AAV CHIMERAS

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 62/639,466, filed on March 6, 2018, the entire disclosure of which is incorporated by reference herein.

BACKGROUND

Adeno-associated virus (AAV) particles are commonly used for research and also for gene therapy applications, including several in clinical development.

Methods and compositions for producing recombinant adeno-associated virus (rAAV) particles, in both small and large scale, are useful for research, pre-clinical, and clinical applications.

SUMMARY

Recombinant AAV particle production can involve culturing cells, introducing to those cells AAV genes and genes of interest that are desired to be packaged in rAAV particles, and allowing the cells to package (or produce) rAAV particles. Cells that package or produce rAAV particles are also referred to herein as“producer cells.” AAV genes that are introduced to a producer cell generally include rep , cap , helper genes and inverted terminal repeats (ITRs) which flank one or more genes of interest. In the last decade numerous AAV cap genes from multiple natural serotypes and variants have been utilized for different gene therapy applications. In contrast, variation of rep and ITR sequences and how they influence rAAV particle packaging has not been explored. This application is related, at least in part, to the finding that both rep and ITR sequences can be varied to improve the packaging of rAAV particles of difference serotypes. In some embodiments, recombinant Rep proteins (e.g., chimeric Rep proteins) and/or genes encoding them as described in this application can be used in the production of rAAV particles comprising recombinant rAAV nucleic acids including one or more genes of interest flanked by ITR sequences (e.g., of different serotypes) as described in this application.

Accordingly, in one aspect, provided herein is a composition comprising a nucleic acid comprising a rep gene, wherein the rep gene is chimeric. In some embodiments, a rep gene comprises an N-terminus and a C-terminus (c). In some embodiments, an N terminus comprises an N-terminus domain (n), a DNA binding domain (d), and a helicase domain (h). In some embodiments, a C terminus comprises a NLS/p40 promoter domain (y) and a Zinc finger domain (z). In some embodiments, a rep gene is of serotype AAV1, AAV2, AAV3, AAV4, AAV6, AAV 12, AAV13, AAV1 and AAV2, or AAV5 and AAV2, or is chimeric.

In some embodiments, an N terminus is of AAV 1 serotype and the C terminus is of AAV2 serotype. In some embodiments, an N terminus is of AAV2 serotype and the C terminus is of AAV1 serotype. In some embodiments, an N terminus is of AAV2 serotype and the C terminus is of AAV5 serotype. In some embodiments, an N terminus is of AAV5 serotype and the C terminus is of AAV2 serotype.

In some embodiments, n, d, y, and z domains are of AAV2 serotype and an h domain is of AAV1 serotype. In some embodiments, n, h, y, and z domains are of AAV2 serotype and a d domain is of AAV1 serotype. In some embodiments, d, h, y, and z domains are of AAV2 serotype and a n domain is of AAV1 serotype. In some embodiments, n, d, and h domains are of AAV1 serotype and y and z domains are of AAV1 serotype. In some embodiments, d and h domains are of AAV1 serotype and n, y and z domains are of AAV2 serotype. In some embodiments, n and d domains are of AAV 1 serotype and h, y, and z domains is of AAV2 serotype.

In some embodiments, n, d, and h domains are of AAV2 serotype and y and z domains are of AAV3 serotype. In some embodiments, a rep gene having n, d, and h domains are of AAV2 serotype and y and z domains are of AAV3 serotype has a start codon of sequence ACG. In some embodiments, a rep gene is of AAV3 serotype, and has a start codon of sequence ATG.

In some embodiments, a rep gene is of AAV4 serotype, and has a start codon of sequence ACG.

In some embodiments, a rep gene is of AAV2 serotype, and has a start codon of sequence ACG.

In some embodiments, n and h domains are of AAV8 serotype and d, y and z domains are of AAV2 serotype. In some embodiments, n and d domains are of AAV1 serotype and h, y, and z domains are of AAV2 serotype.

In some embodiments, a rep gene is of AAV2 serotype, and has a start codon of sequence ACG. In some embodiments, a rep gene is of AAV7 serotype, and has a start codon of sequence ACG.

In some embodiments, n and h domains are of AAV8 serotype and the d, y, and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG. In some embodiments, n, h and d domains are of AAV 1 serotype and the y and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG. In some embodiments, n and h domains are of AAV8 serotype, the following nucleotides are deleted in the d domain: T574, C592, C607, A637, G644, AND C657 according to SEQ ID NO: 125 (and resulting in SEQ ID NO: 126), y and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG.

In some embodiments, any one of the compositions described herein further comprises a nucleic acid comprising a cap gene. The cap gene may be of any serotype (e.g.,

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13).

In some embodiments, the nucleic acid comprising the rep gene and the nucleic acid comprising the cap gene are comprised by a nucleic acid vector. In some embodiments, a nucleic acid vector comprising nucleic acid comprising a rep gene and the nucleic acid comprising a cap gene further comprises a nucleic acid comprising a pair of ITRs. In some embodiments, a gene of interest is flanked by the pair of ITRs.

Accordingly, in one aspect, provided herein is a method of packaging a recombinant adeno-associated virus (AAV) particle comprising contacting a cell that expresses a rep gene of a first serotype with a recombinant nucleic acid that comprises a pair of inverted terminal repeats (ITRs) of a second serotype. In some embodiments, a rep gene is expressed by transfecting or infecting the cell with a nucleic acid encoding the rep gene. In some embodiments, a rep gene is chimeric. A chimeric rep gene is one that comprises

corresponding nucleic acid bases of more than AAV one serotype. In some embodiments, a rep gene is of serotype 1, 2, 3, 4, 6, 12, 13, 1 and 2, or 5 and 2.

In some embodiments of any one of the methods disclosed herein, Rep proteins encoded by a rep gene of serotype 1 and 2 comprise amino acids of serotype 1 in the N terminus and amino acids of serotype 2 in the C terminus. In some embodiments, Rep proteins encoded by a rep gene of serotype 1 and 2 comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 1 in the C terminus. In some embodiments, Rep proteins encoded by a rep gene of serotype 2 and 5 comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 5 in the C terminus. In some embodiments, Rep proteins encoded by a rep gene of serotype 5 and 2 comprise amino acids of serotype 5 in the N terminus and amino acids of serotype 2 in the C terminus.

In some embodiments of any one of the methods disclosed herein, the first serotype of the rep gene is serotype 1. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 1, 2, 3, 4, or 7. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 1. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 2. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 3. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 4. In some embodiments, the first serotype of the rep gene is serotype 1, and the second serotype of the ITRs is serotype 7.

In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 2, 3, 4, 6, 12, or 13. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 2. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 3. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 4. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 6. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 12. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 6, and the first serotype of the rep gene is serotype 13.

In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 2, 3, 4, 12, or 13. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 2. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 3. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 4. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 12. In some embodiments of any one of the methods disclosed herein, the second serotype of the ITRs is serotype 1, and the first serotype of the rep gene is serotype 13. In some embodiments, the Rep proteins encoded by a rep gene of serotype 1 and 2 comprise amino acids of serotype 1 in the N terminus and amino acids of serotype 2 in the C terminus, and the second serotype of the ITRs is serotype 1. In some embodiments, the Rep proteins encoded by a rep gene of serotype 1 and 2 comprise amino acids of serotype 1 in the N terminus and amino acids of serotype 2 in the C terminus, and the second serotype of the ITRs is serotype 6.

In some embodiments, the Rep proteins encoded by a rep gene of serotype 2 and 1 comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 1 in the C terminus, and the second serotype of the ITRs is serotype 1. In some embodiments, the Rep proteins encoded by a rep gene of serotype 2 and 1 comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 1 in the C terminus, and the second serotype of the ITRs is serotype 6.

In some embodiments, the Rep proteins encoded by a rep gene of serotype 2 and 5 comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 5 in the C terminus, and the second serotype of the ITRs is serotype 2.

In some embodiments, the Rep proteins encoded by a rep gene of serotype 5 and 2 comprise amino acids of serotype 5 in the N terminus and amino acids of serotype 2 in the C terminus, and the second serotype of the ITRs is serotype 5.

In some embodiments, n, d, y, and z domains are of AAV2 serotype and an h domain is of AAV1 serotype. In some embodiments, n, h, y, and z domains are of AAV2 serotype and a d domain is of AAV1 serotype. In some embodiments, d, h, y, and z domains are of AAV2 serotype and a n domain is of AAV1 serotype. In some embodiments, n, d, and h domains are of AAV1 serotype and y and z domains are of AAV1 serotype. In some embodiments, d and h domains are of AAV1 serotype and n, y and z domains are of AAV2 serotype. In some embodiments, n and d domains are of AAV 1 serotype and h, y, and z domains is of AAV2 serotype.

In some embodiments, n, d, and h domains are of AAV2 serotype and y and z domains are of AAV3 serotype. In some embodiments, a rep gene having n, d, and h domains are of AAV2 serotype and y and z domains are of AAV3 serotype has a start codon of sequence ACG. In some embodiments, a rep gene is of AAV3 serotype, and has a start codon of sequence ATG.

In some embodiments, a rep gene is of AAV4 serotype, and has a start codon of sequence ACG. In some embodiments, a rep gene is of AAV2 serotype, and has a start codon of sequence ACG.

In some embodiments, n and h domains are of AAV8 serotype and d, y and z domains are of AAV2 serotype. In some embodiments, n and d domains are of AAV1 serotype and h, y, and z domains are of AAV2 serotype.

In some embodiments, a rep gene is of AAV2 serotype, and has a start codon of sequence ACG. In some embodiments, a rep gene is of AAV7 serotype, and has a start codon of sequence ACG.

In some embodiments, n and h domains are of AAV8 serotype and the d, y, and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG. In some embodiments, n, h and d domains are of AAV 1 serotype and the y and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG. In some embodiments, n and h domains are of AAV8 serotype, the following nucleotides are deleted in the d domain: T574, C592, C607, A637, G644, AND C657 according to SEQ ID NO: 125 (and resulting in SEQ ID NO: 126), y and z domains are of AAV2 serotype, and a rep gene has a start codon of sequence ATG.

In some embodiments, any one of the compositions described herein further comprises a nucleic acid comprising a cap gene. The cap gene may be of any serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13)

In some embodiments of any one of the methods disclosed herein, a cells is also contacted with a recombinant nucleic acid that comprises a cap gene. In some embodiments of any one of the methods disclosed herein, a cell that expresses a rep gene and is contacted with a recombinant nucleic acid that comprises a pair of inverted terminal repeats (ITRs) of a second serotype also expresses a cap gene.

In some aspects, the present application also provides a cell comprising a rep gene of a first serotype and a pair of ITRs of a second serotype. A cell as provided herein may comprise any one of the combinations of ITRs and rep genes disclosed herein. In some embodiments, any one of the cells provided herein further comprises a cap gene.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present application, which can be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. It is to be understood that the data illustrated in the drawings in no way limit the scope of the application.

FIG. 1 shows alignment of rep and ITR sequences of AAV serotypes 1-13.

FIG. 2 shows a structure of an AAV ITR with variations in base pairs found between different AAV serotypes. RBE: Rep binding element where AAV Rep78 and Rep68 proteins bind.

FIG. 3 shows a graphical representation of AAV1 versus AAV2 Rep protein sequence identity.

FIG. 4 is a schematic showing the standard AAV vector production system.

FIG. 5 shows percent sequence identity analysis for AAV ITR and Rep78 for AAV serotypes 1-9.

FIG. 6 shows an overview of an AAV genome is shown with its two open reading frames flanked by inverted terminal repeats (ITRs). The zoom-in shows an illustration of the domains of the Rep proteins and the transcripts leading to the expression of Rep78/68/52/40. Regions of the rep gene used for the generations of hybrids are indicated as lower case letter: n = N-terminus, d = DNA binding domain, h = helicase, c = C-terminus, y = nuclear localization signal (NLS)/p40 promoter, z = Zinc finger domain.

FIGs. 7A-7B show characterization and optimization of the rep gene for AAV 1 vector production. FIG. 7A shows examples of AAV plasmid designs with variations in the rep gene. pR2V 1 denotes a plasmid with a cap gene of AAV 1 sequence, and a rep gene of AAV2 sequence. pR2hlVl denotes a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV2 sequence with the exception that the helicase domain (h) is of AAV1 sequence. pR2dlVl denotes a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV2 sequence with the exception that the DNA binding domain (d) is of AAV1 sequence. pR2nlVl denotes a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV2 sequence with the exception that the N-terminus domain (n) is of AAV1 sequence. pRlc2Vl denotes a plasmid with a cap gene of AAV 1 sequence, and a rep gene of AAV 1 sequence with the exception that the C terminus (c), which consists of the NLS/p40 promoter domain (y) and the zinc-finger domain (z) is of AAV2 sequence. pRlhc2Vl denotes a plasmid with a cap gene of AAV 1 sequence, and a rep gene of AAV 1 sequence with the exception that the C terminus (c) and the helicase domain (h)are of AAV2 sequence. pRldc2Vl denotes a plasmid with a cap gene of AAV 1 sequence, and a rep gene of AAV 1 sequence with the exception that the DNA binding domain (d), and the C terminus (c) are of AAV2 sequence. pRlnc2Vl denotes a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV1 sequence with the exception that the N-terminus domain (n), and the C terminus (c) are of AAV2 sequence.

FIG. 7B shows the genome packaging efficiencies of the plasmids shown in FIG. 7A. The genome packaging efficiency is calculated as the amount of genome packaged in a rAAV particle compared to a particle with capsid proteins of serotype 1 and rep proteins of serotype 2 (reference).

FIG. 8 provides an overview of the newly generated AAV 1 production plasmids and their phenotype. The plasmid names, descriptions of rep genes, VP expressions, and genome packaging efficiencies are shown.

FIGs. 9A-9D provide characterization and optimization of the rep gene for AAV3 vector production. FIG. 9A is a schematic showing examples of the AAV2 and AAV3 rep variations with either the naturally occurring ACG start codon, or a ATG start codon. FIG. 9B shows expression of capsid proteins or VP proteins and Rep proteins for the plasmids shown in FIG. 9A. AAV3 Rep78 is not visible with the ACG start codon. FIG. 9C provides yield of vector genomes per l5cm plate (xlO ¹² ) of ACG-R2C3, ACG-R3V3, and ATG-R3V3 as shown in FIG. 9A. FIG. 9D is a chart showing the plasmid names and descriptions of the AAV3 expression plasmids tested.

FIGs. 10A-10D provide characterization and optimization of the rep gene for AAV4 vector production. FIG. 10A is a schematic showing examples of the AAV2 and AAV4 rep variations with either the naturally occurring ACG start codon, or a ATG start codon. FIG. 10B shows expression of capsid proteins or VP proteins and Rep proteins for the plasmids shown in FIG. 10A. The asterisk denotes known cross-reactivity of the Al antibody. FIG. 10C provides yield of vector genomes per l5cm plate (xlO ¹² ) of ACG-R2C3, ACG-R3V3, and ATG-R3V3 as shown in FIG. 10A.4. FIG. 10D is a chart showing the names and descriptions of AAV4 expression plasmids.

FIGs. 11A-11D provide characterization and optimization of the rep gene for AAV5 vector production. FIG. 11A is a schematic showing examples of the AAV2 and AAV5 rep variations with either the naturally occurring ACG start codon, or a ATG start codon. FIG. 11B shows expression of capsid proteins or VP proteins and Rep proteins for the plasmids shown in FIG. 10A. AAV5 Rep78 is not visible with the ACG start codon. FIG. 11C shows the plasmid yield per l5cm plate (xlO ¹² ) of ACG-R2V5, ACG-R5V5, and ATG-R5V5. FIG. 10D is a chart showing the names and descriptions of AAV5 expression plasmids, all of which contain the AAV5 cap gene. FIGs. 12A-12D provide characterization and optimization of the rep gene for AAV6 vector production. . FIG. 12A shows expression of capsid proteins or VP proteins and Rep proteins for denoted plasmids, as well as their yields relative to the control (untransfected cells). FIG. 12B provides genome packaging efficiency for R8dlc3V6 and Rlhc2V6 relative to R2V6. FIG. 12C is a chart showing the names and descriptions of AAV6 expression plasmids.

FIGs. 13A-13D provide characterization and optimization of the rep gene for AAV7 vector production. FIG. 13A is a schematic showing examples of the AAV2 and AAV7 rep variations with either the naturally occurring ACG start codon, or a ATG start codon. FIG. 13B shows expression of capsid proteins or VP proteins and Rep proteins for the plasmids shown in FIG. 13A. FIG. 13C shows the plasmid yield per l5cm plate (xlO ¹² ) of ACG- R2V7, ACG-R7V7, and ATG-R7V7. FIG. 13D is a chart showing the names and descriptions of AAV7 expression plasmids.

FIGs. 14A-14B provide characterization and optimization of the rep gene for AAV8 vector production. FIG. 14A shows the plasmid yield per l5cm plate (gp) for R2V8, R8c2V8, Rlc2V8, R8nlc2V8, R8dlc2V8, and R8hlc2V8. FIG. 14B shows schematics of example AAV1, AAV2 and AAV8 rep variations.

FIGs. 15A-15B show an example of the ratio of genome-containing AAV8 particles for‘standard’ AAV vector production compared to the vector production using rep chimeras as described herein.

FIG. 16A is a chart showing the names and descriptions of AAV8 expression plasmids, along with their genome packaging efficiencies and expression of VP proteins relative to pR2V8. FIG. 16B shows nucleotides are deleted in the DNA binding (d) domain of AAV8 for the last hybrid listed in FIG. 16A.

DETAILED DESCRIPTION

To package rAAV particles, the viral genome that is found between two flanking ITRs is replaced with one or more genes of interest along with one or more control sequences (e.g., a promoter). Generally, when constructing rAAV particles, a gene to be packaged is flanked by cis-active ITRs while the rep and cap genes, which are in encoded in the wild- type genome, can be supplied in trans. The cap gene encodes capsid proteins that encapsidate packaged genetic material. The rep gene encodes proteins involved in replication of viral DNA. In the last decade, numerous AAV cap genes from multiple natural serotypes and variants have been utilized for different gene therapy applications. Generally, ITRs and rep gene of serotype 2 are used for packaging rAAV particles of various serotypes. The present application provides novel methods and compositions for packaging rAAV particles using ITRs and rep genes of different serotypes. As used herein,“packaging of rAAV particles” implies packing of nucleic acid sequences that are flanked by ITRs, which may comprises one or more genes of interest, into rAAV particles.

The inventors of the present application have explored how the sequences of ITRs and rep genes can be varied to improve the packaging of rAAV particles. Accordingly, provided herein are compositions of nucleic acids (e.g., comprised in vectors such as plasmids) that comprise ITRs and/or rep of different serotypes, including chimeric rep genes, for use in transfecting a producer cell, as well as cells that express a Rep proteins of a serotype that is different from the serotype of the ITRs used in producing rAAV particles. As defined herein, a“chimeric” AAV gene (e.g., rep or cap), also referred to as a“hybrid” AAV gene, or chimeric” AAV protein (e.g., Rep (e.g., Rep78, Rep68, Rep52, or Rep40) or capsid protein (e.g., VP1, VP2, and VP3)), also referred to as a“hybrid” AAV protein, is gene or protein having nucleotides or amino acids of more than one AAV serotype, respectively.

Methods of using ITRs and rep genes of different serotypes to improve rAAV particle packaging are also disclosed herein. In some embodiments, chimeric ITRs and/or chimeric rep genes are used for rAAV particle packaging.

AAV structure

The AAV genome is built of single-stranded deoxyribonucleic acid (ssDNA), which is either positive- or negative-sensed. At each end of the DNA strand is an inverted terminal repeat (ITR). Between the ITRs are two open reading frames (ORFs): rep and cap. The cap ORF contains overlapping nucleotide sequences of capsid proteins: VP1, VP2 and VP3, which interact together to form a capsid of an icosahedral symmetry. The serotype of an AAV particle is attributed to the sequence of comprising capsid proteins.

FIG. 2 shows the structure of an AAV ITR. Each AAV ITR forms a hairpin, which contributes to so-called self-priming that allows primase-independent synthesis of the second DNA strand. ITRs are required for integration of AAV DNA into host DNA, efficient encapsidation and generation of a fully assembled DNAse-resistant AAV particle. ITRs are generally considered to be required in cis next to the one or more genes that are desired to be packaged into a rAAV particle. SEQ ID NOs: 1-7 correspond to examples of wild-type ITR sequences of serotypes 1-7 (AAV1-AAV7), respectively. Example sequence of wild-type AAV 1 ITR:

ttgcccactccctctctgcgcgctcgctcgctcggtggggcctgcggaccaaaggtc cgcagacggcagagctctgctctgccggcc ccaccgagcgagcgagcgcgcagagagggagtgggcaactccatcactaggggtaatcgc (SEQ ID NO: 1)

Example sequence of wild-type AAV2 ITR:

ttggccactccctctctgcgcgctcgctcgctcactgaggccgggcgaccaaaggtc gcccgacgcccgggctttgcccgggcggc ctcagtgagcgagcgagcgcgcagagagggagtggccaactccatcactaggggttcct (SEQ ID NO: 2)

Example sequence of wild-type AAV3 ITR:

tggccactccctctatgcgcactcgctcgctcggtggggcctggcgaccaaaggtcg ccagacggacgtgctttgcacgtccggccc caccgagcgagcgagtgcgcatagagggagtggccaactccatcactagaggtatggca (SEQ ID NO: 3)

Example sequence of wild-type AAV4 ITR:

ttggccactccctctatgcgcgctcgctcactcactcggccctggagaccaaaggtc tccagactgccggcctctggccggcagggc cgagtgagtgagcgagcgcgcatagagggagtggccaactccatcatctaggtttgccca c (SEQ ID NO: 4)

Example sequence of wild-type AAV5 ITR:

ctctcccccctgtcgcgttcgctcgctcgctggctcgtttgggggggtggcagctca aagagctgccagacgacggccctctggccgt cgcccccccaaacgagccagcgagcgagcgaacgcgacaggggggagagtgccacactct caagcaagggggttttgtaagcag tgat (SEQ ID NO: 5)

Example sequence of wild-type AAV6 ITR:

ttggccactccctctctgcgcgctcgctcgctcactgaggccgggcgaccaaaggtc gcccgacgcccgggctttgcccgggcggc ctcagtgagcgagcgagcgcgcagagagggagtggccaactccatcactaggggttcct (SEQ ID NO: 6)

Example sequence of wild-type AAV7 ITR:

ttggccactccctctatgcgcgctcgctcgctcggtggggcctgcggaccaaaggtc cgcagacggcagagctctgctctgccggcc ccaccgagcgagcgagcgcgcatagagggagtggccaactccatcactaggggtaccgc (SEQ ID NO: 7)

The rep ORF is composed of four overlapping genes encoding Rep proteins required for the AAV life cycle. The names of the four Rep proteins depict their sizes in kilodaltons (kDa): Rep78, Rep68, Rep52 and Rep40. Rep78 and Rep68 bind the hairpin formed by the ITR in the self-priming act and cleave at a specific region, designated terminal resolution site, within the hairpin. All four Rep proteins bind to ATP and possess helicase activity. They upregulate the transcription from the p40 promoter, and downregulate both p5 and pl9 promoter activity.

SEQ ID NOs: 8-20 correspond to example sequences of wild-type AAV rep genes of serotypes 1-13, respectively.

SEQ ID NOs: 21-33 correspond to example sequences of wild-type AAV Rep78 protein of serotypes 1-13, respectively. Rep78 has 621 amino acids. Rep68 comprises of amino acids 1-529 of Rep78 and a sequence LARGHSL (SEQ ID NO: 38) in the C terminus. Rep52 comprises amino acids 225-621 of Rep78. Rep40 comprises of amino acids 225-621 of Rep78 and LARGHSL (SEQ ID NO: 38) in the C terminus.

Example of wild-type AAV 1 rep nucleic acid sequence:

atgccgggcttctacgagatcgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcgtttgtgagctggg tggccgagaaggaatgggagctgcccccggattctgacatggatctgaatctgattgagc aggcacccctgaccgtggccgagaag ctgcagcgcgacttcctggtccaatggcgccgcgtgagtaaggccccggaggccctcttc tttgttcagttcgagaagggcgagtcct acttccacctccatattctggtggagaccacgggggtcaaatccatggtgctgggccgct tcctgagtcagattagggacaagctggtg cagaccatctaccgcgggatcgagccgaccctgcccaactggttcgcggtgaccaagacg cgtaatggcgccggaggggggaac aaggtggtggacgagtgctacatccccaactacctcctgcccaagactcagcccgagctg cagtgggcgtggactaacatggagga gtatataagcgcctgtttgaacctggccgagcgcaaacggctcgtggcgcagcacctgac ccacgtcagccagacccaggagcaga acaaggagaatctgaaccccaattctgacgcgcctgtcatccggtcaaaaacctccgcgc gctacatggagctggtcgggtggctgg tggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacatct ccttcaacgccgcttccaactcgcggt cccagatcaaggccgctctggacaatgccggcaagatcatggcgctgaccaaatccgcgc ccgactacctggtaggccccgctccg cccgcggacattaaaaccaaccgcatctaccgcatcctggagctgaacggctacgaacct gcctacgccggctccgtctttctcggct gggcccagaaaaggttcgggaagcgcaacaccatctggctgtttgggccggccaccacgg gcaagaccaacatcgcggaagccat cgcccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactttcccttcaa tgattgcgtcgacaagatggtgatctggtg ggaggagggcaagatgacggccaaggtcgtggagtccgccaaggccattctcggcggcag caaggtgcgcgtggaccaaaagtg caagtcgtccgcccagatcgaccccacccccgtgatcgtcacctccaacaccaacatgtg cgccgtgattgacgggaacagcacca ccttcgagcaccagcagccgttgcaggaccggatgttcaaatttgaactcacccgccgtc tggagcatgactttggcaaggtgacaaa gcaggaagtcaaagagttcttccgctgggcgcaggatcacgtgaccgaggtggcgcatga gttctacgtcagaaagggtggagcca acaaaagacccgcccccgatgacgcggataaaagcgagcccaagcgggcctgcccctcag tcgcggatccatcgacgtcagacg cggaaggagctccggtggactttgccgacaggtaccaaaacaaatgttctcgtcacgcgg gcatgcttcagatgctgtttccctgcaag acatgcgagagaatgaatcagaatttcaacatttgcttcacgcacgggacgagagactgt tcagagtgcttccccggcgtgtcagaatc tcaaccggtcgtcagaaagaggacgtatcggaaactctgtgccattcatcatctgctggg gcgggctcccgagattgcttgctcggcct gcgatctggtcaacgtggacctggatgactgtgtttctgagcaataa (SEQ ID NO: 8) Example of wild-type AAV2 rep nucleic acid sequence:

atgccggggttttacgagattgtgattaaggtccccagcgaccttgacgggcatctg cccggcatttctgacagctttgtgaactgggtg gccgagaaggaatgggagttgccgccagattctgacatggatctgaatctgattgagcag gcacccctgaccgtggccgagaagctg cagcgcgactttctgacggaatggcgccgtgtgagtaaggccccggaggcccttttcttt gtgcaatttgagaagggagagagctactt ccacatgcacgtgctcgtggaaaccaccggggtgaaatccatggttttgggacgtttcct gagtcagattcgcgaaaaactgattcaga gaatttaccgcgggatcgagccgactttgccaaactggttcgcggtcacaaagaccagaa atggcgccggaggcgggaacaaggt ggtggatgagtgctacatccccaattacttgctccccaaaacccagcctgagctccagtg ggcgtggactaatatggaacagtatttaa gcgcctgtttgaatctcacggagcgtaaacggttggtggcgcagcatctgacgcacgtgt cgcagacgcaggagcagaacaaagag aatcagaatcccaattctgatgcgccggtgatcagatcaaaaacttcagccaggtacatg gagctggtcgggtggctcgtggacaagg ggattacctcggagaagcagtggatccaggaggaccaggcctcatacatctccttcaatg cggcctccaactcgcggtcccaaatcaa ggctgccttggacaatgcgggaaagattatgagcctgactaaaaccgcccccgactacct ggtgggccagcagcccgtggaggaca tttccagcaatcggatttataaaattttggaactaaacgggtacgatccccaatatgcgg cttccgtctttctgggatgggccacgaaaaa gttcggcaagaggaacaccatctggctgtttgggcctgcaactaccgggaagaccaacat cgcggaggccatagcccacactgtgc ccttctacgggtgcgtaaactggaccaatgagaactttcccttcaacgactgtgtcgaca agatggtgatctggtgggaggaggggaa gatgaccgccaaggtcgtggagtcggccaaagccattctcggaggaagcaaggtgcgcgt ggaccagaaatgcaagtcctcggcc cagatagacccgactcccgtgatcgtcacctccaacaccaacatgtgcgccgtgattgac gggaactcaacgaccttcgaacaccag cagccgttgcaagaccggatgttcaaatttgaactcacccgccgtctggatcatgacttt gggaaggtcaccaagcaggaagtcaaag actttttccggtgggcaaaggatcacgtggttgaggtggagcatgaattctacgtcaaaa agggtggagccaagaaaagacccgccc ccagtgacgcagatataagtgagcccaaacgggtgcgcgagtcagttgcgcagccatcga cgtcagacgcggaagcttcgatcaac tacgcagacaggtaccaaaacaaatgttctcgtcacgtgggcatgaatctgatgctgttt ccctgcagacaatgcgagagaatgaatca gaattcaaatatctgcttcactcacggacagaaagactgtttagagtgctttcccgtgtc agaatctcaacccgtttctgtcgtcaaaaagg cgtatcagaaactgtgctacattcatcatatcatgggaaaggtgccagacgcttgcactg cctgcgatctggtcaatgtggatttggatga ctgcatctttgaacaataa (SEQ ID NO: 9)

Example of wild-type AAV3 rep nucleic acid sequence:

atgccggggttctacgagattgtcctgaaggtcccgagtgacctggacgagcacctg ccgggcatttctaactcgtttgttaactgggtg gccgagaaggaatgggagctgccgccggattctgacatggatccgaatctgattgagcag gcacccctgaccgtggccgaaaagct tcagcgcgagttcctggtggagtggcgccgcgtgagtaaggccccggaggccctcttttt tgtccagttcgaaaagggggagaccta cttccacctgcacgtgctgattgagaccatcggggtcaaatccatggtggtcggccgcta cgtgagccagattaaagagaagctggtg acccgcatctaccgcggggtcgagccgcagcttccgaactggttcgcggtgaccaaaacg cgaaatggcgccgggggcgggaac aaggtggtggacgactgctacatccccaactacctgctccccaagacccagcccgagctc cagtgggcgtggactaacatggacca gtatttaagcgcctgtttgaatctcgcggagcgtaaacggctggtggcgcagcatctgac gcacgtgtcgcagacgcaggagcagaa caaagagaatcagaaccccaattctgacgcgccggtcatcaggtcaaaaacctcagccag gtacatggagctggtcgggtggctggt ggaccgcgggatcacgtcagaaaagcaatggattcaggaggaccaggcctcgtacatctc cttcaacgccgcctccaactcgcggtc ccagatcaaggccgcgctggacaatgcctccaagatcatgagcctgacaaagacggctcc ggactacctggtgggcagcaacccg ccggaggacattaccaaaaatcggatctaccaaatcctggagctgaacgggtacgatccg cagtacgcggcctccgtcttcctgggct gggcgcaaaagaagttcgggaagaggaacaccatctggctctttgggccggccacgacgg gtaaaaccaacatcgcggaagccat cgcccacgccgtgcccttctacggctgcgtaaactggaccaatgagaactttcccttcaa cgattgcgtcgacaagatggtgatctggt gggaggagggcaagatgacggccaaggtcgtggagagcgccaaggccattctgggcggaa gcaaggtgcgcgtggaccaaaag tgcaagtcatcggcccagatcgaacccactcccgtgatcgtcacctccaacaccaacatg tgcgccgtgattgacgggaacagcacc accttcgagcatcagcagccgctgcaggaccggatgtttaaatttgaacttacccgccgt ttggaccatgactttgggaaggtcaccaa acaggaagtaaaggactttttccggtgggcttccgatcacgtgactgacgtggctcatga gttctacgtcagaaagggtggagctaaga aacgccccgcctccaatgacgcggatgtaagcgagccaaaacggcagtgcacgtcacttg cgcagccgacaacgtcagacgcgga agcaccggcggactacgcggacaggtaccaaaacaaatgttctcgtcacgtgggcatgaa tctgatgctttttccctgtaaaacatgcg agagaatgaatcaaatttccaatgtctgttttacgcatggtcaaagagactgtggggaat gcttccctggaatgtcagaatctcaacccgt ttctgtcgtcaaaaagaagacttatcagaaactgtgtccaattcatcatatcctgggaag ggcacccgagattgcctgttcggcctgcgat ttggccaatgtggacttggatgactgtgtttctgagcaataa (SEQ ID NO: 10)

Example of wild-type AAV4 rep nucleic acid sequence:

atgccggggttctacgagatcgtgctgaaggtgcccagcgacctggacgagcacctg cccggcatttctgactcttttgtgagctgggt ggccgagaaggaatgggagctgccgccggattctgacatggacttgaatctgattgagca ggcacccctgaccgtggccgaaaagc tgcaacgcgagttcctggtcgagtggcgccgcgtgagtaaggccccggaggccctcttct ttgtccagttcgagaagggggacagct acttccacctgcacatcctggtggagaccgtgggcgtcaaatccatggtggtgggccgct acgtgagccagattaaagagaagctgg tgacccgcatctaccgcggggtcgagccgcagcttccgaactggttcgcggtgaccaaga cgcgtaatggcgccggaggcgggaa caaggtggtggacgactgctacatccccaactacctgctccccaagacccagcccgagct ccagtgggcgtggactaacatggacc agtatataagcgcctgtttgaatctcgcggagcgtaaacggctggtggcgcagcatctga cgcacgtgtcgcagacgcaggagcaga acaaggaaaaccagaaccccaattctgacgcgccggtcatcaggtcaaaaacctccgcca ggtacatggagctggtcgggtggctg gtggaccgcgggatcacgtcagaaaagcaatggatccaggaggaccaggcgtcctacatc tccttcaacgccgcctccaactcgcg gtcacaaatcaaggccgcgctggacaatgcctccaaaatcatgagcctgacaaagacggc tccggactacctggtgggccagaacc cgccggaggacatttccagcaaccgcatctaccgaatcctcgagatgaacgggtacgatc cgcagtacgcggcctccgtcttcctgg gctgggcgcaaaagaagttcgggaagaggaacaccatctggctctttgggccggccacga cgggtaaaaccaacatcgcggaagc catcgcccacgccgtgcccttctacggctgcgtgaactggaccaatgagaactttccgtt caacgattgcgtcgacaagatggtgatct ggtgggaggagggcaagatgacggccaaggtcgtagagagcgccaaggccatcctgggcg gaagcaaggtgcgcgtggaccaa aagtgcaagtcatcggcccagatcgacccaactcccgtgatcgtcacctccaacaccaac atgtgcgcggtcatcgacggaaactcg accaccttcgagcaccaacaaccactccaggaccggatgttcaagttcgagctcaccaag cgcctggagcacgactttggcaaggtc accaagcaggaagtcaaagactttttccggtgggcgtcagatcacgtgaccgaggtgact cacgagttttacgtcagaaagggtgga gctagaaagaggcccgcccccaatgacgcagatataagtgagcccaagcgggcctgtccg tcagttgcgcagccatcgacgtcaga cgcggaagctccggtggactacgcggacaggtaccaaaacaaatgttctcgtcacgtggg tatgaatctgatgctttttccctgccggc aatgcgagagaatgaatcagaatgtggacatttgcttcacgcacggggtcatggactgtg ccgagtgcttccccgtgtcagaatctcaa cccgtgtctgtcgtcagaaagcggacgtatcagaaactgtgtccgattcatcacatcatg gggagggcgcccgaggtggcctgctcg gcctgcgaactggccaatgtggacttggatgactgtgacatggaacaataa (SEQ ID NO: 11)

Example of wild-type AAV5 rep nucleic acid sequence:

atggctaccttctatgaagtcattgttcgcgtcccatttgacgtggaggaacatctg cctggaatttctgacagctttgtggactgggtaac tggtcaaatttgggagctgcctccagagtcagatttaaatttgactctggttgaacagcc tcagttgacggtggctgatagaattcgccgc gtgttcctgtacgagtggaacaaattttccaagcaggagtccaaattctttgtgcagttt gaaaagggatctgaatattttcatctgcacac gcttgtggagacctccggcatctcttccatggtcctcggccgctacgtgagtcagattcg cgcccagctggtgaaagtggtcttccagg gaattgaaccccagatcaacgactgggtcgccatcaccaaggtaaagaagggcggagcca ataaggtggtggattctgggtatattc ccgcctacctgctgccgaaggtccaaccggagcttcagtgggcgtggacaaacctggacg agtataaattggccgccctgaatctgg aggagcgcaaacggctcgtcgcgcagtttctggcagaatcctcgcagcgctcgcaggagg cggcttcgcagcgtgagttctcggct gacccggtcatcaaaagcaagacttcccagaaatacatggcgctcgtcaactggctcgtg gagcacggcatcacttccgagaagcag tggatccaggaaaatcaggagagctacctctccttcaactccaccggcaactctcggagc cagatcaaggccgcgctcgacaacgc gaccaaaattatgagtctgacaaaaagcgcggtggactacctcgtggggagctccgttcc cgaggacatttcaaaaaacagaatctgg caaatttttgagatgaatggctacgacccggcctacgcgggatccatcctctacggctgg tgtcagcgctccttcaacaagaggaacac cgtctggctctacggacccgccacgaccggcaagaccaacatcgcggaggccatcgccca cactgtgcccttttacggctgcgtgaa ctggaccaatgaaaactttccctttaatgactgtgtggacaaaatgctcatttggtggga ggagggaaagatgaccaacaaggtggttg aatccgccaaggccatcctggggggctcaaaggtgcgggtcgatcagaaatgtaaatcct ctgttcaaattgattctacccctgtcattg taacttccaatacaaacatgtgtgtggtggtggatgggaattccacgacctttgaacacc agcagccgctggaggaccgcatgttcaaa tttgaactgactaagcggctcccgccagattttggcaagattactaagcaggaagtcaag gacttttttgcttgggcaaaggtcaatcag gtgccggtgactcacgagtttaaagttcccagggaattggcgggaactaaaggggcggag aaatctctaaaacgcccactgggtgac gtcaccaatactagctataaaagtctggagaagcgggccaggctctcatttgttcccgag acgcctcgcagttcagacgtgactgttgat cccgctcctctgcgaccgctcaattggaattcaaggtatgattgcaaatgtgactatcat gctcaatttgacaacatttctaacaaatgtgat gaatgtgaatatttgaatcggggcaaaaatggatgtatctgtcacaatgtaactcactgt caaatttgtcatgggattcccccctgggaaa aggaaaacttgtcagattttggggattttgacgatgccaataaagaacagtaa (SEQ ID NO: 12)

Example of wild-type AAV6 rep nucleic acid sequence:

atgccggggttttacgagattgtgattaaggtccccagcgaccttgacgagcatctg cccggcatttctgacagctttgtgaactgggtg gccgagaaggaatgggagttgccgccagattctgacatggatctgaatctgattgagcag gcacccctgaccgtggccgagaagctg cagcgcgacttcctggtccagtggcgccgcgtgagtaaggccccggaggccctcttcttt gttcagttcgagaagggcgagtcctactt ccacctccatattctggtggagaccacgggggtcaaatccatggtgctgggccgcttcct gagtcagattagggacaagctggtgcag accatctaccgcgggatcgagccgaccctgcccaactggttcgcggtgaccaagacgcgt aatggcgccggaggggggaacaag gtggtggacgagtgctacatccccaactacctcctgcccaagactcagcccgagctgcag tgggcgtggactaacatggaggagtat ataagcgcgtgtttaaacctggccgagcgcaaacggctcgtggcgcacgacctgacccac gtcagccagacccaggagcagaaca aggagaatctgaaccccaattctgacgcgcctgtcatccggtcaaaaacctccgcacgct acatggagctggtcgggtggctggtgg accggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacatctcct tcaacgccgcctccaactcgcggtcc cagatcaaggccgctctggacaatgccggcaagatcatggcgctgaccaaatccgcgccc gactacctggtaggccccgctccgcc cgccgacattaaaaccaaccgcatttaccgcatcctggagctgaacggctacgaccctgc ctacgccggctccgtctttctcggctgg gcccagaaaaggttcggaaaacgcaacaccatctggctgtttgggccggccaccacgggc aagaccaacatcgcggaagccatcg cccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactttcccttcaacg attgcgtcgacaagatggtgatctggtgg gaggagggcaagatgacggccaaggtcgtggagtccgccaaggccattctcggcggcagc aaggtgcgcgtggaccaaaagtgc aagtcgtccgcccagatcgatcccacccccgtgatcgtcacctccaacaccaacatgtgc gccgtgattgacgggaacagcaccacc ttcgagcaccagcagccgttgcaggaccggatgttcaaatttgaactcacccgccgtctg gagcatgactttggcaaggtgacaaagc aggaagtcaaagagttcttccgctgggcgcaggatcacgtgaccgaggtggcgcatgagt tctacgtcagaaagggtggagccaac aagagacccgcccccgatgacgcggataaaagcgagcccaagcgggcctgcccctcagtc gcggatccatcgacgtcagacgcg gaaggagctccggtggactttgccgacaggtaccaaaacaaatgttctcgtcacgcgggc atgcttcagatgctgtttccctgcaaaac atgcgagagaatgaatcagaatttcaacatttgcttcacgcacgggaccagagactgttc agaatgtttccccggcgtgtcagaatctca accggtcgtcagaaagaggacgtatcggaaactctgtgccattcatcatctgctggggcg ggctcccgagattgcttgctcggcctgc gatctggtcaacgtggatctggatgactgtgtttctgagcaataa (SEQ ID NO: 13)

Example of wild-type AAV7 rep nucleic acid sequence:

atgccgggtttctacgagatcgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcgtttgtgaactgggt ggccgagaaggaatgggagctgcccccggattctgacatggatctgaatctgatcgagca ggcacccctgaccgtggccgagaag ctgcagcgcgacttcctggtccaatggcgccgcgtgagtaaggccccggaggccctgttc tttgttcagttcgagaagggcgagagct acttccaccttcacgttctggtggagaccacgggggtcaagtccatggtgctaggccgct tcctgagtcagattcgggagaagctggtc cagaccatctaccgcggggtcgagcccacgctgcccaactggttcgcggtgaccaagacg cgtaatggcgccggcggggggaac aaggtggtggacgagtgctacatccccaactacctcctgcccaagacccagcccgagctg cagtgggcgtggactaacatggagga gtatataagcgcgtgtttgaacctggccgaacgcaaacggctcgtggcgcagcacctgac ccacgtcagccagacgcaggagcag aacaaggagaatctgaaccccaattctgacgcgcccgtgatcaggtcaaaaacctccgcg cgctacatggagctggtcgggtggctg gtggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacatc tccttcaacgccgcctccaactcgcg gtcccagatcaaggccgcgctggacaatgccggcaagatcatggcgctgaccaaatccgc gcccgactacctggtggggccctcg ctgcccgcggacattaaaaccaaccgcatctaccgcatcctggagctgaacgggtacgat cctgcctacgccggctccgtctttctcg gctgggcccagaaaaagttcgggaagcgcaacaccatctggctgtttgggcccgccacca ccggcaagaccaacattgcggaagc catcgcccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactttccctt caacgattgcgtcgacaagatggtgatct ggtgggaggagggcaagatgacggccaaggtcgtggagtccgccaaggccattctcggcg gcagcaaggtgcgcgtggaccaaa agtgcaagtcgtccgcccagatcgaccccacccccgtgatcgtcacctccaacaccaaca tgtgcgccgtgattgacgggaacagca ccaccttcgagcaccagcagccgttgcaggaccggatgttcaaatttgaactcacccgcc gtctggagcacgactttggcaaggtgac gaagcaggaagtcaaagagttcttccgctgggccagtgatcacgtgaccgaggtggcgca tgagttctacgtcagaaagggcggag ccagcaaaagacccgcccccgatgacgcggatataagcgagcccaagcgggcctgcccct cagtcgcggatccatcgacgtcaga cgcggaaggagctccggtggactttgccgacaggtaccaaaacaaatgttctcgtcacgc gggcatgattcagatgctgtttccctgca aaacgtgcgagagaatgaatcagaatttcaacatttgcttcacacacggggtcagagact gtttagagtgtttccccggcgtgtcagaat ctcaaccggtcgtcagaaaaaagacgtatcggaaactctgcgcgattcatcatctgctgg ggcgggcgcccgagattgcttgctcggc ctgcgacctggtcaacgtggacctggacgactgcgtttctgagcaataa (SEQ ID NO: 14)

Example of wild-type AAV8 rep nucleic acid sequence:

atgccgggcttctacgagatcgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcgtttgtgaactggg tggccgagaaggaatgggagctgcccccggattctgacatggatcggaatctgatcgagc aggcacccctgaccgtggccgagaa gctgcagcgcgacttcctggtccaatggcgccgcgtgagtaaggccccggaggccctctt ctttgttcagttcgagaagggcgagag ctactttcacctgcacgttctggtcgagaccacgggggtcaagtccatggtgctaggccg cttcctgagtcagattcgggaaaagcttg gtccagaccatctacccgcggggtcgagccccaccttgcccaactggttcgcggtgacca aagacgcggtaatggcgccggcggg ggggaacaaggtggtggacgagtgctacatccccaactacctcctgcccaagactcagcc cgagctgcagtgggcgtggactaaca tggaggagtatataagcgcgtgcttgaacctggccgagcgcaaacggctcgtggcgcagc acctgacccacgtcagccagacgca ggagcagaacaaggagaatctgaaccccaattctgacgcgcccgtgatcaggtcaaaaac ctccgcgcgctatatggagctggtcg ggtggctggtggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcct cgtacatctccttcaacgccgcctcc aactcgcggtcccagatcaaggccgcgctggacaatgccggcaagatcatggcgctgacc aaatccgcgcccgactacctggtgg ggccctcgctgcccgcggacattacccagaaccgcatctaccgcatcctcgctctcaacg gctacgaccctgcctacgccggctccg tctttctcggctgggctcagaaaaagttcgggaaacgcaacaccatctggctgtttggac ccgccaccaccggcaagaccaacattgc ggaagccatcgcccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactt tcccttcaatgattgcgtcgacaagatgg tgatctggtgggaggagggcaagatgacggccaaggtcgtggagtccgccaaggccattc tcggcggcagcaaggtgcgcgtgga ccaaaagtgcaagtcgtccgcccagatcgaccccacccccgtgatcgtcacctccaacac caacatgtgcgccgtgattgacgggaa cagcaccaccttcgagcaccagcagcctctccaggaccggatgtttaagttcgaactcac ccgccgtctggagcacgactttggcaag gtgacaaagcaggaagtcaaagagttcttccgctgggccagtgatcacgtgaccgaggtg gcgcatgagttttacgtcagaaagggc ggagccagcaaaagacccgcccccgatgacgcggataaaagcgagcccaagcgggcctgc ccctcagtcgcggatccatcgacg tcagacgcggaaggagctccggtggactttgccgacaggtaccaaaacaaatgttctcgt cacgcgggcatgcttcagatgctgtttcc ctgcaaaacgtgcgagagaatgaatcagaatttcaacatttgcttcacacacggggtcag agactgctcagagtgtttccccggcgtgt cagaatctcaaccggtcgtcagaaagaggacgtatcggaaactctgtgcgattcatcatc tgctggggcgggctcccgagattgcttg ctcggcctgcgatctggtcaacgtggacctggatgactgtgtttctgagcaataa (SEQ ID NO: 15)

Example of wild-type AAVrH.8 rep nucleic acid sequence:

atgccgggcttctacgagattgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcttttgtgaactgggt ggccgagaaggaatgggagctgcccccggattctgacatggatcggaatctgatcgagca ggcacccctgaccgtggccgagaag ctgtagcgcgacttcctggtccaatggcgccgcgtgagtaaggccccggaggccctcttc tttgttcagttcgagaagggcgagagct actttcacctgcacgttctggtcgagaccacgggggtcaagtccatggtgctaggccgct tcctgagtcagattcgggagaagctggtc cagaccatctaccgcgggatcgagccgaccctgcccaactggttcgcggtgaccaagacg cgtaatggcgccggcggggggaac aaggtggtggacgagtgctacatccccaactacctcctgcccaagactcagcccgagctg cagtgggcgtggactaacatggagga gtatataagcgcgtgcttgaacctggccgagcgcaaacggctcgtggcgcagcacctgac ccacgtcagccagacgcaggagcag aacaaggagaatctgaaccccaattctgacgcgcccgtgatcaggtcaaaaacctccgcg cgctacatggagctggtcgggtggctg gtggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacatc tccttcaacgccgcctccaactcgcg gtcccagatcaaggccgcgctggacaatgccggcaagatcatggcgctgaccaaatccgc gcccgactacctggtaggcccttcact tccggtggacattacgcagaaccgcatctaccgcatcctgcagctcaacggctacgaccc tgcctacgccggctccgtctttctcggct gggcacaaaagaagttcgggaaacgcaacaccatctggctgtttgggccggccaccacgg gaaagaccaacatcgcagaagccat tgcccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactttcccttcaa cgattgcgtcgacaagatggtgatctggtg ggaggagggcaagatgacggccaaggtcgtggagtccgccaaggccattctcggcggcag caaggtgcgcgtggaccaaaagtg caagtcgtccgcccagatcgaccccactcccgtgatcgtcacctccaacaccaacatgtg cgccgtgattgacgggaacagcaccac cttcgagcaccagcagcctctccaggaccggatgtttaagttcgaactcacccgccgtct ggagcacgactttggcaaggtgacaaag caggaagtcaaagagttcttccgctgggccagtgatcacgtgaccgaggtggcgcatgag ttttacgtcagaaagggcggagccag caaaagacccgcccccgatgacgcggataaaagcgagcccaagcgggcctgcccctcagt cgcggatccatcgacgtcagacgc ggaaggagctccggtggactttgccgacaggtaccaaaacaaatgttctcgtcacgcggg catgcttcagatgctgcttccctgcaaa acgtgcgagagaatgaatcagaatttcaacatttgcttcacacacggggtcagagactgc tcagagtgtttccccggcgtgtcagaatct caaccggtcgtcagaaagaggacgtatcggaaactctgtgcgattcatcatctgctgggg cgggctcccgagattgcttgctcggcct gcgatctggtcaacgtggacctggatgactgtgtttctgagcaataa (SEQ ID NO: 16)

Example of wild-type AAV10 rep nucleic acid sequence:

atgccgggcttctacgagatcgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcgtttgtgaactggg tggccgagaaggaatgggagctgcccccggattctgacatggatcggaatctgatcgagc aggcacccctgaccgtggccgagaa gctgcagcgcgacttcctggtccactggcgccgcgtgagtaaggccccggaggccctctt ctttgttcagttcgagaagggcgagtcc tactttcacctgcacgttctggtcgagaccacgggggtcaagtccatggtcctgggccgc ttcctgagtcagatcagagacaggctggt gcagaccatctaccgcggggtagagcccacgctgcccaactggttcgcggtgaccaagac gcgaaatggcgccggcggggggaa caaggtggtggacgagtgctacatccccaactacctcctgcccaagacgcagcccgagct gcagtgggcgtggactaacatggagg agtatataagcgcgtgtctgaacctcgcggagcgtaaacggctcgtggcgcagcacctga cccacgtcagccagacgcaggagca gaacaaggagaatctgaacccgaattctgacgcgcccgtgatcaggtcaaaaacctccgc gcgctacatggagctggtcgggtggct ggtggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacat ctccttcaacgccgcctccaactcgc ggtcccagatcaaggccgcgctggacaatgccggaaagatcatggcgctgaccaaatccg cgcccgactacctggtaggcccgtcc ttacccgcggacattaaggccaaccgcatctaccgcatcctggagctcaacggctacgac cccgcctacgccggctccgtcttcctgg gctgggcgcagaaaaagttcggtaaaaggaatacaatttggctgttcgggcccgccacca ccggcaagaccaacatcgcggaagcc atcgcccacgccgtgcccttctacggctgcgtcaactggaccaatgagaactttcccttc aacgattgcgtcgacaagatggtgatctg gtgggaggagggcaagatgaccgccaaggtcgtggagtccgccaaggccattctgggcgg aagcaaggtgcgcgtcgaccaaaa gtgcaagtcctcggcccagatcgaccccacgcccgtgatcgtcacctccaacaccaacat gtgcgccgtgatcgacgggaacagca ccaccttcgagcaccagcagcccctgcaggaccgcatgttcaagttcgagctcacccgcc gtctggagcacgactttggcaaggtga ccaagcaggaagtcaaagagttcttccgctgggctcaggatcacgtgactgaggtgacgc atgagttctacgtcagaaagggcggag ccaccaaaagacccgcccccagtgacgcggatataagcgagcccaagcgggcctgcccct cagttgcggagccatcgacgtcaga cgcggaagcaccggtggactttgcggacaggtaccaaaacaaatgttctcgtcacgcggg catgcttcagatgctgtttccctgcaag acatgcgagagaatgaatcagaatttcaacgtctgcttcacgcacggggtcagagactgc tcagagtgcttccccggcgcgtcagaat ctcaacctgtcgtcagaaaaaagacgtatcagaaactgtgcgcgattcatcatctgctgg ggcgggcacccgagattgcgtgttcggc ctgcgatctcgtcaacgtggacttggatgactgtgtttctgagcaataa (SEQ ID NO: 17)

Example of wild-type AAV 11 rep nucleic acid sequence:

atgccgggcttctacgagatcgtgatcaaggtgccgagcgacctggacgagcacctg ccgggcatttctgactcgtttgtgaactggg tggccgagaaggaatgggagctgcccccggattctgacatggatcggaatctgatcgagc aggcacccctgaccgtggccgagaa gctgcagcgcgacttcctggtccactggcgccgcgtgagtaaggccccggaggccctctt ctttgttcagttcgagaagggcgagtcc tacttccacctccacgttctcgtcgagaccacgggggtcaagtccatggtcctgggccgc ttcctgagtcagatcagagacaggctggt gcagaccatctaccgcggggtcgagcccacgctgcccaactggttcgcggtgaccaagac gcgaaatggcgccggcggggggaa caaggtggtggacgagtgctacatccccaactacctcctgcccaagacccagcccgagct gcagtgggcgtggactaacatggagg agtatataagcgcgtgtctaaacctcgcggagcgtaaacggctcgtggcgcagcacctga cccacgtcagccagacgcaggagca gaacaaggagaatctgaacccgaattctgacgcgcccgtgatcaggtcaaaaacctccgc gcgctacatggagctggtcgggtggct ggtggaccggggcatcacctccgagaagcagtggatccaggaggaccaggcctcgtacat ctccttcaacgccgcctccaactcgc ggtcccagatcaaggccgcgctggacaatgccggaaagatcatggcgctgaccaaatccg cgcccgactacctggtaggcccgtcc ttacccgcggacattaaggccaaccgcatctaccgcatcctggagctcaacggctacgac cccgcctacgccggctccgtcttcctgg gctgggcgcagaaaaagttcggtaaacgcaacaccatctggctgtttgggcccgccacca ccggcaagaccaacatcgcggaagc catagcccacgccgtgcccttctacggctgcgtgaactggaccaatgagaactttccctt caacgattgcgtcgacaagatggtgatct ggtgggaggagggcaagatgaccgccaaggtcgtggagtccgccaaggccattctgggcg gaagcaaggtgcgcgtggaccaaa agtgcaagtcctcggcccagatcgaccccacgcccgtgatcgtcacctccaacaccaaca tgtgcgccgtgatcgacgggaacagc accaccttcgagcaccagcagccgctgcaggaccgcatgttcaagttcgagctcacccgc cgtctggagcacgactttggcaaggtg accaagcaggaagtcaaagagttcttccgctgggctcaggatcacgtgactgaggtggcg catgagttctacgtcagaaagggcgga gccaccaaaagacccgcccccagtgacgcggatataagcgagcccaagcgggcctgcccc tcagttccggagccatcgacgtcag acgcggaagcaccggtggactttgcggacaggtaccaaaacaaatgttctcgtcacgcgg gcatgcttcagatgctgtttccctgcaa gacatgcgagagaatgaatcagaatttcaacgtctgcttcacgcacggggtcagagactg ctcagagtgcttccccggcgcgtcaga atctcaacccgtcgtcagaaaaaagacgtatcagaaactgtgcgcgattcatcatctgct ggggcgggcacccgagattgcgtgttcg gcctgcgatctcgtcaacgtggacttggatgactgtgtttctgagcaataa (SEQ ID NO: 18) Example of wild-type AAV12 rep nucleic acid sequence:

atgccggggttctacgaggtggtgatcaaggtgcccagcgacctggacgagcacctg cccggcatttctgactcctttgtgaactggg tggccgagaaggaatgggagttgcccccggattctgacatggatcagaatctgattgagc aggcacccctgaccgtggccgagaag ctgcagcgcgagttcctggtggaatggcgccgagtgagtaaatttctggaggccaagttt tttgtgcagtttgaaaagggggactcgta ctttcatttgcatattctgattgaaattaccggcgtgaaatccatggtggtgggccgcta cgtgagtcagattagggataaactgatccag cgcatctaccgcggggtcgagccccagctgcccaactggttcgcggtcacaaagacccga aatggcgccggaggcgggaacaag gtggtggacgagtgctacatccccaactacctgctccccaaggtccagcccgagcttcag tgggcgtggactaacatggaggagtat ataagcgcctgtttgaacctcgcggagcgtaaacggctcgtggcgcagcacctgacgcac gtctcccagacccaggagggcgaca aggagaatctgaacccgaattctgacgcgccggtgatccggtcaaaaacctccgccaggt acatggagctggtcgggtggctggtg gacaagggcatcacgtccgagaagcagtggatccaggaggaccaggcctcgtacatctcc ttcaacgcggcctccaactcccggtc gcagatcaaggcggccctggacaatgcctccaaaatcatgagcctcaccaaaacggctcc ggactatctcatcgggcagcagcccg tgggggacattaccaccaaccggatctacaaaatcctggaactgaacgggtacgaccccc agtacgccgcctccgtctttctcggctg ggcccagaaaaagtttggaaagcgcaacaccatctggctgtttgggcccgccaccaccgg caagaccaacatcgcggaagccatc gcccacgcggtccccttctacggctgcgtcaactggaccaatgagaactttcccttcaac gactgcgtcgacaaaatggtgatttggtg ggaggagggcaagatgaccgccaaggtcgtagagtccgccaaggccattctgggcggcag caaggtgcgcgtggaccaaaaatg caaggcctctgcgcagatcgaccccacccccgtgatcgtcacctccaacaccaacatgtg cgccgtgattgacgggaacagcacca ccttcgagcaccagcagcccctgcaggaccggatgttcaagtttgaactcacccgccgcc tcgaccacgactttggcaaggtcacca agcaggaagtcaaggactttttccggtgggcggctgatcacgtgactgacgtggctcatg agttttacgtcacaaagggtggagctaa gaaaaggcccgccccctctgacgaggatataagcgagcccaagcggccgcgcgtgtcatt tgcgcagccggagacgtcagacgc ggaagctcccggagacttcgccgacaggtaccaaaacaaatgttctcgtcacgcgggtat gctgcagatgctctttccctgcaagacg tgcgagagaatgaatcagaattccaacgtctgcttcacgcacggtcagaaagattgcggg gagtgctttcccgggtcagaatctcaac cggtttctgtcgtcagaaaaacgtatcagaaactgtgcatccttcatcagctccgggggg cacccgagatcgcctgctctgcttgcgac caactcaaccccgatttggacgattgccaatttgagcaataa (SEQ ID NO: 19)

Example of wild-type AAV 13 rep nucleic acid sequence:

atgccgggattctacgagattgtcctgaaggtgcccagcgacctggacgagcacctg cctggcatttctgactcttttgtaaactgggtg gcggagaaggaatgggagctgccgccggattctgacatggatctgaatctgattgagcag gcacccctaaccgtggccgaaaagct gcaacgcgaattcctggtcgagtggcgccgcgtgagtaaggccccggaggccctcttctt tgttcagttcgagaagggggacagcta cttccacctacacattctggtggagaccgtgggcgtgaaatccatggtggtgggccgcta cgtgagccagattaaagagaagctggtg acccgcatctaccgcggggtcgagccgcagcttccgaactggttcgcggtgaccaagacg cgtaatggcgccggaggcgggaaca aggtggtggacgactgctacatccccaactacctgctccccaagacccagcccgagctcc agtgggcgtggactaatatggaccagt atttaagcgcctgtttgaatctcgcggagcgtaaacggctggtggcgcagcatctgacgc acgtgtcgcagacgcaggagcagaaca aagagaaccagaatcccaattctgacgcgccggtgatcagatcaaaaacctccgcgaggt acatggagctggtcgggtggctggtg gaccgcgggatcacgtcagaaaagcaatggatccaggaggaccaggcctcttacatctcc ttcaacgccgcctccaactcgcggtca caaatcaaggccgcactggacaatgcctccaaatttatgagcctgacaaaaacggctccg gactacctggtgggaaacaacccgccg gaggacattaccagcaaccggatctacaaaatcctcgagatgaacgggtacgatccgcag tacgcggcctccgtcttcctgggctgg gcgcaaaagaagttcgggaagaggaacaccatctggctctttgggccggccacgacgggt aaaaccaacatcgctgaagctatcgc ccacgccgtgcccttttacggctgcgtgaactggaccaatgagaactttccgttcaacga ttgcgtcgacaagatggtgatctggtggg aggagggcaagatgacggccaaggtcgtggagtccgccaaggccattctgggcggaagca aggtgcgcgtggaccaaaagtgca agtcatcggcccagatcgacccaactcccgtcatcgtcacctccaacaccaacatgtgcg cggtcatcgacggaaattccaccacctt cgagcaccaacaaccactccaagaccggatgttcaagttcgagctcaccaagcgcctgga gcacgactttggcaaggtcaccaagc aggaagtcaaggactttttccggtgggcgtcagatcacgtgactgaggtgtctcacgagt tttacgtcagaaagggtggagctagaaa gaggcccgcccccaatgacgcagatataagtgagcccaagcgggcctgtccgtcagttgc gcagccatcgacgtcagacgcggaa gctccggtggactacgcggacaggtaccaaaacaaatgttctcgtcacgtgggcatgaat ctgatgctttttccctgccggcaatgcga gagaatgaatcagaatgtggacatttgcttcacgcacggggtcatggactgtgccgagtg cttccccgtgtcagaatctcaacccgtgt ctgtcgtcagaaagcggacatatcagaaactgtgtccgattcatcacatcatggggaggg cgcccgaggtggcttgttcggcctgcga tctggccaatgtggacttggatgactgtgacatggagcaataa (SEQ ID NO: 20)

Example of wild-type AAV1 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVSWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLHILVETTGVKSM VLGRFLS QIRDK LV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPAPPADIKTNRIYRILELN GYEPAY AGS VFLGWAQKRFGKRNTIWLFGPATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWAQDHVTEVAHEFYVRKGGANKRPAPDDADKSEPKRACP S V ADPS TS D AEG AP VDFADR Y QNKC S RH AGMLQMLFPCKTCERMN QNFNICFTHGT RDCSECFPGVSESQPVVRKRTYRKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSEQ

(SEQ ID NO: 21)

Example of wild-type AAV2 Rep78 amino acid sequence:

MPGF YEIVIKVPS DLD GHLPGIS DS FVNW V AEKEWELPPDS DMDLNLIEQ APLT V AE KLQRDFLTE WRRV S KAPE ALFF V QFEKGES YFHMH VLVETT G VKS M VLGRFLS QIRE KLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDECYIPNYLLPKTQPELQWAWTN MEQ YLS ACLNLTERKRLV AQHLTH V S QTQEQNKEN QNPN S D AP VIRS KTS ARYMEL VGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYL V GQQPVEDIS SNRIYKILELN GYDPQ Y AAS VFLGW ATKKFGKRNTIWLFGP ATTGKT NIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGS KVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRL DHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVR ES V AQPS TS D AE AS IN Y ADRY QNKC S RH V GMNLMLFPCRQCERMN QN S NICFTHGQ KDCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ

(SEQ ID NO: 22)

Example of wild-type AAV3 Rep78 amino acid sequence:

MPGF YEIVLK VPS DLDEHLPGIS N S FVNW V AEKEWELPPDS DMDPNLIEQ APLT V AE KLQREFLVE WRRV S KAPE ALFF V QFEKGET YFHLH VLIETIG VKS M V V GR Y V S QIKE KLVTRIYRGVEPQLPNWFA VTKTRN GAGGGNKVVDDC YIPNYLLPKTQPELQW AW TNMDQYLSACLNLAERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYM ELV GWLVDRGITS EKQWIQED Q AS YIS FN A AS NS RS QIKA ALDN AS KIMS LTKT APD YLV GS NPPEDITKNRIY QILELN G YDPQ Y A AS VFLGW AQKKF GKRNTIWLF GP ATTG KTNIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAIL GGSKVRVDQKCKSSAQIEPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELT RRLDHDF GKVTKQE VKDFFRW AS DH VTD V AHEFY VRKGG AKKRP AS ND AD V SEPK RQCTS LAQPTTS D AE AP AD Y ADR Y QNKC S RH V GMNLMLFPCKTCERMN QIS NVCFT HGQRDC GECFPGMS ES QP V S V VKKKT Y QKLCPIHHILGR APEIAC S ACDLAN VDLDD CVSEQ (SEQ ID NO: 23)

Example of wild-type AAV4 Rep78 amino acid sequence:

MPGFYEIVLKVPSDLDEHLPGISDSFVSWVAEKEWELPPDSDMDLNLIEQAPLTVAE KLQREFLVE WRRV S KAPE ALFF V QFEKGDS YFHLHILVET V G VKS M V V GRY V S QIKE KLVTRIYRGVEPQLPNWFA VTKTRNGAGGGNKVVDDCYIPNYLLPKTQPELQW AW TNMDQYISACLNLAERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYM ELV GWLVDRGITS EKQWIQED Q AS YIS FN A AS NS RS QIKA ALDN AS KIMS LTKT APD YLV GQNPPEDIS S NRI YRILEMN G YDPQ Y A AS VFLGW AQKKF GKRNTIWLF GP ATTG KTNIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAIL GGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELT KRLEHDF GKVTKQE VKDFFRW AS DHVTEVTHEFY VRKGG ARKRPAPND ADIS EPKR ACPSVAQPSTSDAEAPVDYADRYQNKCSRHVGMNLMLFPCRQCERMNQNVDICFT HGVMDCAECFPVSESQPVSVVRKRTYQKLCPIHHIMGRAPEVACSACELANVDLDD CDMEQ (SEQ ID NO: 24)

Example of wild-type AAV5 Rep78 amino acid sequence:

MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADR IRR VFLYE WNKF S KQES KFF V QFEKGS E YFHLHTLVETS GIS S M VLGR Y V S QIRAQLV KV VF QGIEPQIND W V AITKVKKGG ANKV VDS G YIP A YLLPKV QPELQW A WTNLDE Y KLAALNLEERKRLVAQFLAES S QRS QE AAS QREFS ADPVIKS KTS QKYMALVNWLV EHGITSEKQWIQENQESYLSFNSTGNSRSQIKAALDNATKIMSLTKSAVDYLVGSSVP ED IS KNRIW QIFEMN G YDP A Y AGS ILY GWCQRS FNKRNT VWLY GP ATT GKTNIAE AI AHTVPFYGCVNWTNENFPFNDCVDKMLIWWEEGKMTNKVVESAKAILGGSKVRVD QKCKSSVQIDSTPVIVTSNTNMCVVVDGNSTTFEHQQPLEDRMFKFELTKRLPPDFG KITKQEVKDFFAW AKVN QVPVTHEFKVPRELAGTKGAEKSLKRPLGD VTNTS YKS L EKR ARLS F VPETPRS S D VT VDP APLRPLNWN S RYDC KCD YH AQFDNIS NKCDECE YL NRGKNGCICHNVTHCQICHGIPPWEKENLSDFGDFDDANKEQ (SEQ ID NO: 25)

Example of wild-type AAV6 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLV QWRRV S RAPE ALFFV QFEKGES YFHLHILVETTGVKSM VLGRFLS QIRDK LV QTIYRGIEPTLPNWF A VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AHDLTH V S QTQEQNKENLNPN S D AP VIRS KT S ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN AAS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPAPPADIKTNRIYRILELNGYDPAYAGSVFLGWAQKRFGKRNTIWLFGPATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWAQDHVTEVAHEFYVRKGGANKRPAPDDADKSEPKRACP S V ADPS TS D AEG AP VDFADR Y QNKC S RH AGMLQMLFPCKTCERMN QNFNICFTHGT RDCSECFPGVSESQPVVRKRTYRKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSEQ

(SEQ ID NO: 26)

Example of wild-type AAV7 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLV QWRRV S RAPE ALFFV QFEKGES YFHLH VLVETTGVKSM VLGRFLS QIREK LV QTIYRGVEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPSLPADIKTNRIYRILELNGYDPAYAGSVFLGWAQKKFGKRNTIWLFGP ATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWASDHVTEVAHEFYVRKGGASKRPAPDDADISEPKRACPS VADPSTSDAEGAPVDFADRYQNKCSRHAGMIQMLFPCKTCERMNQNFNICFTHGVR DCLECFPGVSESQPVVRKKTYRKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSEQ

(SEQ ID NO: 27)

Example of wild-type AAV8 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLH VLVETTGVKSM VLGRFLS QIREK LGPDHLPAGSSPTLPNWFAVTKDAVMAPAGGNKVVDECYIPNYLLPKTQPELQWA WTNMEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S D AP VIRS KTS ARY MELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS AP D YLV GPS LP ADIT QNRIYRILALN G YDP A Y AGS VFLGW AQKKF GKRNTIWLFGP ATT GKTNIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAI LGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFEL TRRLEHDF GKVTKQE VKEFFRW AS DH VTE V AHEFY VRKGG AS KRP APDD ADKS EP KRACPS V ADPS TS D AEG AP VDF ADR Y QNKC S RH AGMLQMLFPC KTCERMN QNFNIC FTHG VRDC S ECFPG V S ES QP V VRKRT YRKLC AIHHLLGRAPEIAC S ACDLVNVDLDD CVSEQ (SEQ ID NO:28)

Example of wild-type AAVrh.8 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLH VLVETTGVKSM VLGRFLS QIREK LV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPS LP VDITQNRIYRILQLN G YDP AY AGS VFLGW AQKKF GKRNTIWLF GP ATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWASDHVTEVAHEFYVRKGGAS KRP APDD ADKSEPKRACP S V ADPS TS D AEG AP VDFADR Y QNKC S RH AGMLQMLLPC KTCERMN QNFNICFTHG VRDCSECFPGVSESQPVVRKRTYRKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSE

Q (SEQ ID NO: 29)

Example of wild-type AAV10 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLVHWRRV S KAPE ALFF V QFEKGES YFHLH VLVETT G VKS M VLGRFLS QIRDR LV QTIYRGVEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S D AP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPS LP ADIKANRIYRILELN G YDP A Y AGS VFLGW AQKKF GKRNTIWLFGP ATT GKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWAQDHVTEVTHEFYVRKGGATKRPAPSDADISEPKRACPS VAEPSTSDAEAPVDFADRYQNKCSRHAGMLQMLFPCKTCERMNQNFNVCFTHGVR DCSECFPGASESQPVVRKKTYQKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSEQ

(SEQ ID NO: 30)

Example of wild-type AAV11 Rep78 amino acid sequence:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLVHWRRV S KAPE ALFF V QFEKGES YFHLH VLVETT G VKS M VLGRFLS QIRDR LV QTIYRGVEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPS LP ADIKANRIYRILELN G YDP AY AGS VFLGW AQKKF GKRNTIWLFGP ATT GKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLE HDFGKVTKQEVKEFFRWAQDHVTEVAHEFYVRKGGATKRPAPSDADISEPKRACPS VPEPSTSDAEAPVDFADRYQNKCSRHAGMLQMLFPCKTCERMNQNFNVCFTHGVR DCSECFPGASESQPVVRKKTYQKLCAIHHLLGRAPEIACSACDLVNVDLDDCVSEQ

(SEQ ID NO: 31)

Example of wild-type AAV12 Rep78 amino acid sequence: MPGF YE VVIKVPS DLDEHLPGIS DS FVNW V AEKEWELPPDS DMD QNLIEQ APLT V AE KLQREFLVE WRRV S KFLE AKFF V QFEKGDS YFHLHILIEIT G VKS M V V GRY V S QIRDK LIQRIYRGVEPQLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKV QPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEGDKENLNPN S D AP VIRS KT S ARYMELV GWLVDKGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AS KIMS LTKT APD YLIG QQPV GDITTNRIYKILELN GYDPQY A AS VFLGW AQKKFGKRNTIWLFGPATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KAS AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLD HDFGKVTKQEVKDFFRWAADHVTDVAHEFYVTKGGAKKRPAPSDEDISEPKRPRVS FAQPETSDAEAPGDFADRYQNKCSRHAGMLQMLFPCKTCERMNQNSNVCFTHGQK DCGECFPGSESQPVSVVRKTYQKLCILHQLRGAPEIACSACDQLNPDLDDCQFEQ

(SEQ ID NO: 32)

Example of wild-type AAV13 Rep78 amino acid sequence:

MPGF YEIVLK VPS DLDEHLPGIS DS FVNW V AEKEWELPPDS DMDLNLIEQ APLT V AE KLQREFLVE WRRV S KAPE ALFF V QFEKGDS YFHLHILVET V G VKS M V V GRY V S QIKE KLVTRIYRGVEPQLPNWFA VTKTRN GAGGGNKVVDDC YIPNYLLPKTQPELQW AW TNMDQYLSACLNLAERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYM ELV GWLVDRGITS EKQWIQED Q AS YIS FN A AS NS RS QIKA ALDN AS KFMS LTKT APD YLV GNNPPEDIT S NRIYKILEMN G YDPQ Y A AS VFLGW AQKKF GKRNTIWLF GP ATTG KTNIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAIL GGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELT KRLEHDF GKVTKQE VKDFFRW AS DH VTE V S HEF Y VRKGG ARKRP APND ADIS EPKR ACPSVAQPSTSDAEAPVDYADRYQNKCSRHVGMNLMLFPCRQCERMNQNVDICFT HGVMDCAECFPVSESQPVSVVRKRTYQKLCPIHHIMGRAPEVACSACDLANVDLDD CDMEQ (SEQ ID NO: 33)

As defined herein, a rep gene or Rep protein comprises an N-terminus and a C- terminus (c), wherein the N terminus comprises an N-terminus domain (n), a DNA binding domain (d), and a helicase domain (h), and C terminus (c) comprises a NLS/p40 promoter domain (y) and a Zinc finger domain (z). Table 1 provides example sequences of these domains for different AAV serotypes. Table 1: Example sequences of rep gene and Rep protein domains for different AAV serotypes

In some embodiments, disclosed herein is a chimeric rep gene. In some

embodiments, a chimeric rep gene has at least one domain (e.g., n, d, h, y, or z) or at least one terminus (e.g., N terminus or C terminus) that is of a serotype that is different than the serotype of majority of the rep gene, or the serotypes of the other domains or terminus. In some embodiments, the N terminus is of serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13) different than the serotype of the C terminus (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). In some embodiments, the N terminus is of one serotype and the C-terminus is of a second serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13).

In some embodiments, the n domain is of AAV serotype 1, and each of the d, h, y, and z are of a serotype other than AAV1 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, each of the d, h, y, and z domains may be of the same serotype (e.g., 2, 3, 4, 5, 6, 7,

8, 9, 10, 11, 12, or 13). In some embodiments, each of the d, h, y, and z domains may be of different serotypes relative to each other, e.g., d, h, and y may be of AAV2 serotype, while z may be of AAV3 serotype. In some embodiments, the n domain is of AAV serotype 2, and each of the d, h, y, and z domains are of a serotype other than AAV2 (e.g., 1, 3, 4, 5, 6, 7, 8,

9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 3, and each of the d, h, y, and z domains are of a serotype other than AAV3 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 4, and each of the d, h, y, and z domains are of a serotype other than AAV4 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 5, and each of the d, h, y, and z domains are of a serotype other than AAV5 (e.g., 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 6, and each of the d, h, y, and z domains are of a serotype other than AAV6 (e.g., 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 7, and each of the d, h, y, and z domains are of a serotype other than AAV7 (e.g., 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 8, and each of the d, h, y, and z domains are of a serotype other than AAV8 (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 9, and each of the d, h, y, and z domains are of a serotype other than AAV9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 10, and each of the d, h, y, and z domains are of a serotype other than AAV10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 11, and each of the d, h, y, and z domains are of a serotype other than AAV11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

12, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 12, and each of the d, h, y, and z domains are of a serotype other than AAV12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 13). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype

13, and each of the d, h, y, and z domains are of a serotype other than AAV13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12). The serotypes of each of the d, h, y, and z domains may be the same, or may be different from each other.

In some embodiments, the d domain is of AAV serotype 1, and each of the n, h, y, and z are of a serotype other than AAV1 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, each of the n, h, y, and z domains may be of the same serotype (e.g., 2, 3, 4, 5, 6, 7,

8, 9, 10, 11, 12, or 13). In some embodiments, each of the n, h, y, and z domains may be of different serotypes relative to each other, e.g., n, h, and y may be of AAV2 serotype, while z may be of AAV3 serotype. In some embodiments, the d domain is of AAV serotype 2, and each of the n, h, y, and z domains are of a serotype other than AAV2 (e.g., 1, 3, 4, 5, 6, 7, 8,

9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 3, and each of the n, h, y, and z domains are of a serotype other than AAV3 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 4, and each of the n, h, y, and z domains are of a serotype other than AAV4 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 5, and each of the n, h, y, and z domains are of a serotype other than AAV5 (e.g., 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 6, and each of the n, h, y, and z domains are of a serotype other than AAV6 (e.g., 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 7, and each of the n, h, y, and z domains are of a serotype other than AAV7 (e.g., 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the n domain is of AAV serotype 8, and each of the n, h, y, and z domains are of a serotype other than AAV8 (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 9, and each of the n, h, y, and z domains are of a serotype other than AAV9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 10, and each of the n, h, y, and z domains are of a serotype other than AAV10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 11, and each of the n, h, y, and z domains are of a serotype other than AAV11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

12, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype 12, and each of the n, h, y, and z domains are of a serotype other than AAV12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 13). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other. In some embodiments, the d domain is of AAV serotype

13, and each of the n, h, y, and z domains are of a serotype other than AAV13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12). The serotypes of each of the n, h, y, and z domains may be the same, or may be different from each other.

In some embodiments, the h domain is of AAV serotype 1, and each of the d, n, y, and z are of a serotype other than AAV1 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, each of the d, n, y, and z domains may be of the same serotype (e.g., 2, 3, 4, 5, 6, 7,

8, 9, 10, 11, 12, or 13). In some embodiments, each of the d, n, y, and z domains may be of different serotypes relative to each other, e.g., d, n, and y may be of AAV2 serotype, while z may be of AAV3 serotype. In some embodiments, the h domain is of AAV serotype 2, and each of the d, n, y, and z domains are of a serotype other than AAV2 (e.g., 1, 3, 4, 5, 6, 7, 8,

9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 3, and each of the d, n, y, and z domains are of a serotype other than AAV3 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 4, and each of the d, n, y, and z domains are of a serotype other than AAV4 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 5, and each of the d, n, y, and z domains are of a serotype other than AAV5 (e.g., 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 6, and each of the d, n, y, and z domains are of a serotype other than AAV6 (e.g., 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 7, and each of the d, n, y, and z domains are of a serotype other than AAV7 (e.g., 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 8, and each of the d, n, y, and z domains are of a serotype other than AAV8 (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 9, and each of the d, n, y, and z domains are of a serotype other than AAV9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 10, and each of the d, n, y, and z domains are of a serotype other than AAV10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 11, and each of the d, n, y, and z domains are of a serotype other than AAV11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

12, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype 12, and each of the d, n, y, and z domains are of a serotype other than AAV12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 13). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other. In some embodiments, the h domain is of AAV serotype

13, and each of the d, n, y, and z domains are of a serotype other than AAV13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12). The serotypes of each of the d, n, y, and z domains may be the same, or may be different from each other.

In some embodiments, the y domain is of AAV serotype 1, and each of the n, d, h, and z are of a serotype other than AAV1 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, each of the n, d, h, and z domains may be of the same serotype (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). In some embodiments, each of the n, d, h, and z domains may be of different serotypes relative to each other, e.g., d, h may be of AAV2 serotype, while z may be of AAV3 serotype. In some embodiments, the y domain is of AAV serotype 2, and each of the n, d, h, and z domains are of a serotype other than AAV2 (e.g., 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 3, and each of the n, d, h, and z domains are of a serotype other than AAV3 (e.g., 1, 2, 4, 5, 6, 7, 8,

9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 4, and each of the n, d, h, and z domains are of a serotype other than AAV4 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 5, and each of the n, d, h, and z domains are of a serotype other than AAV5 (e.g., 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 6, and each of the n, d, h, and z domains are of a serotype other than AAV6 (e.g., 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 7, and each of the n, d, h, and z domains are of a serotype other than AAV7 (e.g., 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 8, and each of the n, d, h, and z domains are of a serotype other than AAV8 (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 9, and each of the n, d, h, and z domains are of a serotype other than AAV9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 10, and each of the n, d, h, and z domains are of a serotype other than AAV10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 11, and each of the n, d, h, and z domains are of a serotype other than AAV11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 12, and each of the n, d, h, and z domains are of a serotype other than AAV12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 13). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other. In some embodiments, the y domain is of AAV serotype 13, and each of the n, d, h, and z domains are of a serotype other than AAV13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12). The serotypes of each of the n, d, h, and z domains may be the same, or may be different from each other.

In some embodiments, the z domain is of AAV serotype 1, and each of the n, d, h, and y are of a serotype other than AAV1 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, each of the n, d, h, and y domains may be of the same serotype (e.g., 2, 3, 4, 5, 6, 7,

8, 9, 10, 11, 12, or 13). In some embodiments, each of the n, d, h, and y domains may be of different serotypes relative to each other, e.g., d, h may be of AAV2 serotype, while z may be of AAV3 serotype. In some embodiments, the z domain is of AAV serotype 2, and each of the n, d, h, and y domains are of a serotype other than AAV2 (e.g., 1, 3, 4, 5, 6, 7, 8, 9, 10,

11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 3, and each of the n, d, h, and y domains are of a serotype other than AAV3 (e.g., 1, 2, 4, 5, 6, 7, 8,

9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 4, and each of the n, d, h, and y domains are of a serotype other than AAV4 (e.g., 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 5, and each of the n, d, h, and y domains are of a serotype other than AAV5 (e.g., 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 6, and each of the n, d, h, and y domains are of a serotype other than AAV6 (e.g., 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 7, and each of the n, d, h, and y domains are of a serotype other than AAV7 (e.g., 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 8, and each of the n, d, h, and y domains are of a serotype other than AAV8 (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 9, and each of the n, d, h, and y domains are of a serotype other than AAV9 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 10, and each of the n, d, h, and y domains are of a serotype other than AAV10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 11, and each of the n, d, h, and y domains are of a serotype other than AAV11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 12, and each of the n, d, h, and y domains are of a serotype other than AAV12 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 13). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other. In some embodiments, the z domain is of AAV serotype 13, and each of the n, d, h, and y domains are of a serotype other than AAV13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,

11, or 12). The serotypes of each of the n, d, h, and y domains may be the same, or may be different from each other.

FIGs. 7-16 provide examples of chimeric rep genes. It is to be understood that any combination of domains may be of a serotype that is different from the serotypes of the other domains. For example, only one domain may have a serotype that is different from the serotypes of the other domain. In some embodiments, all five domains have different serotypes. In some embodiments, the domains of a chimeric rep gene is of two different serotypes (e.g., Rlh2, i.e., an h domain of AAV2 and other domains of AAV1). In some embodiments, the domains of a chimeric rep gene is of three different serotypes (e.g.,

Rlc3h4, i.e, a C terminus of AAV3, a h domain of AAV4 and n and d domains of AA1). In some embodiments, the domains of a chimeric rep gene is of four different serotypes (e.g., Rlh2d3y4, i.e., an h domain of AA2, d domain of AAV3, y domain of AAV3 and n and y domains of AAV1). In some embodiments, the domains of a chimeric rep gene is of five different serotypes (e.g., Rln2d3h4y8).

In some embodiments, a domain is truncated. In some embodiments a domain of a chimeric rep gene is truncated on the N terminal end of the domain. In some embodiments, a chimeric rep gene is truncated on the C terminal end of the domain. In some embodiments, a domain is modified such that non-contiguous nucleotides are deleted. In some embodiments, a domain is truncated by 1-18 nucleotides (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 nucleotides). For example, a d domain may be truncated by 6 nucleotides on either the N terminal end or the C terminal end. In some embodiments, any of the rep genes described herein comprises a start codon with the sequence ACG. In some embodiments, any of the rep genes described herein comprises a start codon with the sequence other than or different from ACG. In some embodiments, a start codon that has a sequence that is different from ACG is ATG.

It is also to be understood that the present disclosure also provides any chimeric Rep proteins that are encoded by any one of the chimeric rep genes disclosed herein, as well as any chimeric rep genes that may encode any one of the chimeric Rep proteins as disclosed herein.

In some embodiments of the present application, a Rep protein is chimeric in that it comprises amino acid sequences from more than one AAV serotype. In some embodiments, a chimeric Rep protein may comprise an N terminus comprising amino acids from one AAV serotype (e.g., AAV1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13) and a C terminus comprising amino acids from another AAV serotype (e.g., AAV1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13). For example, a Rep protein may comprise an N terminus comprising corresponding amino acids of AAV 1 Rep protein, and a C terminus comprising corresponding amino acids of AAV2 Rep protein (e.g., SEQ ID NO: 34 for Rep78 comprising an N term of AAV1 and a C term of AAV2). A Rep protein may comprise an N terminus comprising corresponding amino acids of AAV2 Rep protein, and a C terminus comprising corresponding amino acids of AAV1 Rep protein (e.g., SEQ ID NO: 35 for Rep78 comprising an N term of AAV2 and a C term of AAV1). In another non-limiting example, a Rep protein comprises an N terminus comprising corresponding amino acids of AAV2 Rep protein, and a C terminus comprising corresponding amino acids of AAV5 Rep protein (e.g., SEQ ID NO: 36 for Rep78 comprising an N term of AAV2 and a C term of AAV5). In another non-limiting example, a Rep protein comprises an N terminus comprising corresponding amino acids of AAV5 Rep protein, and a C terminus comprising corresponding amino acids of AAV2 Rep protein (e.g., SEQ ID NO: 37 for Rep78 comprising an N term of AAV5 and a C term of AAV2). In some embodiments, a Rep protein comprises corresponding amino acids of more than two AAV serotypes (e.g., three, four, or five AAV serotypes). A non-limiting example of a Rep protein comprising corresponding amino acids of three AAV serotypes is Rep protein with corresponding amino acids from AAV1, AAV2 and AAV5. The term“corresponding amino acids” as used herein means amino acids in positions that align with each other in amino acid sequences of different AAV serotypes. In some embodiments, the corresponding amino acids between two AAV serotypes have the same positions. In some embodiments, corresponding amino acids between two AAV serotypes are in positions that are 1-5 amino acids shifted from each other. Methods of aligning amino acid sequences are known in the art, and algorithms to perform such alignments are also readily available. See e.g., Michael S.

Rosenberg, Sequence Alignment: Methods, Models, Concepts, and Strategies, 2009,

http://www.istor.Org/stable/l0. l525/i.cttlpps7t· For example, alignment of AAV ITRs and/or Rep proteins can be performed using Protein BLAST,

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PRQGRAM=blastp&a mp;PAGE TYPE=BlastSearch&B LAST SPEC=blast2seq&LINK LQC=blasttab.

Example of Rep78 amino acid sequence with an AAV1 N term and an AAV2 C term:

MPGFYEIVIKVPSDLDEHLPGISDSFVSWVAEKEWELPPDSDMDLNLIEQAPLTVAE K LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLHILVETTGVKSM VLGRFLS QIRDK LV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLV GQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNI AEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSK VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLD HDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVRE S V AQPS TS DAE AS IN Y ADR Y QNKCS RH V GMNLMLFPCRQCERMN QN S NICFTHGQK DCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ

(SEQ ID NO: 34)

Example of Rep78 amino acid sequence with an AAV2 N term and an AAV1 C term:

MPGF YEIVIKVPS DLD GHLPGIS DS FVNW V AEKEWELPPDS DMDLNLIEQ APLT V AE KLQRDFLTE WRRV S KAPE ALFF V QFEKGES YFHMH VLVETT G VKS M VLGRFLS QIRE KLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDECYIPNYLLPKTQPELQWAWTN MEQ YLS ACLNLTERKRLV AQHLTH V S QTQEQNKEN QNPN S D AP VIRS KTS ARYMEL

V GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YL

V GP APP ADIKTNRIYRILELN G YEP AY AGS VFLGW AQKRF GKRNTIWLF GP ATT GKT NIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGG SKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRR LEHDFGKVTKQEVKEFFRWAQDHVTEVAHEFYVRKGGANKRPAPDDADKSEPKRA CPSVADPSTSDAEGAPVDFADRYQNKCSRHAGMLQMLFPCKTCERMNQNFNICFTH GTRDCSECFPGVSESQPVVRKRTYRKLCAIHHLLGRAPEIACSACDLVNVDLDDCVS EQ (SEQ ID NO: 35)

Example of Rep78 amino acid sequence with an AAV2 N term and an AAV5 C term:

MPGF YEIVIKVPS DLD GHLPGIS DS FVNW V AEKEWELPPDS DMDLNLIEQ APLT V AE KLQRDFLTE WRRV S KAPE ALFF V QFEKGES YFHMH VLVETT G VKS M VLGRFLS QIRE KLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDECYIPNYLLPKTQPELQWAWTN MEQ YLS ACLNLTERKRLV AQHLTH V S QTQEQNKEN QNPN S D AP VIRS KTS ARYM AL VNWLVEHGITS EKQWIQEN QES YLS FN S TGN S RS QIKA ALDN ATKIMS LTKS A VD YL VGS S VPEDIS KNRIW QIFEMN G YDP A Y AGS IFY GWCQRS FNKRNT VWFY GP ATTGK TNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMFIWWEEGKMTNKVVESAKAIFGG SKVRVDQKCKSSVQIDSTPVIVTSNTNMCVVVDGNSTTFEHQQPFEDRMFKFEFTKR FPPDFGKITKQEVKDFFAWAKVNQVPVTHEFKVPREFAGTKGAEKSFKRPFGDVTN TS YKS FEKRARFS F VPETPRS S D VT VDP APFRPFNWN S R YDCKCD YH AQFDNIS NKC DECEYFNRGKNGCICHNVTHCQICHGIPPWEKENFSDFGDFDDANKEQ (SEQ ID NO: 36)

Example of Rep78 amino acid sequence with an AAV5 N term and an AAV2 C term:

MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVAD R IRR VFLYE WNKF S KQES KFF V QFEKGS E YFHLHTLVETS GIS S M VLGR Y V S QIRAQLV KV VF QGIEPQIND W V AITKVKKGG ANKV VDS G YIP A YLLPKV QPELQW A WTNLDE Y KLA ALNLEERKRLV AQFLAES S QRS QE A AS QREFS ADP VIKS KTS QKYMEL V GWLV DKGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIMS LTKT APD YLV GQQP VEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAI AHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRV DQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDF GKVTKQE VKDFFRW AKDH V VE VEHEF Y VKKGG AKKRP APS D ADIS EPKRVRES V A QPSTSDAEASINYADRYQNKCSRHVGMNLMLFPCRQCERMNQNSNICFTHGQKDCL ECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ (SEQ ID NO: 37)

Examples of non-limiting chimeric Rep proteins and nucleic acid sequences encoding them:

Rlc2 amino acid sequence: MPGFYEIVIKVPSDLDEHLPGISDSFVSWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLHILVETTG VKSM VLGRFLS QIRDK LV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S DAP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN AAS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPAPPADIKTNRIYRILELN GYEPAY AGS VFLGWAQKRFGKRNTIWLFGPATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLD HDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVRE S V AQPS TS DAE AS IN Y ADR Y QNKCS RHV GMNLMLFPCRQCERMN QN S NICFTHGQK DCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ

(SEQ ID NO: 188)

R1 hc2 amino acid:

MPGFYEIVIKVPSDLDEHLPGISDSFVSWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLHILVETTG VKSM VLGRFLS QIRDK LV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S D AP VIRS KTS ARYMELV GWLVDRGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLV GQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNI AEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSK VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLD HDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVRE S V AQPS TS DAE AS IN Y ADR Y QNKCS RH V GMNLMLFPCRQCERMN QN S NICFTHGQK DCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ

(SEQ ID NO: 189)

R2dl amino acid:

TPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIRD KLV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWT NMEEYIS ACLNLAERKRLVAQHLTHV S QTQEQNKENLNPNSD APVIRS KTS ARYMEL

V GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIMS LTKT APD YL

V GQQPVEDIS SNRIYKILELN GYDPQ Y AAS VFLGW ATKKFGKRNTIWLFGP ATTGKT NIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGS KVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRL DHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVR ES V AQPS TS DAE AS IN Y ADRY QNKC S RHV GMNLMLFPCRQCERMN QN S NICFTHGQ KDCLECFPVSEDNASQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCI FEQ (SEQ ID NO: 190)

R2hl amino acid:

TPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEK LQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREK LIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDECYIPNYLLPKTQPELQWAWTN MEQ YLS ACLNLTERKRLV AQHLTH V S QTQEQNKEN QNPN S D AP VIRS KTS ARYMEL

V GWLVD KGITS EKQ WIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YL

V GP APP ADIKTNRIYRILELN G YEP AY AGS VFLGW AQKRF GKRNTIWLF GP ATT GKT NIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGG SKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRR LDHDF GKVTKQE VKDFFRW AKDH V VE VEHEFY VKKGG AKKRP APS D ADIS EPKR V RES V AQPS TS DAE AS IN Y ADR Y QNKCS RH V GMNLMLFPCRQCERMN QN S NICFTHG QKDCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFE

Q (SEQ ID NO: 191)

R8dl c2 amino acid:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLV QWRRV S RAPE ALFFV QFEKGES YFHLH VLVETTGVKSM VLGRFLS QIRD KLV QTIYRGIEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWT NMEEYIS ACLNLAERKRLVAQHLTHV S QTQEQNKENLNPNSD APVIRS KTS ARYMEL

V GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YL

V GPS LP ADIT QNRIYRILALN G YDP A Y AGS VFLGW AQKKFGKRNTIWLF GP ATT GKT NIAEAIAHAVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGG SKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRR LDHDF GKVTKQE VKDFFRW AKDH VVE VEHEFY VKKGG AKKRP APS D ADIS EPKR V RES V AQPS TS DAE AS IN Y ADR Y QNKCS RHV GMNLMLFPCRQCERMN QN S NICFTHG QKDCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFE

Q (SEQ ID NO: 192) R8pl/2c2 amino acid:

MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDRNLIEQAPLTVAEK LQRDFLV QWRRV S KAPE ALFFV QFEKGES YFHLH VLVETTGVKSM VLGRFLS QIREK LV QTIYRGVEPTLPNWFA VTKTRN GAGGGNKVVDEC YIPNYLLPKTQPELQW AWTN MEE YIS ACLNLAERKRLV AQHLTH V S QTQEQNKENLNPN S D AP VIRS KTS ARYMELV GWLVDRGITS EKQWIQEDQ AS YIS FN A AS NS RS QIKA ALDN AGKIM ALTKS APD YLV GPS LP ADIT QNRIYRILALN G YDP A Y AGS VFLGW AQKKF GKRNTIWLF GP ATTGKTNI AE AIAH A VPF Y GC VNWTNENFPFNDC VD KM VIWWEEGKMT AKV VES AKAILGGS K VRVDQKC KS S AQIDPTP VIVTS NTNMC A VID GN S TTFEHQQPLQDRMFKFELTRRLD HDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEPKRVRE S V AQPS TS DAE AS IN Y ADR Y QNKCS RH V GMNLMLFPCRQCERMN QN S NICFTHGQK DCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDDCIFEQ

(SEQ ID NO: 193)

Rlc2 sene sequence:

ATGCCGGGCTTCTACGAGATCGTGATCAAGGTGCCGAGCGACCTGGACGAGCAC

CTGCCGGGCATTTCTGACTCGTTTGTGAGCTGGGTGGCCGAGAAGGAATGGGAG

CTGCCCCCGGATTCTGACATGGATCTGAATCTGATTGAGCAGGCACCCCTGACCG

TGGCCGAGAAGCTGCAGCGCGACTTCCTGGTCCAATGGCGCCGCGTGAGTAAGG

CCCCGGAGGCCCTCTTCTTTGTTCAGTTCGAGAAGGGCGAGTCCTACTTCCACCT

CCATATTCTGGTGGAGACCACGGGGGTCAAATCCATGGTGCTGGGCCGCTTCCTG

AGTCAGATTAGGGACAAGCTGGTGCAGACCATCTACCGCGGGATCGAGCCGACC

CTGCCCAACTGGTTCGCGGTGACCAAGACGCGTAATGGCGCCGGAGGGGGGAAC

AAGGTGGTGGACGAGTGCTACATCCCCAACTACCTCCTGCCCAAGACTCAGCCC

GAGCTGCAGTGGGCGTGGACTAACATGGAGGAGTATATAAGCGCCTGTTTGAAC

CTGGCCGAGCGCAAACGGCTCGTGGCGCAGCACCTGACCCACGTCAGCCAGACC

CAGGAGCAGAACAAGGAGAATCTGAACCCCAATTCTGACGCGCCTGTCATCCGG

TCAAAAACCTCCGCGCGCTACATGGAGCTGGTCGGGTGGCTGGTGGACCGGGGC

ATCACCTCCGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCGTACATCTCCTTC

AACGCCGCTTCCAACTCGCGGTCCCAGATCAAGGCCGCTCTGGACAATGCCGGC

AAGATCATGGCGCTGACCAAATCCGCGCCCGACTACCTGGTAGGCCCCGCTCCG

CCCGCGGACATTAAAACCAACCGCATCTACCGCATCCTGGAGCTGAACGGCTAC

GAACCTGCCTACGCCGGCTCCGTCTTTCTCGGCTGGGCCCAGAAAAGGTTCGGGA AGCGCAACACCATCTGGCTGTTTGGGCCGGCCACCACGGGCAAGACCAACATCG

CGGAAGCCATCGCCCACGCCGTGCCCTTCTACGGCTGCGTCAACTGGACCAATGA

GAACTTTCCCTTCAATGATTGCGTCGACAAGATGGTGATCTGGTGGGAGGAGGG

GAAGATGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAA

GGTGCGCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGT

GATCGTCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGAC

CTTCGAACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGC

CGTCTGGATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCC

GGTGGGCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGG

GTGGAGCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAAC

GGGTGCGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCA

ACTACGCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGA

TGCTGTTTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTT

CACTCACGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCC

GTTTCTGTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGG

GAAAGGTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGA

CT GC AT CTTT G A AC A AT A A (SEQ ID NO: 194)

Rlhc2 sene sequence:

ATGCCGGGCTTCTACGAGATCGTGATCAAGGTGCCGAGCGACCTGGACGAGCAC

CTGCCGGGCATTTCTGACTCGTTTGTGAGCTGGGTGGCCGAGAAGGAATGGGAG

CTGCCCCCGGATTCTGACATGGATCTGAATCTGATTGAGCAGGCACCCCTGACCG

TGGCCGAGAAGCTGCAGCGCGACTTCCTGGTCCAATGGCGCCGCGTGAGTAAGG

CCCCGGAGGCCCTCTTCTTTGTTCAGTTCGAGAAGGGCGAGTCCTACTTCCACCT

CCATATTCTGGTGGAGACCACGGGGGTCAAATCCATGGTGCTGGGCCGCTTCCTG

AGTCAGATTAGGGACAAGCTGGTGCAGACCATCTACCGCGGGATCGAGCCGACC

CTGCCCAACTGGTTCGCGGTGACCAAGACGCGTAATGGCGCCGGAGGGGGGAAC

AAGGTGGTGGACGAGTGCTACATCCCCAACTACCTCCTGCCCAAGACTCAGCCC

GAGCTGCAGTGGGCGTGGACTAACATGGAGGAGTATATAAGCGCCTGTTTGAAC

CTGGCCGAGCGCAAACGGCTCGTGGCGCAGCACCTGACCCACGTCAGCCAGACC

CAGGAGCAGAACAAGGAGAATCTGAACCCCAATTCTGACGCGCCTGTCATCCGG

TCAAAAACCTCCGCGCGCTACATGGAGCTGGTCGGGTGGCTGGTGGACCGGGGC

ATCACCTCCGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCATACATCTCCTTC

AATGCGGCCTCCAACTCGCGGTCCCAAATCAAGGCTGCCTTGGACAATGCGGGA AAGATTATGAGCCTGACTAAAACCGCCCCCGACTACCTGGTGGGCCAGCAGCCC

GTGGAGGACATTTCCAGCAATCGGATTTATAAAATTTTGGAACTAAACGGGTACG

ATCCCCAATATGCGGCTTCCGTCTTTCTGGGATGGGCCACGAAAAAGTTCGGCAA

GAGGAACACCATCTGGCTGTTTGGGCCTGCAACTACCGGGAAGACCAACATCGC

GGAGGCCATAGCCCACACTGTGCCCTTCTACGGGTGCGTAAACTGGACCAATGA

GAACTTTCCCTTCAACGACTGTGTCGACAAGATGGTGATCTGGTGGGAGGAGGG

GAAGATGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAA

GGTGCGCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGT

GATCGTCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGAC

CTTCGAACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGC

CGTCTGGATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCC

GGTGGGCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGG

GTGGAGCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAAC

GGGTGCGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCA

ACTACGCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGA

TGCTGTTTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTT

CACTCACGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCC

GTTTCTGTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGG

GAAAGGTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGA

CT GC AT CTTT G A AC A AT A A (SEQ ID NO: 195)

R2dl sene sequence:

ACGCCGGGGTTTTACGAGATTGTGATTAAGGTCCCCAGCGACCTTGACGAGCATC

TGCCCGGCATTTCTGACAGCTTTGTGAACTGGGTGGCCGAGAAGGAATGGGAGTT

GCCGCCAGATTCTGACATGGATCTGAATCTGATTGAGCAGGCACCCCTGACCGTG

GCCGAGAAGCTGCAGCGCGACTTTCTGACGGAATGGCGCCGTGTGAGTAAGGCC

CCGGAGGCCCTTTTCTTTGTGCAATTTGAGAAGGGAGAGAGCTACTTCCACATGC

ACGTGCTCGTGGAAACCACCGGGGTGAAATCCATGGTGCTGGGCCGCTTCCTGA

GTCAGATTAGGGACAAGCTGGTGCAGACCATCTACCGCGGGATCGAGCCGACCC

TGCCCAACTGGTTCGCGGTGACCAAGACGCGTAATGGCGCCGGAGGGGGGAACA

AGGTGGTGGACGAGTGCTACATCCCCAACTACCTCCTGCCCAAGACTCAGCCCG

AGCTGCAGTGGGCGTGGACTAACATGGAGGAGTATATAAGCGCCTGTTTGAACC

TGGCCGAGCGCAAACGGCTCGTGGCGCAGCACCTGACCCACGTCAGCCAGACCC

AGGAGCAGAACAAGGAGAATCTGAACCCCAATTCTGACGCGCCTGTCATCCGGT CAAAAACCTCCGCGCGCTACATGGAGCTGGTCGGGTGGCTGGTGGACCGGGGCA

TCACCTCCGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCATACATCTCCTTCA

ATGCGGCCTCCAACTCGCGGTCCCAAATCAAGGCTGCCTTGGACAATGCGGGAA

AGATTATGAGCCTGACTAAAACCGCCCCCGACTACCTGGTGGGCCAGCAGCCCG

TGGAGGACATTTCCAGCAATCGGATTTATAAAATTTTGGAACTAAACGGGTACGA

TCCCCAATATGCGGCTTCCGTCTTTCTGGGATGGGCCACGAAAAAGTTCGGCAAG

AGGAACACCATCTGGCTGTTTGGGCCTGCAACTACCGGGAAGACCAACATCGCG

GAGGCCATAGCCCACACTGTGCCCTTCTACGGGTGCGTAAACTGGACCAATGAG

AACTTTCCCTTCAACGACTGTGTCGACAAGATGGTGATCTGGTGGGAGGAGGGG

AAGATGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAAG

GTGCGCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGTG

ATCGTCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGACCT

TCGAACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGCC

GTCTGGATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCCG

GTGGGCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGGG

TGGAGCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAACG

GGTGCGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCAA

CTACGCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGAT

GCTGTTTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTTC

ACTCACGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCCG

TTTCTGTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGGG

AAAGGTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGAC

TGC ATCTTTGAAC AAT AA (SEQ ID NO: 196)

R2hl sene sequence:

ACGCCGGGGTTTTACGAGATTGTGATTAAGGTCCCCAGCGACCTTGACGAGCATC

TGCCCGGCATTTCTGACAGCTTTGTGAACTGGGTGGCCGAGAAGGAATGGGAGTT

GCCGCCAGATTCTGACATGGATCTGAATCTGATTGAGCAGGCACCCCTGACCGTG

GCCGAGAAGCTGCAGCGCGACTTTCTGACGGAATGGCGCCGTGTGAGTAAGGCC

CCGGAGGCCCTTTTCTTTGTGCAATTTGAGAAGGGAGAGAGCTACTTCCACATGC

ACGTGCTCGTGGAAACCACCGGGGTGAAATCCATGGTTTTGGGACGTTTCCTGAG

TCAGATTCGCGAAAAACTGATTCAGAGAATTTACCGCGGGATCGAGCCGACTTTG

CCAAACTGGTTCGCGGTCACAAAGACCAGAAATGGCGCCGGAGGCGGGAACAA

GGTGGTGGATGAGTGCTACATCCCCAATTACTTGCTCCCCAAAACCCAGCCTGAG CTCCAGTGGGCGTGGACTAATATGGAACAGTATTTAAGCGCCTGTTTGAATCTCA

CGGAGCGTAAACGGTTGGTGGCGCAGCATCTGACGCACGTGTCGCAGACGCAGG

AGCAGAACAAAGAGAATCAGAATCCCAATTCTGATGCGCCGGTGATCAGATCAA

AAACTTCAGCCAGGTACATGGAGCTGGTCGGGTGGCTCGTGGACAAGGGGATTA

CCTCGGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCGTACATCTCCTTCAACG

CCGCTTCCAACTCGCGGTCCCAGATCAAGGCCGCTCTGGACAATGCCGGCAAGA

TCATGGCGCTGACCAAATCCGCGCCCGACTACCTGGTAGGCCCCGCTCCGCCCGC

GGACATTAAAACCAACCGCATCTACCGCATCCTGGAGCTGAACGGCTACGAACC

TGCCTACGCCGGCTCCGTCTTTCTCGGCTGGGCCCAGAAAAGGTTCGGGAAGCGC

AACACCATCTGGCTGTTTGGGCCGGCCACCACGGGCAAGACCAACATCGCGGAA

GCCATCGCCCACGCCGTGCCCTTCTACGGCTGCGTCAACTGGACCAATGAGAACT

TTCCCTTCAATGATTGCGTCGACAAGATGGTGATCTGGTGGGAGGAGGGGAAGA

TGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAAGGTGC

GCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGTGATCG

TCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGACCTTCGA

ACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGCCGTCTG

GATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCCGGTGG

GCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGGGTGGA

GCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAACGGGTG

CGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCAACTAC

GCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGATGCTGT

TTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTTCACTCA

CGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCCGTTTCT

GTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGGGAAAG

GTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGACTGCA

TCTTTGAACAATAA (SEQ ID NO: 197)

R8dlc2 sene sequence:

ATGCCGGGCTTCTACGAGATCGTGATCAAGGTGCCGAGCGACCTGGACGAGCAC

CTGCCGGGCATTTCTGACTCGTTTGTGAACTGGGTGGCCGAGAAGGAATGGGAG

CTGCCCCCGGATTCTGACATGGATCGGAATCTGATCGAGCAGGCACCCCTGACCG

TGGCCGAGAAGCTGCAGCGCGACTTCCTGGTCCAATGGCGCCGCGTGAGTAAGG

CCCCGGAGGCCCTCTTCTTTGTTCAGTTCGAGAAGGGCGAGAGCTACTTTCACCT

GCACGTTCTGGTCGAGACCACGGGGGTCAAGTCCATGGTGCTGGGCCGCTTCCTG AGTCAGATTAGGGACAAGCTGGTGCAGACCATCTACCGCGGGATCGAGCCGACC

CTGCCCAACTGGTTCGCGGTGACCAAGACGCGTAATGGCGCCGGAGGGGGGAAC

AAGGTGGTGGACGAGTGCTACATCCCCAACTACCTCCTGCCCAAGACTCAGCCC

GAGCTGCAGTGGGCGTGGACTAACATGGAGGAGTATATAAGCGCCTGTTTGAAC

CTGGCCGAGCGCAAACGGCTCGTGGCGCAGCACCTGACCCACGTCAGCCAGACC

CAGGAGCAGAACAAGGAGAATCTGAACCCCAATTCTGACGCGCCTGTCATCCGG

TCAAAAACCTCCGCGCGCTATATGGAGCTGGTCGGGTGGCTGGTGGACCGGGGC

ATCACCTCCGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCGTACATCTCCTTC

AACGCCGCCTCCAACTCGCGGTCCCAGATCAAGGCCGCGCTGGACAATGCCGGC

AAGATCATGGCGCTGACCAAATCCGCGCCCGACTACCTGGTGGGGCCCTCGCTG

CCCGCGGACATTACCCAGAACCGCATCTACCGCATCCTCGCTCTCAACGGCTACG

ACCCTGCCTACGCCGGCTCCGTCTTTCTCGGCTGGGCTCAGAAAAAGTTCGGGAA

ACGCAACACCATCTGGCTGTTTGGACCCGCCACCACCGGCAAGACCAACATTGC

GGAAGCCATCGCCCACGCCGTGCCCTTCTACGGCTGCGTCAACTGGACCAATGA

GAACTTTCCCTTCAATGATTGCGTCGACAAGATGGTGATCTGGTGGGAGGAGGG

GAAGATGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAA

GGTGCGCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGT

GATCGTCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGAC

CTTCGAACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGC

CGTCTGGATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCC

GGTGGGCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGG

GTGGAGCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAAC

GGGTGCGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCA

ACTACGCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGA

TGCTGTTTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTT

CACTCACGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCC

GTTTCTGTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGG

GAAAGGTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGA

CT GC AT CTTT G A AC A AT A A (SEQ ID NO: 198)

R8pl/2c2 sene sequence:

ATGCCGGGCTTCTACGAGATCGTGATCAAGGTGCCGAGCGACCTGGACGAGCAC

CTGCCGGGCATTTCTGACTCGTTTGTGAACTGGGTGGCCGAGAAGGAATGGGAG

CTGCCCCCGGATTCTGACATGGATCGGAATCTGATCGAGCAGGCACCCCTGACCG TGGCCGAGAAGCTGCAGCGCGACTTCCTGGTCCAATGGCGCCGCGTGAGTAAGG

CCCCGGAGGCCCTCTTCTTTGTTCAGTTCGAGAAGGGCGAGAGCTACTTTCACCT

GCACGTTCTGGTCGAGACCACGGGGGTCAAGTCCATGGTGCTAGGCCGCTTCCTG

AGTCAGATTCGGGAAAAGCTGGTCCAGACCATCTACCGCGGGGTCGAGCCCACC

TTGCCCAACTGGTTCGCGGTGACCAAGACGCGTAATGGCGCCGGGGGGGGGAAC

AAGGTGGTGGACGAGTGCTACATCCCCAACTACCTCCTGCCCAAGACTCAGCCC

GAGCTGCAGTGGGCGTGGACTAACATGGAGGAGTATATAAGCGCGTGCTTGAAC

CTGGCCGAGCGCAAACGGCTCGTGGCGCAGCACCTGACCCACGTCAGCCAGACG

CAGGAGCAGAACAAGGAGAATCTGAACCCCAATTCTGACGCGCCCGTGATCAGG

TCAAAAACCTCCGCGCGCTATATGGAGCTGGTCGGGTGGCTGGTGGACCGGGGC

ATCACCTCCGAGAAGCAGTGGATCCAGGAGGACCAGGCCTCGTACATCTCCTTC

AACGCCGCCTCCAACTCGCGGTCCCAGATCAAGGCCGCGCTGGACAATGCCGGC

AAGATCATGGCGCTGACCAAATCCGCGCCCGACTACCTGGTGGGGCCCTCGCTG

CCCGCGGACATTACCCAGAACCGCATCTACCGCATCCTCGCTCTCAACGGCTACG

ACCCTGCCTACGCCGGCTCCGTCTTTCTCGGCTGGGCTCAGAAAAAGTTCGGGAA

ACGCAACACCATCTGGCTGTTTGGACCCGCCACCACCGGCAAGACCAACATTGC

GGAAGCCATCGCCCACGCCGTGCCCTTCTACGGCTGCGTCAACTGGACCAATGA

GAACTTTCCCTTCAATGATTGCGTCGACAAGATGGTGATCTGGTGGGAGGAGGG

GAAGATGACCGCCAAGGTCGTGGAGTCGGCCAAAGCCATTCTCGGAGGAAGCAA

GGTGCGCGTGGACCAGAAATGCAAGTCCTCGGCCCAGATAGACCCGACTCCCGT

GATCGTCACCTCCAACACCAACATGTGCGCCGTGATTGACGGGAACTCAACGAC

CTTCGAACACCAGCAGCCGTTGCAAGACCGGATGTTCAAATTTGAACTCACCCGC

CGTCTGGATCATGACTTTGGGAAGGTCACCAAGCAGGAAGTCAAAGACTTTTTCC

GGTGGGCAAAGGATCACGTGGTTGAGGTGGAGCATGAATTCTACGTCAAAAAGG

GTGGAGCCAAGAAAAGACCCGCCCCCAGTGACGCAGATATAAGTGAGCCCAAAC

GGGTGCGCGAGTCAGTTGCGCAGCCATCGACGTCAGACGCGGAAGCTTCGATCA

ACTACGCAGACAGGTACCAAAACAAATGTTCTCGTCACGTGGGCATGAATCTGA

TGCTGTTTCCCTGCAGACAATGCGAGAGAATGAATCAGAATTCAAATATCTGCTT

CACTCACGGACAGAAAGACTGTTTAGAGTGCTTTCCCGTGTCAGAATCTCAACCC

GTTTCTGTCGTCAAAAAGGCGTATCAGAAACTGTGCTACATTCATCATATCATGG

GAAAGGTGCCAGACGCTTGCACTGCCTGCGATCTGGTCAATGTGGATTTGGATGA

CT GC AT CTTT G A AC A AT A A (SEQ ID NO: 199) Methods of packaging particles

Methods of producing rAAV particles are known in the art and reagents are commercially available (see, e.g., Zolotukhin et al. Production and purification of serotype 1, 2, and 5 recombinant adeno-associated viral vectors. Methods 28 (2002) 158-167; and U.S. Patent Publication Numbers US20070015238 and US20120322861, which are incorporated herein by reference; and plasmids and kits available from ATCC and Cell Biolabs, Inc.).

Generally, rAAV production involves culturing cells, introducing AAV genes and any genes of interest (e.g., flanked by ITRs) desired to be packaged to the cells, and allowing the cells to produce or package rAAV. The last step is followed by harvesting rAAV particles and subsequent purification steps. AAV genes and any genes desired to be packaged into rAAV particles may be introduced to cells by either transfection methods (e.g., using plasmid vectors and a transfection agent) or infection methods (e.g., using a viral vector).

In some embodiments, one or more genes of interest, rep gene (e.g., encoding a wild- type or recombinant, for example chimeric, Rep protein as described in this application), cap gene and helper genes (e.g., Ela gene, a Elb gene, a E4 gene, a E2a gene, and a VA gene) are introduced to a cell wherein the genes are comprised in one or more vectors (e.g., plasmids) such that the cell gets transfected or infected by the vectors. For clarity, helper genes are genes that encode helper proteins Ela, Elb, E4, E2a, and VA. In some

embodiments, only one or more genes of interest and the control elements to which they are operably linked are comprised in one vector, while one or more of the rep , cap and helper genes are comprised in comprised in one or more of separate vectors. For example, a first vector may comprise one more genes of interest, while a second vector may comprise rep , cap and helper genes. In some embodiments, a first vector may comprise one more genes of interest, while a second vector may comprise rep , and a third vector may comprise helper genes and cap. In some embodiments, a first vector may comprise one more genes of interest, while a second vector may comprise rep , and a third vector may comprise helper genes, and a forth vector may comprise cap.

In some embodiments, a nucleic acid vector used to deliver a gene of interest or AAV gene to a producer cell is circular. In some embodiments, a nucleic acid vector is single- stranded. In some embodiments, a nucleic acid vector is double- stranded. In some embodiments, a double-stranded nucleic acid vector may be, for example, a self

complimentary vector that contains a region of the nucleic acid vector that is complementary to another region of the nucleic acid vector, initiating the formation of the double

strandedness of the nucleic acid vector. In some embodiments of any one of the methods disclosed herein, the regions of nucleic acid (e.g., heterologous nucleic acid regions) that is flanked by ITRs comprises one or more genes of interest. Regions of nucleic acid flanked by ITRs may also comprise control elements that are operably linked to one or more genes of interest. In some embodiments either a rep gene or a cap gene or both the rep and cap genes are flanked by ITRs.

In some embodiments, a cell to which one or more genes of interest are introduced already comprise one or more of one rep gene, cap gene, and/or helper genes useful to package rAAV particles. As a non-limiting example, a cell may already comprise rep and express Rep proteins Rep78, Rep68, Rep52, and Rep40. Such a cell that expresses Rep proteins can be introduced to vectors comprising ITR-flanked genes of interest, and vectors that express cap and helper genes. In some embodiments, a cell may already comprise rep and helper genes.

Methods of transfecting a cell are known in the art. Non-limiting methods of transfecting cells are CaP04-mediated transfection, transfection using lipids or polymeric molecules such as Polyethylenimine (PEI), and electroporation. Cells can also be introduced to nucleic acid using using viral vectors (e.g., HSV vectors or baculovirus).

After introducing one or more of one or more genes of interest, rep gene, cap gene, and helper genes to a cell in a manner that they enter the cell by transfection or infection, the cell is incubated under conditions in which rAAV particles will be produced in the cell and escape from the cell. The rAAV particles can then be purified using any method known the art or described herein, e.g., by iodixanol step gradient, CsCl gradient, chromatography, or polyethylene glycol (PEG) precipitation.

Improving packaging of AAV particles using combinations of ITRs and rep of different serotypes, and or chimeric rep genes

Disclosed here are combinations of rep and ITRs of different serotypes such that their use in any method to produce or package rAAV particles results in greater packaging or production efficiency compared to similar conditions in which ITRs and rep gene of the same serotype are used. Accordingly, disclosed herein is also a method of packaging a rAAV particle comprising contacting a cell that expresses a rep gene of a first serotype with a recombinant nucleic acid comprising a pair of ITRs of a second serotype. In some embodiments, the first serotype and the second serotype are the same. In some embodiments, the first and second serotypes are different. In some embodiments on any one of the rAAV particle producing methods disclosed herein, the rep gene is expressed in any one of the producer cells disclosed herein by transfected or infecting the cells with a nucleic acid encoding the rep gene.

In some embodiments, a first serotype of rep gene is any one of serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13. In some embodiments, a second serotype of AAV ITRs is any one of serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13. In some embodiments, any one of the first serotype for rep is used with any serotype for ITRs. For example, rep of serotype 1 can be used with ITRs of any one of serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13. As another example, rep of serotype 2 can be used with ITRs of any one of serotypes 1, 2, 3, 4,

5, 6, 7, 8, 9, 10, 11, 12, and 13, and so on.

In some embodiments, rep of serotype 1 is used with ITRs or serotype 1, 2, 3, 4, or 7.

In some embodiments, ITRs of serotype 6 are used with rep of serotype 2, 3, 4, 6, 12, or 13. In some embodiments, ITRs of serotype 1 are used with rep of serotype 2, 3, 4, 12, or 13.

In some embodiments, a rep gene is chimeric. A chimeric AAV gene is one which comprises amino acids of more than one serotype. SEQ ID NOs 34-37 provide examples of chimeric Rep78 proteins. In some embodiments, ITRs of serotype 6 are used with chimeric rep of serotype 1 and 2. In some embodiments, ITRs of serotype 1 are used with chimeric rep of serotype 1 and 2. In some embodiments, ITRs of serotype 2 are used with chimeric rep of serotype 2 and 5. In some embodiments, ITRs of serotype 5 are used with chimeric rep of serotype 2 and 5.

Chimeric rep genes and Rep proteins are described above and may be used in any one of the methods of packaging rAAV particles as described herein.

In some embodiments, chimeric Rep proteins may comprise corresponding amino acids of a first serotype in the N terminus and corresponding amino acids of a second serotype in the C terminus. For example, a Rep protein may comprise amino acids of serotype 1 in the N terminus and amino acids of serotype 2 in the C terminus. In some embodiments, a Rep protein may comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 1 in the C terminus. In some embodiments, a Rep protein may comprise amino acids of serotype 2 in the N terminus and amino acids of serotype 5 in the C terminus. In some embodiments, a Rep protein may comprise amino acids of serotype 5 in the N terminus and amino acids of serotype 2 in the C terminus. It is to be understood that a chimeric rep gene may be used in combination with ITRs of any serotype for producing rAAV particles or any serotype or pseudo-serotype. Table 2 provides examples of combinations of rep serotypes that can be used with ITRs of different serotypes to improve rAAV particle production. It is to be understood that, in addition the combinations of ITRs and rep genes provided in Table 2, any one chimeric rep genes or chimeric Rep proteins can be used in combination with any one of the ITRs as described herein, which in turn can be used with any one of the cap genes and capsid proteins described herein for producing rAAV particles.

Table 2. Examples of ITR and Rep combinations (including examples of chimeras) to be generated and tested

1. AAV l_ITR+AAV l_Rep

2. AAV2_ITR+AAV l_Rep

3. AAV3_ITR+AAV l_Rep

4. AAV4_ITR+AAV l_Rep

5. AAV7_ITR+AAV l_Rep

6. AAV 6_ITR+ A A V 2_Rep

7. AAV 6_ITR+A A V 3_Rep

8. AAV 6_ITR+ A A V 4_Rep

9. AAV 6_ITR+A A V 6_Rep

10. AAV 6_ITR+ A A V 12_Rep

11. AAV 6_ITR+ A A V 13_Rep

12. AAV l_ITR+AAV2_Rep

13. AAV l_ITR+AAV3_Rep

14. AAV l_ITR+AAV4_Rep

15. AAV l_ITR+AAV l2_Rep

16. AAV l_ITR+AAVl3_Rep

17. AAV6_ITR+AAV lN/2C_chimeric_Rep

18. AAV l_ITR+AAV 1 N/2C_chimeric_Rep

19. AAV 6_ITR+ A A V 2N/ 1 C_chimeric_Rep

20. AAV l_ITR+AAV2N/lC_chimeric_Rep

21. AAV 2_ITR+ A A V 2N/5 C_chimeric_Rep

22. AAV 5_ITR+A A V5N/2C_chimeric_Rep

Producer cells

Provided herein are cells used to produce rAAV particles using the combinations of ITRs, cap and/or rep of different serotypes as disclosed herein. Accordingly, in some embodiments, a producer cell as disclosed herein comprises rep of a first AAV serotype and ITRs of a second AAV serotype. In some embodiments, a producer cell as disclosed herein comprises a combination of rep and ITRs, wherein the serotypes of the rep and ITRs are any one of the combinations disclosed herein.

In some embodiments, the packaging is performed in a helper cell or producer cell, such as a mammalian cell or an insect cell. Exemplary mammalian cells include, but are not limited to, HEK293 cells, COS cells, HeLa cells, BHK cells, or CHO cells (see, e.g., ATCC® CRL-1573™, ATCC® CRL-1651™, ATCC® CRL-1650™, ATCC® CCL-2, ATCC® CCL- 10™, or ATCC® CCL-61™). Exemplary insect cells include, but are not limited to Sf9 cells (see, e.g., ATCC® CRL-1711™). The helper cell may comprises rep and/or cap genes that encode the Rep protein and/or Cap proteins for use in a method described herein. In some embodiments, the packaging is performed in vitro.

Improvement in rAAV particle yield

Recombinant AAV particle yields may improve by using any one of the methods described herein compared to rAAV production processes that are the same with the exception of the particular combination of serotypes of ITR and Rep proteins. In some embodiments, particle yields are defined by the amount of rAAV particles produced. In some embodiments, particle yields are defined by the amount of full rAAV particles (i.e., those that contain nucleic acid or genomes) produced. In some embodiments, yields of rAAV particles are increased relative to when ITRs of serotype 2 are used for packaging rAAV. In some embodiments, the yield of rAAV production involving any one of the particular combination of serotypes of ITR and Rep protein may increase by 2-20% (e.g., 2-4%. 2-10%, 5-10%, 5- 20%, 15-20% or 10-20%), or even by up to 5-10 fold or lOO-fold or more (e.g., up to 2-fold, up to 3-fold, up to 5-fold, up to lO-fold, up to 20-fold, up to 50-fold, or up to lOO-fold or more) compared to rAAV production processes wherein an ITR of serotype 2 is used.

Recombinant AAV particle yields may improve by using any one of the chimeric rep genes described herein compared to rAAV particles produced using production processes that use rep genes of serotype that is a wild-type serotype closest to the majority of the

nucleotides in the chimeric gene. For example, the packaging or particle yields for particles produced using ITRs of AAV2, cap of AAV3, and a chimeric rep of serotype 2 except for having a h domain of serotype 8 (R2h8) may be compared to packaging yields for particles produced using ITRs of AAV2, cap of AAV3 and rep of AAV2. In some embodiments, packaging yields as described herein are compared to that of particles of the same serotype made with ITRs of AAV2 and rep of AAV2. In some embodiments, particle yields achieved by using any one of the chimeric rep genes as described herein is improved by at least 1.5- fold (e.g., at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least lO-fold).

Methods of measuring packaging of rAAV particles is known in the art. For example, the quantity of genome can be measured using methods such as PCR (e.g., quantitative PCR). Quantities of capsids or particles can be measured using protein-based assays such as ELISA. In some embodiments, electron microscopy (e.g., cryo-electron microscopy) can be used to differentiate visually empty capsids from full capsids (i.e. those that comprise nucleic acid or genomes).

Cap genes and capsid proteins

A rAAV particle or particle within an rAAV preparation may be of any AAV serotype, including any derivative or pseudotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 2/1, 2/5, 2/8, 2/9, 3/1, 3/5, 3/8, or 3/9). A cap gene may be used to package the rAAV genome or any gene of interest flanked by any one of the ITRs as described herein. As a result, a rAAV particle produced from any one of the methods described herein can be of any serotype or pseudotype, which in turn may use any one of the chimeric rep genes described herein. A rAAV particle produced using any one of the methods disclosed herein (e.g., with any one of the rep genes, any one of the cap genes, and/or any one of the ITRs described here) can be used to deliver a gene of interest to a cell (e.g., a cell in a subject’s body, or an in vitro cell), or to treat a condition or disease in a subject.

The serotype of an rAAV viral particle refers to the serotype of the capsid proteins of the recombinant virus. Non-limiting examples of derivatives and pseudotypes include rAAV2/l, rAAV2/5, rAAV2/8, rAAV2/9, AAV2-AAV3 hybrid, AAVrh.lO, AAVhu.l4, AAV3a/3b, AAVrh32.33, AAV-HSC15, AAV-HSC17, AAVhu.37, AAVrh.8, CHt-P6, AAV2.5, AAV6.2, AAV2i8, AAV-HSC15/17, AAVM41, AAV9.45, AAV6(Y445F/Y73lF), AAV2.5T, AAV-HAE1/2, AAV clone 32/83, AAVShHlO, AAV2 (Y->F), AAV8 (Y733F), AAV2.15, AAV2.4, AAVM41, and AAVr3.45. In some embodiments, cap proteins have one or more amino acid substitutions. Such AAV serotypes and derivatives/pseudotypes, and methods of producing such derivatives/pseudotypes are known in the art (see, e.g., Mol Ther. 2012 Apr ;20(4) : 699-708. doi: 10. l038/mt.20l 1.287. Epub 2012 Jan 24. The AAV vector toolkit: poised at the clinical crossroads. Asokan Al, Schaffer DV, Samulski RJ.). In some embodiments, the rAAV particle is a pseudotyped rAAV particle, which comprises (a) a nucleic acid vector comprising ITRs from one serotype (e.g., AAV2, AAV3) and (b) a capsid comprised of capsid proteins derived from another serotype (e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, or AAV 10). Methods for producing and using pseudotyped rAAV vectors are known in the art (see, e.g., Duan et al., J. Virol., 75:7662-7671, 2001; Halbert et al., J. Virol., 74:1524-1532, 2000; Zolotukhin et ah, Methods, 28:158-167, 2002; and Auricchio et al., Hum. Molec. Genet., 10:3075-3081, 2001).

Helper genes and vectors

In some embodiments, the one or more helper vectors (e.g., plasmids) include a first helper plasmid comprising a rep gene and/or a cap gene, and a second helper plasmid comprising one or more of the following helper genes: Ela gene, Elb gene, E4 gene, E2a gene, and VA gene. For clarity, helper genes are genes that encode helper proteins Ela, Elb, E4, E2a, and VA. In some embodiments, the cap gene is modified such that one or more of the proteins VP1, VP2, and VP3 do not get expressed. In some embodiments, the cap gene is modified such that VP2 does not get expressed. Methods for making such modifications are known in the art (Lux et al. (2005), J Virology, 79: 11776-87)

Helper plasmids, and methods of making such plasmids, are known in the art and commercially available (see, e.g., pDF6, pRep, pDM, pDG, pDPlrs, pDP2rs, pDP3rs, pDP4rs, pDP5rs, pDP6rs, pDG(R484E/R585E), and pDP8.ape plasmids from

PlasmidFactory, Bielefeld, Germany; other products and services available from Vector Biolabs, Philadelphia, PA; Cellbiolabs, San Diego, CA; Agilent Technologies, Santa Clara, Ca; and Addgene, Cambridge, MA; pxx6; Grimm et al. (1998), Novel Tools for Production and Purification of Recombinant Adeno associated Virus Vectors, Human Gene Therapy,

Vol. 9, 2745-2760; Kem, A. et al. (2003), Identification of a Heparin-Binding Motif on Adeno- Associated Virus Type 2 Capsids, Journal of Virology, Vol. 77, 11072-11081.;

Grimm et al. (2003), Helper Virus-Free, Optically Controllable, and Two-Plasmid-Based Production of Adeno-associated Virus Vectors of Serotypes 1 to 6, Molecular Therapy, Vol.

7, 839-850; Kronenberg et al. (2005), A Conformational Change in the Adeno-Associated Virus Type 2 Capsid Leads to the Exposure of Hidden VP1 N Termini, Journal of Virology, Vol. 79, 5296-5303; and Moullier, P. and Snyder, R.O. (2008), International efforts for recombinant adeno-associated viral vector reference standards, Molecular Therapy, Vol. 16, 1185-1188). Plasmids that encode wild-type AAV coding regions for specific serotypes are also know and available. For example pSub20l is a plasmid that comprises the coding regions of the wild-type AAV2 genome (Samulski et al. (1987), J Virology, 6:3096-3101). Gene of interest and control elements

A gene of interest is a gene that encodes a protein of interest. A protein of interest may be a detectable marker or a therapeutic protein. A detectable marker is a molecule that can be visualized (e.g., using a naked eye or under a microscope). In some embodiments, the detectable marker is a fluorescent molecule, a bioluminescent molecule, or a molecule that provides color (e.g., b-galactosidase, b-lactamases, b-glucuronidase, and spheriodenone). In some embodiments, a detectable marker is a fluorescent protein or functional peptide or functional polypeptide thereof.

In some embodiments, a gene of interest encodes a therapeutic protein. In some embodiments, a therapeutic gene encodes an antibody, a peptibody, a growth factor, a clotting factor, a hormone, a membrane protein, a cytokine, a chemokine, an activating or inhibitory peptide acting on cell surface receptors or ion channels, a cell-permeant peptide targeting intracellular processes, a thrombolytic, an enzyme, a bone morphogenetic proteins, a nuclease or other protein used for gene editing, an Fc-fusion protein, an anticoagulant, a nuclease, guide RNA or other nucleic acid, or protein for gene editing.

In some embodiments, the nucleic acid vector comprises one or more regions comprising a sequence that facilitates expression of the nucleic acid (e.g., the heterologous nucleic acid), e.g., expression control sequences operatively linked to the nucleic acid. Such control elements can be delivered to a producer cell such that it aids in expression of one or more proteins in the producer cells. In some embodiments, a control element is delivered to a producer cells such that it gets packaged with the one or more genes of interest so that the packaged rAAV particle, when used to infect a target cell, tissue, or organ, aids in the expression of the product of the gene of interest in the target cell, tissue, or organ.

Numerous control elements are known in the art. Non-limiting examples of control elements include promoters, insulators, silencers, response elements, introns, enhancers, initiation sites, termination signals, and poly(A) tails. Any combination of such control elements is contemplated herein (e.g., a promoter and an enhancer). To achieve appropriate expression levels of the protein or polypeptide of interest, any of a number of promoters suitable for use in the selected host cell may be employed. The promoter may be, for example, a constitutive promoter, tissue-specific promoter, inducible promoter, or a synthetic promoter. For example, constitutive promoters of different strengths can be used. A nucleic acid vector described herein may include one or more constitutive promoters, such as viral promoters or promoters from mammalian genes that are generally active in promoting transcription. Non-limiting examples of constitutive viral promoters include the Herpes Simplex virus (HSV), thymidine kinase (TK), Rous Sarcoma Virus (RSV), Simian Virus 40 (SV40), Mouse Mammary Tumor Virus (MMTV), Ad E1A, and cytomegalovirus (CMV) promoters. Non-limiting examples of constitutive mammalian promoters include various housekeeping gene promoters, as exemplified by the b-actin promoter (e.g., chicken b-actin promoter) and human elongation factor- 1 a (EF-la) promoter. Inducible promoters and/or regulatory elements may also be contemplated for achieving appropriate expression levels of the protein or polypeptide of interest. Non-limiting examples of suitable inducible promoters include those from genes such as cytochrome P450 genes, heat shock protein genes, metallothionein genes, and hormone-inducible genes, such as the estrogen gene promoter. Another example of an inducible promoter is the tetVPl6 promoter that is responsive to tetracycline. Tissue-specific promoters and/or regulatory elements are also contemplated herein. Non-limiting examples of such promoters that may be used include airway epithelial cell-specific promoters. Synthetic promoters are also contemplated herein. A synthetic promoter may comprise, for example, regions of known promoters, regulatory elements, transcription factor binding sites, enhancer elements, repressor elements, and the like.

In some embodiments, a gene of interest, optionally including one or more control elements, is flanked by ITRs. In some embodiments, a nucleic acid vector comprising the gene of interest flanked by ITRs is an RNA, a DNA, a ssDNA, or a self-complementary DNA molecule. In some embodiments, the nucleic acid vector is packaged into a viral particle using one or more techniques described in this application (e.g., by introducing the nucleic acid vector, for example via transfection, into a producer cell that expresses a chimeric rep gene or a gene that is of a different serotype than the ITRs flanking the gene of interest, wherein the producer cell further optionally expresses one or more cap genes and/or helper genes).

Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present application to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the application in any way whatsoever. All publications cited herein are incorporated by reference for the purposes or subject matter referenced herein.

Use of r AAV particles as produced by methods described herein

A rAAV particle produced using any one of the methods disclosed herein (e.g., with any one of the rep genes, any one of the cap genes, and/or any one of the ITRs described here) can be used to deliver a gene of interest to a cell (e.g., a cell in a subject’s body, or an in vitro cell), or to treat a condition or disease in a subject. In some embodiments, a subject is a mammal (e.g., a human). In some embodiments, a subject is in need of treatment with a gene of interest as described above.

In some embodiments,“administering” or“administration” means providing a material to a subject in a manner that is pharmacologically useful. In some embodiments, a rAAV particle is administered to a subject enterally. In some embodiments, an enteral administration of the essential metal element/s is oral. In some embodiments, a rAAV particle is administered to the subject parenterally. In some embodiments, a rAAV particle is administered to a subject subcutaneously, intraocularly, intravitreally, subretinally, intravenously (IV), intracerebro-ventricularly, intramuscularly, intrathecally (IT), intracistemally, intraperitoneally, via inhalation, topically, or by direct injection to one or more cells, tissues, or organs. In some embodiments, a rAAV particle is administered to the subject by injection into the hepatic artery or portal vein.

To "treat" a disease as the term is used herein, means to reduce the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject.

The compositions described above or elsewhere herein are typically administered to a subject in an effective amount, that is, an amount capable of producing a desirable result. The desirable result will depend upon the active agent being administered. For example, an effective amount of rAAV particles may be an amount of the particles that are capable of transferring an expression construct to a host organ, tissue, or cell. A therapeutically acceptable amount may be an amount that is capable of treating a disease, e.g., Friedreich’s ataxia. As is well known in the medical and veterinary arts, dosage for any one subject depends on many factors, including the subject's size, body surface area, age, the particular composition to be administered, the active ingredient(s) in the composition, time and route of administration, general health, and other drugs being administered concurrently.

In some embodiments, the composition comprises a pharmaceutically acceptable carrier. The term“carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the rAAV particle is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum oil such as mineral oil, vegetable oil such as peanut oil, soybean oil, and sesame oil, animal oil, or oil of synthetic origin. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers. EXAMPLES

Example 1 : Comparison of AAV ITRs and Rep proteins of different serotypes

To begin to explore the impact of using AAV Rep protein and/or AAV ITRs of different serotypes on the genome packaging efficiency, the Rep and available ITR sequences of AAV1 to AAV13 were compared (FIG. 1). The ITR sequences are only available for AAV1-AAV7. AAV1 and AAV6 share high sequence identity in both Rep (99.4%) and Cap (99.2%) proteins. In contrast, their ITR sequences show divergence (81.6%). The AAV6 ITR is identical to that of AAV2 ITR while the Rep and Cap protein sequences are more diverse at 87.3% and 83.4%, respectively. This is consistent with AAV6 being a chimera between AAV1 and AAV2. The AAV1 and AAV6 Rep share high sequence homology (>95.0%) to AAV7, AAV8, AAV9, AAV10, and AAV11, although their Cap protein sequences are more diverse (FIG. 1). Significantly, AAV5 is consistently diverse in its ITR sequence, Rep protein, and Cap proteins compared to the other AAVs (FIG. 1).

An analysis of the locations of the sequence variations within the ITRs shows minor variations in the A-region but higher variation in the D-sequence and the hairpin (B- and C- region) (FIG. 2). The D-sequence is reportedly important for AAV packaging while the sequence in the hairpin is exchangeable as long as the secondary structure is maintained. A graphical representation of the comparison of the AAV1 and AAV2, as an example, shows that variation exists in both the DNA binding and helicase domains (FIG. 3). These observations indicate a level of complexity in these essential viral elements that may relate to their function.

Example 2: Effect of using combination of ITRs and Rep proteins of different serotypes on rAAV particle packaging

First, a comparison between the packaging of AAV6 capsids with Rep proteins of all AAV serotypes is carried out. Vector constructs having a genome flanked by ITRs of AAV1 to AAV6 are used. Existing Rep2 (of AAV2)-cap6 (of AAV6) helper plasmids containing the AAV2 rep gene is substituted by rep genes from other AAV serotypes. These constructs are used to transfect HEK293 cells to generate rAAV6 (rAAVX/6) vectors. AAV vector genomes flanked by ITRs from alternative AAV serotypes are used for AAV6 vector production, starting with matching pairs of ITR and Rep proteins (e.g., AAV1 ITR plus AAV1 rep, or AAV3 ITR plus AAV3 rep, etc.). The resulting vectors are purified by AVB sepharose, which purifies genome-containing as well as empty (no DNA) AAV particles.

The full and empty capsids are separated either by a density gradient (e.g., Iodixanol) or a sedimentation gradient (e.g., Sucrose gradient), and for each sample, a capsid ELISA (with the ADKla antibody) is used to quantify the capsid titer. The individual vector preparations are subsequently analyzed and compared for their empty:full ratio, overall production yield, and gene expression efficiency.

If significant differences in the packaging efficiencies of the same transgenes are observed, a finer analysis of the residue differences in the two Rep domains is carried out along with mutation of certain residues to identify residues important for the differences.

Then, Rep sequences of AAV1 to AAV 13 were compared to determine where differences between them are located. Their role in packaging is then examined. It is known that AAV5 ITRs can only be packaged with the AAV5 Rep proteins, thus chimeras will test both the DNA binding and helicase domains to pinpoint the determinant of this requirement. If significant differences in packaging efficiency or vector productivity are found to be dictated by serotype Rep or ITR, domains are swapped between the viruses (e.g., utilization of the AAV 1 DNA binding domain and/or helicase/ ATPase or the utilization of the D- sequence from AAV1) and tested for their effect on rAAV particle packaging.

Example 3: Effect of using chimeric rep gene to produce rAAV particles of various serotypes.

FIG. 4 shows a schematic of the standard AAV productions system used to produce rAAV particles. A cell, also called a helper or producer cell, is transfected with one or more plasmids comprising genes encoding Rep and capsid proteins, and optionally, a gene of interest between ITRs so that it can be packaged within rAAV particle. The standard technique utilizes various chimeric and modified cap genes but usually rep and ITRs of serotype 2. The following describes experiments and data therefrom in which the rep gene is modified and used with ITRs having sequence of AAV2 to produce capsids of different serotypes. The modified rep genes that were tested are chimeric rep genes having domains that are substituted with domains or other serotypes.

An analysis of the DNA sequence identity for ITR AAV1-7 and Rep78 AAV1-8 was performed (FIG. 5). Sequences for AAV8 ITR, AAV9 ITR, and AAV9 Rep are not available.

FIG. 5 shows percent sequence identity analysis for AAV ITR and Rep78 for AAV serotypes 1-9. FIG. 6 provides a schematic showing the arrangement of rep and cap genes in an AAV genome and various domains of AAV Rep proteins expressed from the rep gene. A schematic of AAV genome is shown with its two open reading frames flanked by inverted terminal repeats (ITRs). The zoom-in shows an illustration of the domains of the Rep proteins and the transcripts leading to the expression of Rep78/68/52/40. The specific domains of the rep gene used for the generations of hybrids are indicated by follows:

n = N-terminus domain,

d = DNA binding domain,

h = helicase domain,

y = NLS/p40 promoter domain, and

z = Zinc finger domain;

wherein the N-terminus as defined herein consists of domains n, d, and h; and the C- terminus (c) consists of domains y and z.

The characterization and optimization of the rep gene for AAV 1 vector production is shown in FIGs. 7A-7B. Swaps between the AAV 1 and AAV2 rep gene were generated to identify the domain responsible for improved genome packaging. The DNA binding domain (DBD, d) plays an important role as the AAV2 DBD significantly affects packaging . The helicase domain (h) is also likely involved with the AAV2 helicase also showing improved packaging. Overall, the variants Rlhc2Vl (i.e., denoting a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV 1 sequence with the exception that the C terminus (c) and the helicase domain (h)are of AAV2 sequence) and R2dlVl (denoting a plasmid with a cap gene of AAV1 sequence, and a rep gene of AAV2 sequence with the exception that the DNA binding domain (d) is of AAV1 sequence), which both have AAV1 DBD and AAV2 helicase, have the best vector genome packaging phenotypes in AAV 1 capsids. Additional data for rep modifications for producing rAAV particles of AAV1 is provided in FIG. 8. For these variants the domains in rep gene are defined as follows: n = N-terminus: aa 1- 102, d = DNA- binding domain: aa 103 - 242, h = helicase domain: aa 243 - 370, c = C-terminus: aa 371 - 621.

The AAV2 rep gene was substituted with the AAV3 rep gene for the production of AAV3 particles (FIGs. 9A-9D). For the standard production system, an ACG-start codon for AAV2 rep was used. Both ACG and ATG start codons were tested with the AAV3 rep gene. With the ATG start codon, AAV3 Rep78 was visible and it was not seen with the ACG start codon. The VP expression of the AAV3 rep constructs was slightly lower compared to the AAV2 rep gene construct. Nonetheless, the genome titer of ATG-R3V3 was comparable to that of ACG-R2V3. Thus, the packaging was slightly better with AAV3 Rep (FIGs. 9A-9D).

Next, the AAV2 rep gene was substituted with the AAV4 rep gene for the production of AAV4 particles (FIGs. 10A-10D). Both ACG and ATG start codons were tested with the AAV4 rep gene. With the ATG start codon AAV4 Rep78 was visible and it was not seen with ACG start codon. The VP1 expression with the AAV4 rep constructs was comparable to that of the AAV2 rep gene construct. Nonetheless, the genome titer of ACG-R4V4 was higher compared to ACG-R2V4. Thus, the packaging might be better with AAV4 Rep compared to AAV2 Rep.

The AAV2 rep gene was substituted with the AAV5 rep gene for the production of AAV5 particles (FIGs. 11A-11D). Both ACG and ATG start codons were tested with the AAV5 rep gene. With the ATG start codon, AAV5 Rep78 was visible and it was not seen with ACG start codon. The VP expression with the AAV5 rep constructs appeared to be slightly lower compared to the AAV2 rep gene construct. However, no packaged genomes had been detected with the AAV5. AAV5 Rep is known to be unable to interact with AAV2 ITRs (see e.g., Chiorini et ah, J Virol. 1999 May;73(5):4293-8).

The AAV2 rep gene was substituted with the AAV6 rep gene for the production of AAV6 vectors (FIGs. 12A-12D). Both ACG and ATG start codons were tested with the AAV6 rep gene. Various Rep hybrids between the AAV serotypes AAV1, AAV2, AAV6 and AAV8 were also analyzed. The best vector genome packaging phenotypes were observed for the Rep variants plasmids R8dlc2V6 and Rlhc2V6. However, both plasmids maintained high VP expression comparable to that of the reference plasmid pR2V6.

The AAV2 rep gene was substituted with the AAV7 rep gene for the production of AAV7 particles (FIGs. 13A-13D). Both ACG and ATG start codons were tested with the AAV7 rep gene. With the ATG start codon AAV7 Rep78 was visible and it was not seen with ACG start codon. The VP expression with the AAV7 rep constructs was lower compared to the AAV2 rep gene construct. Nonetheless, the genome titer of ACG-R7V7 was comparable to ACG-R2V7. Thus, the packaging was better with ACG-R7V7.

Swaps between the AAV1, AAV2, and AAV8 rep genes were generated to identify the domain responsible for improved genome packaging and to optimize the rep gene for AAV8 vector production (FIGs. 14A-14B). The DNA binding domain (DBD) appeared to play an important role for VP expression, as the substitution of the AAV8 DBD with the AAV1 DBD increased VP expression. The Rlc2V8 and R8dlc2V8 hybrids/chimeras package vector genomes more efficiently into AAV8 capsids compared to the AAV2 rep gene. For these variants, the rep domains are defined as follows: n = N-terminus: aa 1-102, d = DNA-binding domain: aa 103 - 224, h = helicase domain: aa 225 - 372, c = C-terminus: aa 373 - 623. The improvement in genome packaging of AAV8 particles using rep chimeras is shown in FIGs. 15A-15B. The utilization of the new rep chimeras Rlc2 and R8dlc2 lead to higher percentages (3- to 4-fold) of genome containing particles.

FIGs. 16A-16B provide data for more rep chimeras to package AAV8 particles. It can be seen that the genome packaging is improved when the listed rep chimeras are used over AAV2 rep.

OTHER EMBODIMENTS

All of the features disclosed in this specification may be combined in any

combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features.

From the above description, one skilled in the art can easily ascertain the essential characteristics of the present application, and without departing from the spirit and scope thereof, can make various changes and modifications of the application to adapt it to various usages and conditions. Thus, other embodiments are also within the claims.

EQUIVALENTS

While several inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the inventive teachings is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present application are directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the inventive scope of the present application.

All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms.

All references, patents and patent applications disclosed herein are incorporated by reference with respect to the subject matter for which each is cited, which in some cases may encompass the entirety of the document.

The indefinite articles“a” and“an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean“at least one.”

The phrase“and/or,” as used herein in the specification and in the claims, should be understood to mean“either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e.,“one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the“and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to“A and/or B”, when used in conjunction with open-ended language such as“comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

As used herein in the specification and in the claims,“or” should be understood to have the same meaning as“and/or” as defined above. For example, when separating items in a list,“or” or“and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as“only one of’ or“exactly one of,” or, when used in the claims,“consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term“or” as used herein shall only be interpreted as indicating exclusive alternatives (i.e.“one or the other but not both”) when preceded by terms of exclusivity, such as“either,”“one of,”“only one of,” or “exactly one of.”“Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law. As used herein in the specification and in the claims, the phrase“at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase“at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example,“at least one of A and B” (or, equivalently,“at least one of A or B,” or, equivalently“at least one of A and/or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another

embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one,

B (and optionally including other elements); etc.

It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited.

In the claims, as well as in the specification above, all transitional phrases such as “comprising,”“including,”“carrying,”“having,� �“containing,”“involving,”“holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases“consisting of’ and“consisting essentially of’ shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03. It should be appreciated that embodiments described in this document using an open-ended transitional phrase (e.g.,“comprising”) are also contemplated, in alternative embodiments, as“consisting of’ and“consisting essentially of’ the feature described by the open-ended transitional phrase. For example, if the application describes“a composition comprising A and B”, the application also contemplates the alternative embodiments“a composition consisting of A and B” and“a composition consisting essentially of A and B”.