CROSS-REFERENCE TO RELATED APPLICATIONS This application is a continuation-in-part of U.S. Application Serial No. 208,997, filed June 17, 1988, which is herein incorporated by reference.

INTRODUCTION

Field of Invention

This invention relates to recombinant proteins, genes, and gene probes and more specifically to such proteins and probes derived from an enterically transmitted nonA/nonB hepatitis viral agent, and to diagnostic methods and vaccine applications which employ the proteins and probes.

Background

Enterically transmitted non-A/non-B (ET-NANB) hepatitis viral agent is the reported cause of hepatitis in several epidemics and sporadic cases in Asia, Africa, and the Indian subcontinent. Infection is usually by water contaminated with feces, although the virus may also spread by close physical contact. The virus does not seem to cause chronic infection.

The viral etiology in ET-NANB has been demonstrated by infection of volunteers with pooled fecal isolates; Immune electron microscopy (IEM) studies have shown virus particles with 27-34 nm diameters in stools from infected individuals. The virus particles reacted with antibodies in serum from infected individuals from geographically distinct regions, suggesting that a

single viral agent or class is responsible for the majority of ET-NANB hepatitis seen worldwide. No antibody reaction was seen in serum from individuals infected with blood-transmitted NANB virus, indicating a different specificity between the two NANB types. In addition to serological differences, the two types of NANB infection show distinct clinical differences. ET-NANB is characteristically an acute infection, often associated with fever and arthralgia, and with portal inflammation and associated bile stasis in liver biopsy specimens (Arankalle). Symptoms are usually resolved within six weeks. Blood-transmitted NANB, by contrast, produces a chronic infection in about 50% of the cases. Fever and arthralgia are rarely seen, and inflammation has a predominantly parenchymal distribution (Khuroo, 1980). The two viral agents can also be distinguished on the basis of primate host susceptibility. ET-NANB, but not the blood-transmitted agent, can be transmitted to cynomolgus monkeys. The blood-transmitted agent is more readily transmitted to chimpanzees than is ET-NANB (Bradley, 1987).

There have been major efforts worldwide to identify and clone viral genomic sequences associated with ET-NANB hepatitis. One goal of this effort, requiring virus-specific genomic sequences, is to identify and characterize the nature of the virus and its protein products. Another goal is to produce recombinant viral proteins which can be used in antibody-based diagnostic procedures and for a vaccine. Despite these efforts, viral sequences associated with ET-NANB hepatitis have not been successfully identified or cloned heretofore, nor have any virus-specific proteins been identified or produced.

Relevant Literature

Arankalle, V.A., et al. , The Lancet, 550 (March 12, 1988) .

Bradley, D.W., et al. , J Gen. Virol. , 69:1 (1988).

Bradley, D.W. et al. , Proc. Nat. Acad. Sci., USA, 84:6277 (1987).

Gravelle, CR. et al. , J. Infect. Diseases, 131:167 (1975). Kane, M.A. , et al., JAMA, 252:3140 (1984).

Khuroo, M.S., Am. J. Med., 48:818 (1980).

Khuroo, M.S., et al. , Am. J. Med. , 68:818 (1983).

Maniatis, T., et al. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory (1982).

Seto, B., et al., Lancet, 11:941 (1984).

Sreenivasan, M.A.m et al., J. Gen. Virol. , 65:1005 (1984). Tabor, E., et al., J. Infect. Pis., 140:789

(1979).

SUMMARY OF THE INVENTION Novel compositions, as well as methods of preparation and use of the compositions are provided, where the compositions comprise viral proteins and fragments thereof derived from the viral agent for ET- NANB. Methods for preparation of ET-NANB viral proteins include isolating ET-NANB genomic sequences which are then cloned and expressed in a host cell. The resultant recombinant viral proteins find use as diagnostic agents and as vaccines. The genomic sequences and fragments thereof find use in preparing ET-NANB viral proteins and as probes for virus detection.

BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows vector constructions and manipulations used in obtaining and sequencing cloned ET-NANB fragment; and Figures 2A-2B are representations of Southern blots in which a radiolabeled ET-NANB probe was hybridized with amplified cDNA fragments prepared from RNA isolated from infected (I) and non-infected (N) bile sources (2A), and from infected (I) and non- infected (N) stool-sample sources (2B).

DESCRIPTION OF SPECIFIC EMBODIMENTS Novel compositions comprising generic sequences and fragments thereof derived from the viral agent for ET-NANB are provided, together with recombinant viral proteins produced using the genomic sequences and methods of using these compositions. The genome of the ET-NANB viral agent is identified as containing a region which is homologous to the 1.33 kb DNA EcoRI insert present in plasmid pTZ- KF1 (ET1.1) carried in E. coli strain BB4 and having ATCC deposit no. 67717. Initial studies sequenced the two terminal regions of the insert and an intermediate region. The 5'-end region of this insert contains the sequence:

1 42

GAT GGA AGG CAC TAA TCT GGC AAG ACC TGT CCC TGT TGC AGC

43 84

TGT TCT ACC ACC CTG CCC CGA GCT CGA ACA GGG CCT TCT CTA

85 126

CCT GCC CCA GGA GCT CAC ACA CCC TGT GAT AGT GTC GTA ACA

127 168

TTT GAA TTA ACA GAC ATT GTG CAC TGC CGC ATG GCC GCC CCG

169 210

AGC CAG CGC AAG GCC GTG CTG TCC ACA CTC GTG GGC CGC TAC

211 GGC.

An intermediate region has the sequence:

691 731

CTA GAG TGT GCT ATT ATG GAG GAG TGT GGG ATG CCG CAG TGG

733 774

CTC ATC CGC CTG TAT CAC CTT ATA AGG TCT GCG TGG ATC TTG

775 816

CAG GCC CCG AAG GAG TCT CTG CGA GGG TTT TGG AAG AAA CAC

817 858 TCC GGT GAG CCC GGC ACT CTT CTA TGG AAT ACT GTC TGG AAT

859 900

ATG GCC GTT ATT ACC CAC TGT TAT GAC TTC CGC GAT TTT CAG

901 942

GTG GCT GCC TTT AAA GGT GAT GAT TCG ATA GTG CTT TGC AGT

943 984

GAG TAT CGT CAG AGT CCA GGA GCT GCT GTC CTG ATC GCC GGC

985 1026

TGT GGC TTG AAG TTG AAG GTA GAT TTC CGC CCG ATC GGT TTG

1027 TAT.

The 3'-end region contains the sequence:

1191 1232

TGA GTA GAG GAT GTT GTT TCC CGT GTT TAT GGG GTT TCC CCT

5

1233 1274

GGA CTC GTT CAT AAC CTG ATT GGC ATG CTA CAG GCT GTT GCT

1275 1316 0 GAT GGC AAG GCA CAT TTC ACT GAG TCA GTA AAA CCA GTG CTC

1317 1327 GAC CGG AAT TC.

5 Additional work has provided the entire sequence, in both directions, as set forth below. The sequence of both strands is provided, since it is not known in which strand the gene is located. However, the sequence in one direction has been designated as the 0 "forward" sequence because of statistical similarities to known proteins. This sequence is set forth below along with the three possible translation sequences. There is one long open reading frame that starts at nucleotide 145 with an isoleucine and extends to the 5 end of the sequence. The two other reading frames have many termination codons. Standard abbreviations for nucleotides and amino acids are used here and elsewhere in this specification.

30 Forward Sequence

R I P P T D G R H Z S G K T C P C C S C

E F R Q L M E G T N L A R P V P V A A V

N S A N Z W K A L I W Q D L S L L Q L F 35 * * * * *

1 11 21 31 41 51 CGAATTCCGCCAACTGATGGAAGGCACTAATCTGGCAAGACCTGTCCCTGTTGCAGCTGT

S T T L P R A R T G P S L P A P G A H H L P P C P E L E Q G L L Y L P Q E L T T Y H P A P S S N R A F S T C P R S S P P

* * * * * *

61 71 81 91 101 111

TCTACCACCCTGCCCCGAGCTCGAACAGGGCCTTCTCTACCTGCCCCAGGAGCTCAC CAC

L Z Z C R N I Z I N R H C A L P H G R P C D S V V T F E L T D I V H C R M A A P

V I V S Z H L N Z Q T L C T A A W P P R

* * * * * *

121 131 141 151 161 171

CTGTGATAGTGTCGTAACATTTGAATTAACAGACATTGTGCACTGCCGCATGGCCGC CCC

E P A Q G R A V H T R G P L R R R T K L S Q R K A V L S T L V G R Y G V A Q S S

A S A R P C C P H S W A A T A S H K A L

* * * - * * *

181 191 201 211 221 231

GAGCCAGCGCAAGGCCGTGCTGTCCACACTCGTGGGCCGCTACGGCGTCGCACAAAG CTC

Y N A S H S D V R D S L A R F I P A I G T M L P T L M F A T L S P V L S R P L A

Q C F P L Z C S R L S R P F Y P G H W P

* * * * * *

241 251 261 271 281 291 TACAATGCTTCCCACTCTGATGTTCGCGACTCTCTCGCCCGTTTTATCCCGGCCATTGGC

P V Q V T T C E L Y E L V E A M V E K G P Y R L Q L V N C T S Z W R P W S R R A

R T G Y N L Z I V R A S G G H G R E G P * * * * * *

301 311 321 331 341 351 CCCGTACAGGTTACAACTTGTGAATTGTACGAGCTAGTGGAGGCCATGGTCGAGAAGGGC

Q D G S A V L E L D L C N R D V S R I T R M A P P S L S L I F A T V T C P G S P G W L R R P Z A Z S L Q P Z R V Q D H L * * * * * *

36l ^' 371 381 391 401 411

CAGGATGGCTCCGCCGTCCTTGAGCTTGATCTTTGCAACCGTGACGTGTCCAGGATC ACC

F F Q K D C N K F T T G E T I A H G K V

S S R K I V T S S P Q V R P L P M V K W

L P E R L Z Q V H H R Z D H C P W Z S G * * * * * *

421 431 441 451 461 471

TTCTTCCAGAAAGATTGTAACAAGTTCACCACAGGTGAGACCATTGCCCATGGTAAA GTG

G Q G I S A W S K T F C A L F G P W F R

A R A S R P G A R P S A P S L A L G S A

P G H L G L E Q D L L R P L W P L V P R * - * * * * *

481 491 501 511 521 531

GGCCAGGGCATCTCGGCCTGGAGCAAGACCTTCTGCGCCCTCTTTGGCCCTTGGTTC CGC

A I E K A I L A L L P Q G V F Y G D A F L L R R L F W P C S L R V C F T V M P L Y Z E G Y S G P A P S G C V L R Z C L Z * * * * * *

541 551 561 571 581 591

GCTATTGAGAAGGCTATTCTGGCCCTGCTCCCTCAGGGTGTGTTTTACGGTGATGCC TTT

D D T V F S A A V A A A K A S M V F E N

M T P S S R R L W P Q Q R H P W C L R M

Z H R L L G G C G R S K G I H G V Z E Z * * * * * *

601 611 621 631 641 651

GATGACACCGTCTTCTCGGCGGCTGTGGCCGCAGCAAAGGCATCCATGGTGTTTGAG AAT

D F S E F D S T Q N N F S L G L E C A I

T F L S L T P P R I T F L W V Z S V L L

L F Z V Z L H P E Z L F S G S R V C Y Y * * * * * *

661 ^' 671 681 691 701 711

GACTTTTCTGAGTTTGACTCCACCCAGAATAACTTTTCTCTGGGTCTAGAGTGTGCT ATT

M E E C G M P Q W L I R L Y H L I R S A W R S V G C R S G S S A C I T L Z G L R G G V W D A A V A H P P V S P Y K V C V * * * * * *

721 731 741 751 761 771

ATGGAGGAGTGTGGGATGCCGCAGTGGCTCATCCGCCTGTATCACCTTATAAGGTCT GCG

W I L Q A P K E S L R G F W K K H S G E G S C R P R R S L C E G F G R N T P V S D L A G P E G V S A R V L E E T L R Z A * * * * * *

781 791 801 811 821 831

TGGATCTTGCAGGCCCCGAAGGAGTCTCTGCGAGGGTTTTGGAAGAAACACTCCGGT GAG

P G T L L W N T V W N M A V I T H C Y D

P A L F Y G I L S G I W P L L P T V M T

R H S S M E Y C L E Y G R Y Y P L L Z L * * * * * *

841 851 861 871 881 891

CCCGGCACTCTTCTATGGAATACTGTCTGGAATATGGCCGTTATTACCCACTGTTAT GAC

F R D F Q V A A F K G D D S I V L C S E

S A I F R W L P L K V M I R Z C F A V S

P R F S G G C L Z R Z Z F D S A L Q Z V * * * * * *

901 911 921 931 941 951

TTCCGCGATTTTCAGGTGGCTGCCTTTAAAGGTGATGATTCGATAGTGCTTTGCAGT GAG

Y R Q S P G A A V L I A G C G L K L K V I V R V Q E L L S Z S P A V A Z S Z R Z

S S E S R S C C P D R R L W L E V E G R

* * * * * *

961 971 981 991 1001 1011

TATCGTCAGAGTCCAGGAGCTGCTGTCCTGATCGCCGGCTGTGGCTTGAAGTTGAAG GTA

D F R P I G L Y A G V V V A P G L G A L I S A R S V C M Q V L W W P P A L A R S F P P D R F V C R C C G G P R P W R A P

* * * * * *

1021 1031 1041 1051 1061 1071

GATTTCCGCCCGATCGGTTTGTATGCAGGTGTTGTGGTGGCCCCCGGCCTTGGCGCG CTC

P D V V R F A G R L T E K N W G P G P E L M L C A S P A G L P R R I G A L A L S

Z C C A L R R P A Y R E E L G P P Z A

* * * * * *

1081 1091 1101 1111 1121 1131

CCTGATGTTGTGCGCTTCGCCGGCCGGCTTACCGAGAAGAATTGGGGCCCTGGCCCT GAG

R A E Q L R L A V S D F L . R K L T N V A G R S S S A S L L V I S S A S S R M Z L

G G A A P P R C Z Z F P P Q A H E C S S

* * * * * *

1141 1151 1161 1171 1181 1191

CGGGCGGAGCAGCTCCGCCTCGCTGTTAGTGATTTCCTCCGCAAGCTCACGAATGTA GCT

Q M C V D V V S R V Y G V S P G L V H N R C V W M L F P V F M G F P L D S F I T

D V C G C C F P C L W G F P W T R S Z P

* * * * * *

1201 1211 1221 1231 1241 1251 CAGATGTGTGTGGATGTTGTTTCCCGTGTTTATGGGGTTTCCCCTGGACTCGTTCATAAC

L I G M L Q A V A D G K A H F T E S V K Z L A C Y R L L L M A R H I S L S Q Z N D W H A T G C C Z W Q G T F H Z V S K T

* * * * * *

1261 1271 1281 1291 1301 1311

CTGATTGGCATGCTACAGGCTGTTGCTGATGGCAAGGCACATTTCACTGAGTCAGTA AAA

P V L D R N S S Q C S T G I R S A R P E F E

* * *

1321 1331 1341 CCAGTGCTCGACCGGAATTCGAGC

The complimentary strand, referred to here as the "reverse sequence," is set forth below in the same manner as the forward sequence set forth above. Several open reading frames, shorter than the long open reading frame found in the forward sequence, can be seen in this reverse sequence.

Reverse Sequence

A R I P V E H W F Y Z L S E M C L A I S L E F R S S T G F T D S V K C A L P S A

S N S G R A L V L L T Q Z N V P C H Q Q

* * * * * *

1 11 21 31 41 51

GCTCGAATTCCGGTCGAGCACTGGTTTTACTGACTCAGTGAAATGTGCCTTGCCATC AGC

N S L Z H A N Q V M N E S R G N P I N T T A C S M P I R L Z T S P G E T P Z T R

Q P V A C Q S G Y E R V Q G K P H K H G

* * * * * *

61 71 81 91 101 111

AACAGCCTGTAGCATGCCAATCAGGTTATGAACGAGTCCAGGGGAAACCCCATAAAC ACG

G N N I H T H L S Y I R E L A E E I T N E T T S T H I Z A T F V S L R R K S L T K Q H P H T S E L H S Z A C G G N H Z Q * * * * * *

121 131 141 151 161 171

GGAAACAACATCCACACACATCTGAGCTACATTCGTGAGCTTGCGGAGGAAATCACT AAC

S E A E L L R P L R A R A P I L L G K P

A R R S C S A R S G P G P Q F F S V S R

R G G A A P P A Q G Q G P N S S R Z A G * * * * * *

181 191 201 211 221 231

AGCGAGGCGGAGCTGCTCCGCCCGCTCAGGGCCAGGGCCCCAATTCTTCTCGGTAAG CCG

A G E A H N I R E R A K A G G H H N T C

P A K R T T S G S A P R P G A T T T P A

R R S A Q H Q G A R Q G R G P P Q H L H * * * * * *

241 251 261 271 281 291

GCCGGCGAAGCGCACAACATCAGGGAGCGCGCCAAGGCCGGGGGCCACCACAACACC TGC

Ϊ Q T D R A E I Y L Q L Q A T A G D Q D

Y K P I G R K S T F N F K P Q P A I R T

T N R S G G N L P S T S S H S R R S G Q * * * * * *

301 311 321 331 341 351

ATACAAACCGATCGGGCGGAAATCTACCTTCAACTTCAAGCCACAGCCGGCGATCAG GAC

S S S W T L T I L T A K H Y R I I T F K

A A P G L Z R Y S L Q S T I E S S P L K

Q L L D S D D T H C K A L S N H H L Z R * * * * * *

361 371 381 391 401 411

AGCAGCTCCTGGACTCTGACGATACTCACTGCAAAGCACTATCGAATCATCACCTTT AAA

G S H L K I A E V I T V G N N G H I P D

A A T Z K S R K S Z Q W V I T A I F Q T

Q P P E N R G S H N S G Z Z R P Y S R Q * * * * * *

421 431 441 451 461 471

GGCAGCCACCTGAAAATCGCGGAAGTCATAACAGTGGGTAATAACGGCCATATTCCA GAC

S I P Z K S A G L T G V F L P K P S Q R V F H R R V P G S P E C F F Q N P R R D Y S I E E C R A H R S V S S K T L A E T * * * * * *

481 491 501 511 521 531

AGTATTCCATAGAAGAGTGCCGGGCTCACCGGAGTGTTTCTTCCAAAACCCTCGCAG AGA

L L R G L Q D P R R P Y K V I Q A D E P

S F G A C K I H A D L I R Z Y R R M S H

P S G P A R S T Q T L Z G D T G G Z A T * * * * * *

541 551 561 571 581 591

CTCCTTCGGGGCCTGCAAGATCCACGCAGACCTTATAAGGTGATACAGGCGGATGAG CCA

L R H P T L L H N S T L Z T Q R K V I L

C G I P H S S I I A H S R P R E K L F W

A A S H T P P Z Z H T L D P E K S Y S G * * * * * *

601 611 621 631 641 651

CTGCGGCATCCCACACTCCTCCATAATAGCACACTCTAGACCCAGAGAAAAGTTATT CTG

G G V K L R K V I L K H H G C L C C G H

V E S N S E K S F S N T M D A F A A A T

W S Q T Q K S H S Q T P W M P L L R P Q * * * * * *

661 671 681 691 701 711

GGTGGAGTCAAACTCAGAAAAGTCATTCTCAAACACCATGGATGCCTTTGCTGCGGC CAC

S R R E D G V I K G I T V K H T L R E Q A A E K T V S S K A S P Z N T P Z G S R

P P R R R C H Q R H H R K T H P E G A G

* * * * * *

721 731 741 751 761 771

AGCCGCCGAGAAGACGGTGTCATCAAAGGCATCACCGTAAAACACACCCTGAGGGAG CAG

G Q N S L L N S A E P R A K E G A E G L A R I A F S I A R N Q G P K R A Q K V L

P E Z P S Q Z R G T K G Q R G R R R S C

* * * * * *

781 791 801 811 821 831

GGCCAGAATAGCCTTCTCAATAGCGCGGAACCAAGGGCCAAAGAGGGCGCAGAAGGT CTT

A P G R D A L A H F T M G N G L T C G E L Q A E M P W P T L P W A M V S P V V N

S R P R C P G P L Y H G Q W S H L W Z T

* * * * * *

841 851 861 871 881 891

GCTCCAGGCCGAGATGCCCTGGCCCACTTTACCATGGGCAATGGTCTCACCTGTGGT GAA

L V T I F L E E G D P G H .V V A K I K L L Q S F W K K V I L D T S R L Q R S S C Y N L S G R R Z S W T R H G C K D Q A

* * * * * *

901 911 921 931 941 951

CTTGTTACAATCTTTCTGGAAGAAGGTGATCCTGGACACGTCACGGTTGCAAAGATC AAG

L K D G G A I L A L L D H G L H Z L V Q S R T A E P S W P F S T M A S T S S Y N

Q G R R S H P G P S R P W P P L A R T I

* * * * * *

961 971 981 991 1001 1011 CTCAAGGACGGCGGAGCCATCCTGGCCCTTCTCGACCATGGCCTCCACTAGCTCGTACAA

F T S C N L Y G A N G R D K T G E R V A S Q V V T C T G P M A G I K R A R E S R H K L Z P V R G Q W P G Z N G R E S R E

* * * * * *

1021 1031 1041 1051 1061 1071

TTCACAAGTTGTAACCTGTACGGGGCCAATGGCCGGGATAAAACGGGCGAGAGAGTC GCG

N I R V G S I V E L C A T P Z R P T S V T S E W E A L Z S F V R R R S G P R V W

H Q S G K H C R A L C D A V A A H E C G

* * * * * *

1081 1091 1101 1111 1121 1131

AACATCAGAGTGGGAAGCATTGTAGAGCTTTGTGCGACGCCGTAGCGGCCCACGAGT GTG

D S T A L R W L G A A M R. Q C T M S V N T A R P C A G S G R P C G S A Q C L L I

Q H G L A L A R G G H A A V H N V C Z F

* * * * * *

1141 1151 1161 1171 1181 1191

GACAGCACGGCCTTGCGCTGGCTCGGGGCGGCCATGCGGCAGTGCACAATGTCTGTT AAT

S N V T T L S Q V V S S W G R Z R R P C Q M L R H Y H R W Z A P G A G R E G P V

K C Y D T I T G G E L L G Q V E K A L F

* * * * * *

1201 1211 1221 1231 1241 1251

TCAAATGTTACGACACTATCACAGGTGGTGAGCTCCTGGGGCAGGTAGAGAAGGCCC TGT

S S S G Q G G R T A A T G T G L A R L V R A R G R V V E Q L Q Q G Q V L P D Z C

E L G A G W Z N S C N R D R S C Q I S A

* * * * * *

1261 1271 1281 1291 1301 1311 TCGAGCTCGGGGCAGGGTGGTAGAACAGCTGCAACAGGGACAGGTCTTGCCAGATTAGTG

P S I S W R N S L P S V G G I F H Q L A E F * * *

1321 1331 1341 CCTTCCATCAGTTGGCGGAATTCG

DETAILED DESCRIPTION OF THE INVENTION

I. Definitions

The terms defined below have the following meaning herein:

1. "Enterically transmitted non-A/non-B (ET-NANB) hepatitis viral agent" means a virus, virus type, or virus class which (1) causes water-borne, infectious hepatitis, (ii) is transmissible in cynomolgus monkeys, (iii) is serologically distinct from hepatitis A virus (ΞAV) and hepatitis B virus (HAB), and (iv) includes a genomic region which is homologous to the 1.33 kb cDNA insert in plasmid pTZ-KFl(ETl.l) carried in E. coli strain BB4 identified by ATCC deposit number 67717.

2. Two double-strand nucleic acid fragments are "homologous" if their opposite strands are capable of hybridizing to one another under moderately stringent hybridization conditions, i.e., where hybridized strands contain at most about 5-10% basepair mismatches. A single-strand nucleic acid species is homologous to a double-strand fragment if it contains a region which is capable of hybridizing to one of the fragment strands under moderately stringent hybridization conditions.

3. A DNA fragment is "derived from" an ET-NANB viral agent if it has the same or substantially the

same basepair sequence as a region of the viral agent genome.

4. A protein is "derived from" an ET-NANB viral agent if it is encoded by an open reading frame of a DNA or RNA fragment derived from an ET-NANB viral agent.

II. Obtaining Cloned ET-NANB Fragments

According to one aspect of the invention, it has been found that a virus-specific DNA clone can be produced by (a) isolating RNA from the bile of a cynomolgus monkey having a known ET-NANB infection, (b) cloning the cDNA fragments to form a fragment library, and (c) screening the library by differential hybridization to radiolabeled cDNAs from infected and non-infected bile sources.

A. cDNA Fragment Mixture

ET-NANB infection in cynomolgus monkeys is initiated by inoculating the animals intravenously with a 10% w/v suspension from human case stools positive for 27-34 nm ET-NANB particles (mean diameter 32 nm) . An infected animal is monitored for elevated levels of alanine aminotransferase, indicating hepatitis infection. ET-NANB infection is confirmed by immunospecific binding of seropositive antibodies to virus-like particles (VLPs), according to published methods (Gravelle). Briefly, a stool (or bile) specimen taken from the infected animal 3-4 weeks after infection is diluted 1:10 with phosphate-buffered saline, and the 10% suspension is clarified by low- speed centrifugation and filtration successively through 1.2 and 0.45 micron filters. The material may be further purified by pelleting through a 30% sucrose cushion (Bradley). The resulting preparation of VLPs is mixed with diluted serum from human patients with known ET-NANB infection. After incubation overnight,

the mixture is centrifuged overnight to pellet immune aggregates, and these are stained and examined by electron microscopy for antibody binding to the VLPs. ET-NANB infection can also be confirmed by seroconversion to VLP-positive serum. Here the serum of the infected animal is mixed as above with 27-34 nm VLPs isolated form the stool specimens of infected human cases and examined by immune electron microscopy for antibody binding to the VLPs. Bile can be collected from ET-NANB positive animals by either cannulating the bile duct and collecting the bile fluid or by draining the bile duct during necropsy. Total RNA is extracted from the bile by hot phenol extraction, as outlined in Example IA. The RNA fragments are used to synthesize corresponding duplex cDNA fragments by random priming, also as referenced in Example IA. The cDNA fragments may be fractionated by gel electrophoresis or density gradient centrifugation to obtain a desired size class of fragments, e.g., 500-4,000 basepair fragments.

Although alternative sources of viral material, such as VLPs obtained from stool samples (as described in Example 4), may be used for producing a cDNA fraction, the bile source is preferred. According to one aspect of the invention, it has been found that bile from ET-NANB-infected monkeys shows a greater number of intact viral particles than material obtained from stool samples, as evidenced by immune electron microscopy. Bile obtained from an ET-NANB infected human or cynomolgus monkey, for use as a source of ET- NANB viral protein or genomic material, or intact virus, forms part of the present invention.

B. cDNA Library and Screening The cDNA fragments from above are cloned into a suitable cloning vector to form a cDNA library. This may be done by equipping blunt-ended fragments with a

suitable end linker, such as an EcoRI sequence, and inserting the fragments into a suitable insertion site of a cloning vector, such as at a unique EcoRI site. After initial cloning, the library may be recloned, if desired, to increase the percentage of vectors containing a fragment insert. The library construction described in Example IB is illustrative. Here cDNA fragments were blunt-ended, equipped with EcoRI ends, and inserted into the EcoRI site of the lambda phage vector gtlO. The library phage, which showed less than 5% fragment inserts, was isolated, and the fragment inserts recloned into the lambda gtlO vector, yielding more than 95% insert-containing phage.

The cDNA library is screened for sequences specific for ET-NANB by differential hybridization to cDNA probes derived from infected and non-infected sources. cDNA fragments from infected and non-infected source bile or stool viral isolates can be prepared as above. Radiolabeling the fragments is by random labeling, nick translation, or end labeling, according to conventional methods (Maniatis, p. 109). The cDNA library from above is screened by transfer to duplicate nitrocellulose filters, and hybridization with both infected-source and non-infected-source (control) radiolabeled probes, as detailed in Example 2. Plaques which show selective hybridization to the infected- source probes are preferably replated at low plating density and rescreened as above, to isolate single clones which are specific for ET-NANB sequences. As indicated in Example 2, sixteen clones which hybridized specifically with infected-source probes were indentified by these procedures. One of the clones, designated lambda gtlO-1.1, contained a 1.33 kilobase fragment insert.

C. ET-NANB Sequences

The basepair sequence of cloned regions of the

ET-NANB fragments from Part B are determined by standard sequencing methods. In one illustrative method, described in Example 3, the fragment insert from the selected cloning vector is excised, isolated by gel electrophoresis, and inserted into a cloning vector whose basepair sequence on either side of the insertion site is known. The particular vector employed in Example 3 is a pTZ-KFl vector shown at the left in Figure 1. The ET-NANB fragment from the gtlO- 1.1 phage was inserted at the unique EcoRI site of the pTZ-KFl plasmid. Recombinants carrying the desired insert were identified by hybridization with the isolated 1.33 kilobase fragment, as described in Example 3. One selected plasmid, identified as pTZ-KFl (ET1.1), gave the expected 1.33 kb fragment after vector digestion with EcoRI. E. coli strain BB4 infected with the pTZ-KFl(ETl.l) plasmid has been deposited with the American Type Culture Collection, Rockville, MD, and is identified by ATCC deposit nubmer 67717.

The pTZ-KFl(ETl.l) plasmid is illustrated at the bottom in Figure 1. The fragment insert has 5' and 3' end regions denoted at A and C, respectively, and an intermediate region, denoted at B. The sequences in these regions were determined by standard dideoxy sequencing and are set forth above. The three short sequences (A, B, and C) are from the same insert strand. As will be seen in Example 3, the B-region sequence was actually determined from the opposite strand, so that the B-region sequence shown above represent the complement of the sequence in the sequenced strand. The base numbers of the partial sequences are approximate.

Later work in the laboratory of the inventors identified the full sequence, also set forth above. Fragments of this total sequence can readily be prepared using restriction endonucleases. Computer

analysis of both the forward and reverse sequence has identified a number of cleavage sites. The specific cleavage sites are summarized (for the forward direction) in the following tables.

Pattern identifier Pattern matched Base number matched ( ^Λ = cleavage site) in "forward" strand

CC'WGG(BstNI) CO/JGG 106, 360, 410, 483

497, 973, 1129, 1243

CC ^Λ SGG(NciI) CCSGG 288, 841, 1063 GAAGANNNNNNNN~(MboII) GAAGA 822, 1116 TCTTC(<-7-MbθII) TCTTC 422, . 611, 849 GCGTC(<-10-Hgal) GCGTC 225 GCATCNNNNN ^* (SfaNI) GCATC 488, 640 GCAGCNNNNNNNN (Bbvl) GCAGC 53, 631, 1149 GCTGC(<-12-Bbvl) GCTGC 919, 979 GGATGNNNNNNNNN"(Fokl) GGATG 363, 734, 1212 CATCC(<-13-F0kI) CATCC 641, 750 GGTGANNNNNNNN"(HphI) GGTGA 454, 589, 835, 931 TCACC(<-7-HphI) TCACC 114, 416, 446, 762 GP ^Λ CGYC(AhaII) GPCGYC 224 GDGCH ^Λ C(BspI1286) GDGCHC 77, 110, 158, 838, 1125, 1324

GPGCY ^Λ C(BanII) GPGCYC 77, 110, 838, 1125

C ^Λ YCGPG(AvaI) CYCGPG 74, 178

Y ^Λ GGCCP(EaeI) YGGCCP 171, 290, 626, 875, 1101

GWGCVTC ( GgiAI ) GWGCWC 77, 110, 158, 1324

C CTTGG(StyI) CCTTGG 529, 1068

P ^Λ GATCY(XhoII) PGATCY 782

CAG ^Λ CTG(PvuII) CAGCTG 54

C ^Λ CATGG(NcoI) CCATGG 344, 468, 644

CGAT ^Λ CG(PvuI) CGATCG 1031

C ^Λ GGCCG(EagI) CGGCCG 1101

G AATTC(EcoRI) GAATTC 2, 1335

GAGCT ^Λ C(SacI) GAGCTC 77, 110

GCATG ^Λ C(SphI) GCATGC 1268

GCC~GGC(NaeI) GCCGGC 994, 1099, 1103

G ^Λ CGCGC(BssHII) GCGCGC 1073

GGGCC~C(ApaI) GGGCCC 1125

TCG ^Λ CGA(NruI) TCGCGA 264

T ^A CTAGA(XbaI) TCTAGA 705

TTT~AAA(DraI) TTTAAA 925

G ^A TGCAC(ApaLI) GTGCAC 158

ACCTGCNNNN~(BpsMI) ACCTGC 99

GCAGG (<-8-BspMI) GCAGGT 1045

GACN ^Λ NNGTC(Tthllll) GACNNNGTC 604

CCANNNN"NTGG(Pf1MI) CCANNNNNTGG 10

CC ^Λ TNAGG(MstII) CCTNAGG 571

GCCNNNN ^Λ NGGC(BglI) GCCNNNNNGGC 216, 359, 738

CCANNNNN'NTGG(BstXI) CCANNNNNNTGG 204

III. ET-NANB Fragments

According to another aspect, the invention includes ET-NANB-specific fragments or probes which hybridize with ET-NANB genomic sequences or cDNA fragments derived therefrom. The fragments may include full-length cDNA fragments such as described in Section II, or may be derived from shorter sequence regions within cloned cDNA fragments. Shorter fragments can be prepared by enzymatic digestion of full-length fragments under conditions which yield desired-sized fragments, as will be described in Section IV. Alternatively, the fragments can be produced by oligonucleotide synthetic methods, using sequences derived from the cDNA fragments. Methods or services for producing selected-sequence oligonucleotide fragments are available.

To confirm that a given ET-NANB fragment is in fact derived from the ET-NANB viral agent, the fragment

can be shown to hybridize selectively with cDNA from infected sources. By way of illustration, to confirm that the 1.33 kb fragment in the pTZ-KFl(El.l) plasmid is ET-NANB in origin, the fragment was excised from the pTZ-KFl(ETl.l) plasmid, purified, and radiolabeled by random labeling. The radiolabeled fragment was hybridized with fractionated cDNAs from infected and non-infected sources to confirm that the probe reacts only with infected-source cDNAs. This method is illustrated in Example 4, where the above radiolabeled 1.33 kb fragment from pTZ-KFl(ETl.l) plasmid was examined for binding to cDNAs prepared from infected and non-infected sources. The infected sources are (1) bile from a cynomolgus monkey infected with a strain of virus derived from stool samples from human patients from Burma with known ET-NANB infections and (2) a viral agent derived from the stool sample of a human ET-NANB patient from Mexico. The cDNAs in each fragment mixture were first amplified by a linker/primer amplification method described in Example 4. Fragment separation was on agarose gel, followed by Southern blotting and then hybridization to bind the radiolabeled 1.33 kb fragment to the fractionated cDNAs. The lane containing cDNAs from the infected sources showed a smeared band of bound probe, as expected (cDNAs amplified by the linker/primer amplification method would be expected to have a broad range of sizes). No probe binding to the amplified cDNAs from the non-infected sources was observed. The results indicate that the 1.33 kb probe is specific for cDNA fragments associated with ET-NANB infection. This same type of study, using ET 1.1 as the probe, has demonstrated hybridization to ET-NANB samples collected from Tashkent, Somalia, Borneo and Pakistan. Secondly, the fact that the probe is specific for ET-NANB related sequences derived from different continents (Asia, Africa and North America) indicates the cloned ET-NANB

Africa sequence is derived from a common ET-NANB virus or virus class responsible for ET-NANB hepatitis infection worldwide.

In a related confirmatory study, probe binding to fractionated genomic fragments prepared from human or cynomolgus monkey genomic DNA was examined. No probe binding was observed to either genomic fraction, demonstrating that the ET-NANB fragment is not an endogenous human or cynomologus fragment. Another confirmation of ET-NANB specific sequences in the fragments is the ability to express ET-NANB proteins from coding regions in the fragments. Section IV below discusses methods of protein expression using the fragments. One important use of the ET-NANB-specific fragments is for identifying ET-NANB-derived cDNAs which contain additional sequence information. The newly identified cDNAs, in turn, yield new fragment probes, allowing further iterations until the entire viral genome is identified and sequenced. Procedures for identifying additional ET-NANB library clones and generating new probes therefrom generally follow the cloning and selection procedures described in Section II. The fragments (and oligonucleotides prepared based on the sequences given above) are also useful as primers for a poly erase chain reaction method of detecting ET-NANB viral genomic material in a patient sample. This diagnostic method will be described in Section V below.

IV. ET-NANB Proteins

As indicated above, ET-NANB proteins can be prepared by expressing open reading-frame coding regions in ET-NANB fragments. In one preferred approach, the ET-NANB fragments used for protein

expression are derived from cloned cDNAs which have been treated to produce desired-size fragments, and preferably random fragments with sizes predominantly between about 100 to about 300 base pairs. Example 5 describes the preparation of such fragments by DNAs digestion. Because it is desired to obtain peptide antigens of between about 30 to about 100 amino acids, the digest fragments are preferably size fractionated, for example by gel electrophoresis, to select those in the approximately 100-300 basepair size range.

A. Expression Vector

The ET-NANB fragments are inserted into a suitable expression vector. One exemplary expression vector is lambda gtll, which contains a unique EcoRI insertion site 53 base pairs upstream of the translation termination codon of the beta-galactosidase gene. Thus, the inserted sequence will be expressed as a beta-galactosidase fusion protein which contains the N-terminal portion of the beta-galactosidase gene, the heterologous peptide, and optionally the C-terminal region of the beta-galactosidase peptide (the C- terminal portion being expressed when the heterologous peptide coding sequence does not contain a translation termination codon). This vector also produces a temperature-sensitive repressor (cl857) which causes viral lysogeny at permissive temperatures, e.g., 32°C, and leads to viral lysis at elevated temperatures, e.g., 42°C. Advantages of this vector include: (1) highly efficient recombinant generation, (2) ability to select lysogenized host cells on the basis of host-cell growth at permissive, but not non-permissive, temperatures, and (3) high levels of recombinant fusion protein production. Further, since phage containing a heterologous insert produces an inactive beta- galactosidase enzyme, phage with inserts can be readily identified by a beta-galactosidase colored-substrate

reaction.

For insertion into the expression vector, the viral digest fragments may be modified, if needed, to contain selected restriction-site linkers, such as EcoRI linkers, according to conventional procedures. Example 1 illustrates methods for cloning the digest fragments into lambda gtll, which includes the steps of blunt-ending the fragments, ligating with EcoRI linkers, and introducing the fragments into EcoRI-cut lambda gtll. The resulting viral genomic library may be checked to confirm that a relatively large (representative) library has been produced. This can be done, in the case of the lambda gtll vector, by infecting a suitable bacterial host, plating the bacteria, and examining the plaques for loss of beta- galactosidase activity. Using the procedures described in Example 1, about 50% of the plaques showed loss of enzyme activity.

B. Peptide Antigen Expression

The viral genomic library formed above is screened for production of peptide antigen (expressed as a fusion protein) which is immunoreactive with antiserum from ET-NANB seropositive individuals. In a preferred screening method, host cells infected with phage library vectors are plated, as above, and the plate is blotted with a nitrocellulose filter to transfer recombinant protein antigens produced by the cells onto the filter. The filter is then reacted with the ET-NANB antiserum, washed to remove unbound antibody, and reacted with reporter-labeled, anti-human antibody, which becomes bound to the filter, in sandwich fashion, through the anti-ET-NANB antibody. Typically phage plaques which are identified by virtue of their production of recombinant antigen of interest are re-examined at a relatively low density for production of antibody-reactive fusion protein.

Several recombinant phage clones which produced immunoreactive recombinant antigen were identified in the procedure.

The selected expression vectors may be used for scale-up production, for purposes of recombinant protein purification. Scale-up production is carried out using one of a variety of reported methods for (a) lysogenizing a suitable host, such as E. coli, with a selected lambda gtll recombinant (b) culturing the transduced cells under conditions that yield high levels of the heterologous peptide, and (c) purifying the recombinant antigen from the lysed cells.

In one preferred method involving the above lambda gtll cloning vector, a high-producer E. coli host, BNN103, is infected with the selected library phage and replica plated on two plates. One of the plates is grown at 32 ^β C, at which viral lysogeny can occur, and the other at 42°C, at which the infecting phage is in a lytic stage and therefore prevents cell growth. Cells which grow at the lower but not the higher temperature are therefore assumed to be successfully lysogenized.

The lysogenized host cells are then grown under liquid culture conditions which favor high production of the fused protein containing the viral insert, and lysed by rapid freezing to release the desired fusion protein.

C. Peptide Purification The recombinant peptide can be purified by standard protein purification procedures which may include differential precipitation, molecular sieve chromatography, ion-exchange chromatography, isoelectric focusing, gel electrophoresis and affinity chromatography. In the case of a fused protein, such as the beta-galactosidase fused protein prepared as above, the protein isolation techniques which are used

can be adapted from those used in isolation of the native protein. Thus, for isolation of a beta- glactosidase fusion protein, the protein can be isolated readily by simple affinity chromatography, by passing the cell lysis material over a solid support having surface-bound anti-beta-galactosidase antibody.

D. Viral Proteins

The ET-NANB protein of the invention may also be derived directly from the ET-NANB viral agent. VLPs isolated from a stool sample from an infected individual, as above, are one suitable source of viral protein material. The VLPs isolated from the stool sample may be further purified by affinity chromatography prior to protein isolation (see below). The viral agent may also be raised in cell culture, which provides a convenient and potentially concentrated source of viral protein. Co-owned U.S. Patent Application Serial No. 846,757, filed April 1, 1986, describes an immortalized trioma liver cell which supports NANB infection in cell culture. The trioma cell line is prepared by fusing human liver cells with a mouse/human fusion partner selected for human chromosome stability. Cells containing the desired NANB viral agent can be identified by immuno- fluorescence methods, employing anti-ET-NANB human antibodies.

The viral agent is disrupted, prior to protein isolation, by conventional methods, which can include sonication, high- or low-salt conditions, or use of detergents.

Purification of ET-NANB viral protein can be carried out by affinity chromatography, using a purified anti-ET-NANB antibody attached according to standard methods to a suitable solid support. The antibody itself may be purified by affinity chromatography, where an immunoreactive recombinant ET-

NANB protein, such as described above, is attached to a solid support, for isolation of anti-ET-NANB antibodies from an immune serum source. The bound antibody is released from the support by standard methods. Alternatively, the anti-ET-NANB antibody may be a monoclonal antibody (Mab) prepared by immunizing a mouse or other animal with recombinant ET-NANB protein, isolating lymphocytes from the animal and immortalizing the cells with a suitable fusion partner, and selecting successful fusion products which react with the recombinant protein immunogen. These in turn may be used in affinity purification procedures, described above, to obtain native ET-NANB antigen.

V. Utility

A. Diagnostic Methods

The particles and antigens of the invention, as well as the genetic material, can be used in diagnostic assays. Methods for detecting the presence of ET-NANB hepatitis comprise analyzing a biological sample such as a blood sample, stool sample or liver biopsy specimen for the presence of an analyte associated with ET-NANB hepatitis virus. The analyte can be a nucleotide sequence which hybridizes with a probe comprising a sequence of at least about 16 consecutive nucleotides, usually 30 to 200 nucleotides, up to substantially the full sequence of the sequences shown above (cDNA sequences). The analyte can be RNA or cDNA. The analyte is typically a virus particle suspected of being ET-NANB or a particle for which this classification is being ruled out. The virus particle can be further characterized as having an RNA viral genome comprising a sequence at least about 80% homologous to a sequence of at least 12 consecutive nucleotides of the "forward" and "reverse" sequences given above, usually at least about 90%

homologous to at least about 60 consecutive nucleotides within the sequences, and may comprise a sequence substantially homologous to the full-length sequences. In order to detect an analyte, where the analyte hybridizes to a probe, the probe may contain a detectable label.

The analyte can also comprise an antibody which recognizes an antigen, such as a cell surface antigen, on a ET-NANB virus particle. The analyte can also be a ET-NANB viral antigen. Where the analyte is an antibody or an antigen, either a labelled antigen or antibody, respectively, can be used to bind to the analyte to form an immunological complex, which can then be detected by means of the label. Typically, methods for detecting analytes such as surface antigens and/or whole particles are based on i munoassays. I munoassays can be conducted either to determine the presence ^" of antibodies in the host that have arisen from infection by ET-NANB hepatitis virus or by assays that directly determine the presence of virus particles or antigens. Such techniques are well known and need not be described here in detail. Exam¬ ples include both heterogeneous and homogeneous immuno- assay techniques. Both techniques are based on the formation of an immunological complex between the virus particle or its antigen and a corresponding specific antibody. Heterogeneous assays for viral antigens typically use a specific monoclonal or polyclonal antibody bound to a solid surface. Sandwich assays are becoming increasingly popular. Homogeneous assays, which are carried out in solution without the presence of a solid phase, can also be used, for example by determining the difference in enzyme activity brought on by binding of free antibody to an enzyme-antigen conjugate. A number of suitable assays are disclosed

in U.S. Patent Nos. 3,817,837, 4,006,360, 3,996,345. When assaying for the presence of antibodies induced by ET-NANB viruses, the viruses and antigens of the invention can be used as specific binding agents to detect either IgG or IgM antibodies. Since IgM anti¬ bodies are typically the first antibodies that appear during the course of an infection, when IgG synthesis may not yet have been initiated, specifically distin¬ guishing between IgM and IgG antibodies present in the blood stream of a host will enable a physician or other investigator to determine whether the infection is recent or chronic.

In one diagnostic configuration, test serum is reacted with a solid phase reagent having surface-bound ET-NANB protein antigen. After binding anti-ET-NANB antibody to the reagent and removing unbound serum components by washing, the reagent is reacted with reporter-labeled anti-human antibody to bind reporter to the reagent in proportion to the amount of bound anti-ET-NANB antibody on the solid support. The reagent is again washed to remove unbound labeled antibody, and the amount of reporter associated with the reagent is determined. Typically, the reporter is an enzyme which is detected by incubating the solid phase in the presence of a suitable fluorometric or colorimetric substrate.

The solid surface reagent in the above assay prepared by known techniques for attaching protein material to solid support material, such as polymeric beads, dip sticks, or filter material. These attachment methods generally include non-specific adsorption of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activate carboxyl, hydroxyl, or aldehyde group.

In a second diagnostic configuration, known as

a homogeneous assay, antibody binding to a solid support produces some change in the reaction medium which can be directly detected in the medium. Known general types of homogeneous assays proposed heretofore include (a) spin-labeled reporters, where antibody binding to the antigen is detected by a change in reported mobility (broadening of the spin splitting peaks), (b) fluorescent reporters, where binding is detected by a change in fluorescence efficiency, (c) enzyme reporters, where antibody binding effects enzyme/substrate interactions, and (d) liposome-bound reporters, where binding leads to liposome lysis and release of encapsulated reporter. The adaptation of these methods to the protein antigen of the present invention follows conventional methods for preparing homogeneous assay reagents.

In each of the assays described above, the assay method involves reacting the serum from a test individual with the protein antigen and examining the antigen for the presence of bound antibody. The examining may involve attaching a labeled anti-human antibody to the antibody being examined, either IgM (acute phase) or IgG (convalescent phase), and measuring the amount of reporter bound to the solid support, as in the first method, or may involve observing the effect of antibody binding on a homogeneous assay reagent, as in the second method.

Also forming part of the invention is an assay system or kit for carrying out the assay method just described. The kit generally includes a support with surface-bound recombinant protein antigen which is (a) immunoreactive with antibodies present in individuals infected with enterically transmitted nonA/nonB viral agent and (b) derived from a viral hepatitis agent whose genome contains a region which is homologous to the 1.33 kb DNA EcoRI insert present in plasmid pTZ- KFl(ETl.l) carried in E. Coli strain BB4, and having

ATCC deposit no. 67717. A reporter-labeled anti-human antibody in the kit is used for detecting surface-bound anti-ET-NANB antibody.

B. Viral Genome Diagnostic Applications

The genetic material of the invention can it¬ self be used in numerous assays as probes for genetic material present in naturally occurring infections. One method for amplification of target nucleic acids, for later analysis by hybridization assays, is known as the polymerase chain reaction or PCR technique. The PCR technique can be applied to detecting virus particles of the invention in suspected pathological samples using oligonucleotide primers spaced apart from each other and based on the genetic sequence set forth above. The primers are complementary to opposite strands of a double stranded DNA molecule and are typically separated by from about 50 to 450 nt or more (usually not more than 2000 nt). This method entails preparing the specific oligonucleotide primers and then repeated cycles of target DNA denaturation, primer binding, and extension with a DNA polymerase to obtain DNA fragments of the expected length based on the primer spacing. Extension products generated from one primer serve as additional target sequences for the other primer. The degree of amplification of a target sequence is controlled by the number of cycles that are performed and is theoretically calculated by the simple formula 2 ⁿ where n is the number of cycles. Given that the average efficiency per cycle ranges from about 65% to 85%, 25 cycles produce from 0.3 to 4.8 million copies of the target sequence. The PCR method is de¬ scribed in a number of publications, including Saiki e_t §!•» Science (1985) 23_0:1350-1354; Saiki et al. , Nature (1986) 3_24_:163-166; and Scharf et al. , Science (1986) 2_3_3:1076-1078. Also see U.S. Patent Nos. 4,683,194; 4,683,195; and 4,683,202.

The invention includes a specific diagnostic method for determination of ET-NANB viral agent, based on selective amplification of ET-NANB fragments. This method employs a pair of single-strand primers derived from non-homologous regions of opposite strands of a DNA duplex fragment, which in turn is derived from an enterically transmitted viral hepatitis agent whose genome contains a region which is homologous to the 1.33 kb DNA EcoRI insert present in plasmid pTZ- KFl(ETl.l) carried in E. coli strain BB4, and having ATCC deposit no. 67717. These "primer fragments," which form one aspect of the invention, are prepared f om ET-NANB fragments such as described in Section III above. The method follows the process for amplifying selected nucleic acid sequences as disclosed in U.S. Patent No. 4,683,202, as discussed above.

C. Peptide Vaccine

Any of the antigens of the invention can be used in preparation of a vaccine. A preferred starting material for preparation of a vaccine is the particle antigen isolated from bile. The antigens are preferably initially recovered as intact particles as described above. However, it is also possible to pre- pare a suitable vaccine from particles isolated from other sources or non-particle recombinant antigens. When non-particle antigens are used (typically soluble antigens), proteins derived from the viral envelope or viral capsid are preferred for use in preparing vac- cines. These proteins can be purified by affinity chromatography, also described above.

If the purified protein is not immunogenic per se, it can be bound to a carrier to make the protein immunogenic. Carriers include bovine serum albumin, keyhole limpet hemocyanin and the like. It is desir¬ able, but not necessary, to purify antigens to be sub¬ stantially free of human protein. However, it is more

important that the antigens be free of proteins, viruses, and other substances not of human origin that may have been introduced by way of, or contamination of, the nutrient medium, cell lines, tissues, or patho- logical fluids from which the virus is cultured or obtained.

Vaccination can be conducted in conventional fashion. For example, the antigen, whether a viral particle or a protein, can be used in a suitable diluent such as water, saline, buffered salines, complete or incomplete adjuvants, and the like. The immunogen is administered using standard techniques for antibody induction, such as by subcutaneous administra¬ tion of physiologically compatible, sterile solutions containing inactivated or attenuated virus particles or antigens. An immune response producing amount of virus particles is typically administered per vaccinizing injection, typically in a volume of one milliliter or less. A specific example of a vaccine composition includes, in a pharmacologically acceptable adjuvant, a recombinant protein or protein mixture derived from- an enterically transmitted nonA/nonB viral hepatitis agent whose genome contains a region which is homologous to the 1.33 kb DNA EcoRI insert present in plasmid pTZ- KFl(ETl.l) carried in E. coli strain BB4, and having ATCC deposit no. 67717. The vaccine is administered at periodic intervals until a significant titer of anti- ET-NANB antibody is detected in the serum. The vaccine is intended to protect against ET-NANB infection.

D. Prophylactic and Therapeutic Antibodies and Antisera

In addition to use as a vaccine, the composi- tions can be used to prepare antibodies to ET-NANB virus particles. The antibodies can be used directly as antiviral agents. To prepare antibodies, a host

animal is immunized using the virus particles or, as appropriate, non-particle antigens native to the virus particle are bound to a carrier as described above for vaccines. The host serum or plasma is collected following an appropriate time interval to provide a composition comprising antibodies reactive with the virus particle. The gamma globulin fraction or the IgG antibodies can be obtained, for example, by use of saturated ammonium sulfate or DEAE Sephadex, or other techniques known to those skilled in the art. The antibodies are substantially free of many of the adverse side effects which may be associated with other anti-viral agents such as drugs.

The antibody compositions can be made even more compatible with the host system by minimizing potential adverse immune system responses. This is accomplished by removing all or a portion of the Fc portion of a foreign species antibody or using an antibody of the same species as the host animal, for example, the use of antibodies from human/human hybridomas.

The antibodies can also be used as a means of enhancing the immune response since antibody-virus complexes are recognized by macrophages. The anti¬ bodies can be administered in amounts similar to those used for other therapeutic administrations of anti¬ body. For example, pooled gamma globulin is admini¬ stered at 0.02-0.1 ml/lb body weight during the early incubation of other viral diseases such as rabies, measles and hepatitis B to interfere with viral entry into cells. Thus, antibodies reactive with the ET-NANB virus particle can be passively administered alone or in conjunction with another anti-viral agent to a host infected with an ET-NANB virus to enhance the immune response and/or the effectiveness of an antiviral drug. Alternatively, anti-ET-NANB-virus antibodies can be induced by administering anti-idiotype anti¬ bodies as immunogens. Conveniently, a purified anti-

ET-NANB-virus antibody preparation prepared as descibed above is used to induce anti-idiotype antibody in a host animal. The composition is administered to the host animal in a suitable diluent. Following administration, usually repeated administration, the host produces anti-idiotype antibody. To eliminate an immunogenic response to the Fc region, antibodies pro¬ duced by the same species as the host animal can be used or the Fc region of the administered antibodies can be removed. Following induction of anti-idiotype antibody in the host animal, serum or plasma is removed to provide an antibody composition. The composition can be purified as described above for anti-ET-NANB- virus antibodies, or by affinity chromatography using anti-ET-NANB-virus antibodies bound to the affinity matrix. The anti-idiotype antibodies produced are similar in conformation to the authentic ET-NANB antigen and may be used to prepare an ET-NANB vaccine rather than using a ET-NANB particle antigen. When used as a means of inducing anti-ET-NANB- virus antibodies in a patient, the manner of injecting the antibody is the same as for vaccination purposes, namely intramuscularly, intraperitoneally, subcutane- ously or the like in an effective concentration in a physiologically suitable diluent with or without adju¬ vant. One or more booster injections may be desirable. The anti-idiotype method of induction of anti-ET-NANB- virus antibodies can alleviate problems which may be caused by passive administration of anti-ET-NANB-virus antibodies, such as an adverse immune response, and those associated with administration of purified blood components, such as infection with as yet undiscovered viruses.

The ET-NANB derived proteins of the invention are also intended for use in producing antiserum designed for pre- or post-exposure prophylaxis. Here an ET-NANB protein, or mixture of proteins is

formulated with a suitable adjuvant and administered by injection to human volunteers, according to known methods for producing human antisera. Antibody response to the injected proteins is monitored, during a several- week period following immunization, by periodic serum sampling to detect the presence an anti- ET-NANB serum antibodies, as described in Section IIA above.

The antiserum from immunized individuals may be administered as a pre-exposure prophylactic measure for individuals who are at risk of contracting infection. The anitserum is also useful in treating an individual post-exposure, analogous to the use of high titer antiserum against hepatitis B virus for post-exposure prophylaxis.

E. Monoclonal Antibodies

For both jji vivo use of antibodies to ET-NANB virus particles and proteins and anti-idiotype anti- bodies and diagnostic use, it may be preferable to use monoclonal antibodies. Monoclonal anti-virus particle antibodies or anti-idiotype antibodies can be produced as follows. The spleen or lymphocytes from an immunized animal are removed and immortalized or used to prepare hybridomas by methods known to those skilled in the art. To produce a human-human hybridoma, a human lymphocyte donor is selected. A donor known to be infected with a ET-NANB virus (where infection has been shown for example by the presence of anti-virus antibodies in the blood or by virus culture) may serve as a suitable lymphocyte donor. Lymphocytes can be isolated from a peripheral blood sample or spleen cells may be used if the donor is subject to splenectomy. Epstein-Barr virus (EBV) can be used to immortalize human lymphocytes or a human fusion partner can be used to produce human-human hybridomas. Primary ^n vitro immunization with peptides can also be used in the

generation of human monoclonal antibodies.

Antibodies secreted by the immortalized cells are screened to determine the clones that secrete anti¬ bodies of the desired specificity. For monoclonal anti-virus particle antibodies, the antibodies must bind to ET-NANB virus particles. For monoclonal anti- idiotype antibodies, the antibodies must bind to anti- virus particle antibodies. Cells producing antibodies of the desired specificity are selected. The following examples illustrate various aspects of the invention, but are in no way intended to limit the scope thereof.

Material The materials used in the following Examples were as follows:

Enzymes: DNAse I and alkaline phosphatase were obtained from Boehringer Mannheim Biochemicals (BMB, Indianapolis, IN); EcoRI, EcoRI methylase, DNA ligase, and DNA Polymerase I, from New England Biolabs (NEB, Beverly MA); and RNase A was obtained from Sigma (St. Louis, MO).

Other reagents: EcoRI linkers were obtained from NEB; and nitro blue tetrazolium (NBT), 5-bromo-4-chloro-3-indolyl phosphate (BCIP)

5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside (X- gal) and isopropyl B-D-thiogalactopyranoside (IPTG) were obtained from Sigma. cDNA synthesis kit and random priming labeling kits are available from Boehringer-Mannheim Biochemical (BMB, Indianapolis, IN).

Eample 1 Preparing cDNA Library

A. Source of ET-NANB virus

Two cynomolgus monkeys (cynos) were

intravenously injected with a 10% suspension of a stool pool obtained from a second-passage cyno (cyno #37) infected with a strain of ET-NANB virus isolated from Burma cases whose stools were positive for ET-NANB, as evidenced by binding of 27-34 nm virus-like particles (VLPs) in the stool to immune serum from a known ET- NANB patient. The animals developed elevated levels of alanine aminotransferase (ALT) between 24-36 days after innoculation, and one excreted 27-34 nm VLPs in its bile in the pre-acute phase of infection.

The bile duct of each infected animal was cannulated and about 1-3 cc of bile was collected daily. RNA was extracted from one bile specimen (cyno #121) by hot phenol extraction, using a standard RNA isolation procedure. Double-strand cDNA was formed from the isolated RNA by a random primer for first- strand generation, using a cDNA synthesis kit obtained from Boehringer-Mannheim (Indianapolis, IN).

B. Cloning the Duplex Fragments

The duplex cDNA fragments were blunt-ended with T4 DNA polymerase under standard conditions (Maniatis, p. 118), then extracted with phenol/chloroform and precipitated with ethanol. The blunt-ended material was ligated with EcoRI linkers under standard conditions (Maniatis, pp. 396-397) and digested with EcoRI to remove redundant linker ends. Non-ligated linkers were removed by sequential isopropanol precipitation. Lambda gtlO phage vector (Huynh) was obtained from Promega Biotec (Madison, WI) . This cloning vector has a unique EcoRI cloning site in the phage cl repressor gene. The cDNA fragments from above were introduced into the EcoRI site by mixing 0.5 - 1.0 ug EcoRI-cleaved gtlO, 0.5-3 μl of the above duplex fragments, 0.5 μl 10X ligation buffer, 0.5 μl ligase (200 units), and distilled water to 5 μl. The mixture

was incubated overnight at 14°C, followed by in vitro packaging, according to standard methods (Maniatis, pp. 256-268).

The packaged phage were used to infect an E__ coli hfl strain, such as strain HG415. Alternatively, E. coli, strain C600 hfl, avialable from Promega Biotec, Madison, WI, could be used. The percentage of recombinant plaques obtained with insertion of the EcoRI-ended fragments was less than 5% by analysis of 20 random plaques.

The resultant cDNA library was plated and phage were eluted from the selection plates by addition of elution buffer. After DNA extraction from the phage, the DNA was digested with EcoRI to release the heterogeneous insert population, and the DNA fragments were fractionated on agarose to remove phage fragments. The 500-4,000 basepair inserts were isolated and recloned into lambda gtlO as above, and the packaged phage was used to infect E. coli strain HG415. The percentage of successful recombinants was greater than 95%. The phage library was plated on E. coli strain HG415, at about 5,000 plaques/plate, on a total of 8 plates.

Example 2 Selecting ET-NANB Cloned Fragments A. cDNA Probes

Duplex cDNA fragments from noninfected and ET- NANB-infected cynomolgus monkeys were prepared as in Example 1. The cDNA fragments were radiolabeled by random priming, using a random-priming labeling kit obtained from Boehringer-Mannheim (Indianapolis, IN).

B. Clone Selection

The plated cDNA library from Example 1 was transferred to each of two nitrocellulose filters, and the phage DNA was fixed on the filters by baking, according to standard methods (Maniatis, pp. 320- 323). The duplicate filters were hybridized with either infected-source or control cDNA probes from above. Autoradiographs of the filters were examined to identify library clones which hybridized with radiolabeled cDNA probes from infected source only, i.e., did not hybridize with cDNA probes from the non¬ infected source. Sixteen such clones, out of a total of about 40,000 clones examined, were identified by this subtraction selection method.

Each of the sixteen clones was picked and replated at low concentration on an agar plate. The clones on each plate were transferred to two nitro¬ cellulose as duplicate lifts, and examined for hybrid¬ ization to radiolabeled cDNA probes from infected and noninfected sources, as above. Clones were selected which showed selective binding for infected-source probes (i.e., binding with infected-source probes and substantially no binding with non-infected-source probes). One of the clones which bound selectively to probe from infected source was isolated for further study. The selected vector was identified as lambda gtlO-1.1, indicated in Figure 1.

Example 3 ET-NANB Sequence Clone lambda gtlO-1.1 from Example 2 was digested with EcoRI to release the heterologous insert, which was separated from the vector fragments by gel electrophoresis. The electrophoretic mobility of the fragment was consistent with a 1.33 kb fragment. This fragment, which contained EcoRI ends, was inserted into the EcoRI site of a pTZ-KFl vector, whose construction and properties are described in co-owned U.S. patent application for "Cloning Vector System and Method for Rare Clone Identification", Serial No. 125, 650, filed November 25, 1987. Briefly, and as illustrated in Figure 1, this plasmid contains a unique EcoRI site adjacent a T7 polymerase promoter site, and plasmid and phage origins of replication. The sequence immediately adjacent each side of the EcoRI site is known. E. coli BB4 bacteria, obtained from Stratagene (La Jolla, CA, were transformed with the plasmid. Radiolabeled ET-NANB probe was prepared by excising the 1.33 kb insert from the lambda gtlO-1.1 phage in Example 2, separating the fragment by gel electrophoresis, and randomly labeling as above. Bacteria transfected with the above pTZ-KFl and containing the desired ET-NANB insert were selected by replica lift and hybridization with the radiolabeled ET-NANB probe, according to methods outlined in Example 2.

One bacterial colony containing a successsful recombinant was used for sequencing a portion of the 1.33 kb insert. This isolate, designated pTZ- KFl(ETl.l), has been deposited with the American Type Culture Collection, and is identified by ATCC deposit no. 67717. Using a standard dideoxy sequencing procedure, and primers for the sequences flanking the EcoRI site, about 200-250 basepairs of sequence from the 5 '-end region and 3'-end region of the insert were

obtained. The sequences are given above in Section II. Later sequencing by the same techniques gave the full sequence in both directions, also given above.

Example 4

Detecting ET-NANB Sequences cDNA fragment mixtures from the bile of noninfected and ET-NANB-infected cynomolgus monkeys were prepared as above. The cDNA fragments obtained from human stool samples were prepared as follows.

Thirty ml of a 10% stool suspension obtained from an individual from Mexico diagnosed as infected with ET- NANB as a result of an ET-NANB outbreak, and a similar volume of stool from a healthy, non-infected individual, were layered over a 30% sucrose density gradient cushion, and centrifuged at 25,000 xg for 6 hr in an SW27 rotor, at 15°C. The pelleted material from the infected-source stool contained 27-34 nm VLP particles characteristic of ET-NANB infection in the infected-stool sample. RNA was isolated from the sucrose-gradient pellets in both the infected and non¬ infected samples, and the isolated RNA was used to produce cDNA fragments as described in Example 1.

The cDNA fragment mixtures from infected and non-infected bile source, and from infected and non¬ infected human-stool source were each amplified by a novel linker/primer replication method described in co- owned patent application serial number 07/208,512 for "DNA Amplification and Subtraction Technique," filed June 17, 1988. Briefly, the fragments in each sample were blunt-ended with DNA Pol I then extracted with phenol/chloroform and precipitated with ethanol. The blunt-ended material was ligated with linkers having the following sequence:

5 '-GGAATTCGCGGCCGCTCG-3 ' 3 '-TTCCTTAAGCGCCGGCGAGC-5 '

The duplex fragements were digested with Nrul to remove linker dimers, mixed with a primer having the sequence 5'-GGAATTCGCGGCCGCTCG-3' , and then heat denatured and cooled to room temperature to form single-strand DNA/primer complexes. The complexes were replicated to form duplex fragments by addition of Thermus aquaticus (Taq) polymerase and all four deoxynucleotides. The replication procedures, involving successive strand denaturation, formation of strand/primer complexes, and replication, was repeated 25 times. The amplified cDNA sequences were fractionated by agarose gel electrophoresis, using a 2% agarose matrix. After transfer of the DNA fragments from the agarose gels to nitrocellulose paper, the filters were hybridized to a random-labeled ^ ² P probe prepared by (i) treating the pTZ-KFl(ETl.l) plasmid from above with EcoRI, (ii) isolating the released 1.33 kb ET-NANB fragment, and (iii) randomly labeling the isolated fragment. The probe hybridization was performed by conventional Southern blotting methods (Maniatis, pp. 382-389). Figure 2 shows the hybridization pattern obtained with cDNAs from infected (I) and non-infected (N) bile sources (2A) and from infected (I) and non¬ infected (N) human stool sources (2B). As seen, the ET-NANB probe hybridized with fragments obtained from both of the infected sources, but was non-homologous to sequences obtained from either of the non-infected sources, thus confirming the specificity of derived sequence.

Southern blots of the radiolabeled 1.33 kb fragment with genomic DNA fragments from both human and cynomologus-monkey DNA were also prepared. No probe hybridization to either of the genomic fragment

mixtures was observed, confirming that the ET-NANB sequence is exogenous to either human or cynomolgus genome.

Example 5

Expressing ET-NANB Proteins

A. Preparing ET-NANB Coding Sequences

The pTZ-KFl(ETl.l) plasmid from Example 2 was digested with EcoRI to release the 1.33 kb ET-NANB insert which was purified from the linearized plasmid by gel electrophoresis. The purified fragment was suspended in a standard digest buffer (0.5M Tris HCl, pH 7.5; 1 mg/ml BSA; lOmM MnCl ₂ ) to a concentration of about 1 mg/ml and digested with DNAse I at room temperature for about 5 minutes. These reaction conditions were determined from a prior calibration study, in which the incubation time required to produce predominantly 100-300 basepair fragments was determined. The material was extracted with phenol/chloroform before ethanol precipitation.

The fragments in the digest mixture were blunt- ended and ligated with EcoRI linkers as in Example 1. The resultant fragments were analyzed by electrophoresis (5-10V/cm) on 1.2% agarose gel, using PhiX174/HaeIII and lambda/HindiII size markers. The 100-300 bp fraction was eluted onto NA45 strips (Schleicher and Schuell), which were then placed into 1.5 ml microtubes with eluting solution (1 M NaCl, 50 mM arginine, pH 9.0), and incubated at 67°C for 30-60 minutes. The eluted DNA was phenol/chloroform extracted and then precipitated with two volumes of ethanol. The pellet was resuspended in 20 μl TE (0.01 M Tris HCl, pH 7.5, 0.001 M EDTA) .

B. Cloning in an Expression Vector

Lambda gtll phage vector (Huynh) was obtained

from Promega Biotec (Madison, WI). This cloning vector has a unique EcoRI cloning site 53 base pairs upstream from the beta-galactosidase translation termination codon. The genomic fragments from above were introduced into the EcoRI site by mixing 0.5-1.0 μg EcoRI-cleaved gtll, 0.3-3 μl of the above sized fragments, 0.5 μl 10X ligation buffer (above), 0.5 μl ligase (200 units), and distilled water to 5 μl. The mixture was incubated overnight at 14°C, followed by iτ\ vitro packaging, according to standard methods (Maniatis, pp. 256-268).

The packaged phage were used to infect E. coli strain KM392, obtained from Dr. Kevin Moore, DNAX (Palo Alto, CA). Alternatively, E. Coli strain Y1090, available from the American Type Culture Collection (ATCC #37197), could be used. The infected bacteria were plated and the resultant colonies were checked for loss of beta-galactosidase activity-(clear plaques) in the presence of X-gal using a standard X-gal substrate plaque assay method (Maniatis). About 50% of the phage plaques showed loss of beta-galactosidase enzyme activity (recombinants).

C. Screening for ET-NANB Recombinant Proteins ET-NANB convalescent antiserum was obtained from patients infected during documented ET-NANB outbreaks in Mexico, Borneo, Pakistan, Somalia, and Burma. The sera were immunoreactive with VLPs in stool specimens from each of several other patients with ET- NANB hepatitis.

A lawn of E. coli KM392 cells infected with about 10^ pfu of the phage stock from above was prepared on a 150 mm plate and incubated, inverted, for 5-8 hours at 37°C. The lawn was overlaid with a nitrocellulose sheet, causing transfer of expressed ET- NANB recombinant protein from the plaques to the paper. The plate and filter were indexed for matching

corresponding plate and filter positions.

The filter was washed twice in TBST buffer (10 mM Tris, pH 8.0, 105 mM NaCl, 0.05% Tween 20), blocked with AIB (TBST buffer with 1% gelatin), washed again in TBST, and incubated overnight after addition of antiserum (diluted to 1:50 in AIB, 12-15 ml/plate). The sheet was washed twice in TBST and then contacted with enzyme-labeled anti-human antibody to attach the labeled antibody at filter sites containing antigen recognized by the antiserum. After a final washing, the filter was developed in a substrate medium containing 33 μl NBT (50 mg/ml stock solution maintained at 5°C) mixed with 16 μl BCIP (50 mg/ml stock solution maintained at 5°C) in 5 ml of alkaline phosphatase buffer (100 mM Tris, 9.5, 100 mM NaCl, 5 mM MgCl ₂ ). Purple color appeared at points of antigen production, as recognized by the antiserum.

D. Screening Plating The areas of antigen production determined in the previous step were replated at about 100-200 pfu on an 82 mm plate. The above steps, beginning with a 5-8 hour incubation, through NBT-BCIP development, were repeated in order to plaque purify phage secreting an antigen capable of reacting with the ET-NANB antibody. The identified plaques were picked and eluted in phage buffer (Maniatis, p. 443).

E. Epitope Identification A series of subclones derived from the original pTZ-KFl (ET1.1) plasmid from Example 2 were isolated using the same techniques described above. Each of these five subclones were immunoreactive with a pool of anti-ET antisera noted in C. The subclones contained short sequences from the "reverse" sequence set forth previously. The beginning and ending points of the sequences in the subclones (relative to the full

"reverse" sequence), are identified in the table below.

TABLE 1

Subclone Position in "Reverse" Sequence

5'-end 3'-end

Yl 522 643

Y2 594 667

Y3 508 665

Y4 558 752

Y5 545 665

Since all of the gene sequences identified in the table must contain the coding sequence for the epitope, it is apparent that the coding sequence for the epitope falls in the region between nucleotide 594 (5'-end) and 643 (3'-end). Genetic sequences equivalent to and complementary to this relatively short sequence are therefore particularly preferred aspects of the present invention, as are peptides produced using this coding region.

A second series of clones identifying an altogether different epitope was isolated with only Mexican serum.

TABLE 2

Subclone Position in "Forward" Sequence

5'end 3' end

ET 2-2 2 193

ET 8-3 2 135

ET 9-1 2 109

ET 13-1 2 101

The coding system for this epitope falls between nucleotide 2 (5'-end) and 101 (3'-end). Genetic sequences related to this short sequence are therefore also preferred, as are peptides produced using this coding region.

While the invention has been described with reference to particular embodiments, methods, construction and use, it will be apparent to those skilled in the art that various changes and modifications can be made without departing from the invention.