Method of assaying HIV-1 tropism for CCR5 and/or CXCR4 co-receptor and/or susceptibility to entry inhibitors

The invention relates to a method of characterising the cellular tropism of

Human Immunodeficiency Virus type 1 (HIV-1), i.e. the capacity of HIV-1 virus to use the CXCR4 and/or CCR5 receptors for cell entry. The invention also relates to a method of assessing susceptibility or resistance of HIV-1 viruses to entry inhibitors, in particular those targeting HIV-1 co-receptors.

The entry of HIV into cell is mediated by several proteins, including the viral envelope proteins gp41 and gp120. Both are derived from the precursor protein gp160 and remain non-covalently bound after the cleavage of gp160. Gp41 spans the viral membrane with endo- and ecto-domains placed inside and outside of the viral membrane region, respectively. The ectodomain is critical to interactions of gp41 with gp120 and ultimately to virus-cell fusion.

The initial step of HIV replication cycle involves attachment of the virion to helper T cells through the interactions of HIV-gp120 glycoprotein with cellular protein CD4. However, HIV-1 requires interaction with CD4 and a co-receptor to trigger fusion of viral and cellular membranes and entry into cells. The most important secondary receptors in vivo are the chemokine receptors CCR5 and CXCR4. Over the course of the infection, the co-receptor usage of HIV-1 changes from a preference for CCR5 to a preference for CXCR4 in about 50% of infected individuals. The switch from CCR5-using to CXCR4-using HIV-1 variants is associated with accelerated CD4+ T-cell decline and progression to AIDS. The phenotypic switch has been associated with mutations in the V3 region of gp120 envelope glycoprotein. In the standard terminology for HIV-1 phenotypes, CCR5-using variants are referred as R5 viruses, CXCR4-using variants are referred as X4 viruses, and variants that are able to use both co-receptors are referred as R5X4 viruses.

Methods of analysing phenotypic characteristics of HIV viruses, including cellular tropism and resistance/susceptibility to cell entry inhibitors, have been described in the art.

For instance Kootstra and Schuitemaker (2005, Methods MoI Biol., 304:317-25) describe that cellular tropism of HIV-1 tropism can be determined on

primary monocyte derived macrophages, established T-cell lines and promonocyte cell lines.

Peters et al. (2006, J. Virol., 80 (3), 6324-6332) disclose determination of tropism using a NL4-3 vector deleted of the envelope region, used for cotransfection of 293T producer cells with a plasmid pSVIII-Env+ (carrying PCR- amplified patients' envelopes). Transfected 293T cells are used in a cell fusion assay with GHOST cells expressing CCR5 or CXCR5 co-receptors and syncytia formation is observed by light microscopy.

In Gray et al. (2005, Virology, 337(2), 384-98), primary virus is isolated from patients' PBMCs and used for infection of Cf2-Luc cells transfected with CD4 and CCR5 or CXCR4. Infection is determined after cell lysis using a luciferase assay.

The article Kulkarni et al. (2005, Virology, 337(1), 68-75) describes a GHOST cell assay, with indicator cells harbouring GFP under control of HIV-2 Tat. Infection is observed using FACS analysis on infected cells. The international patent application WO 02/27321 describes a diagnostic method to determine whether CXCR4 or CCR5 strains are present in a patient infected with HIV, which method relies on a cell fusion assay between cells transformed with an HIV envelope gene variant cloned from an infected patient, and an indicator cell line expressing an HIV envelope-compatible co-receptor. The indicator cell line contains an inducible reporter gene construct which is activated upon fusion with a cell containing a suitable transcriptional activator and/or transcription factor.

The international patent application WO 02/38792 describes a Recombinant Virus Assay (RVA) for phenotypic characterisation of HIV, including determination of HIV tropism and resistance/susceptibility to cell entry inhibitors. The method comprises PCR amplification of a region of the viral genome liable to comprise a mutation, and the transfection of a first host cell with said amplified region together with a vector comprising the parts of HIV genome required for viral replication except for the amplified region, in order to obtain a chimeric virus by homologous recombination. The method then involves the production of viral particles by the first host cell and the infection of a second host cell with the viral particles. The second host cell is chosen so as to be liable to be infected by HIV virus or HIV pseudotyped virus and comprises a marker gene which is activated upon viral

infection. According to an embodiment, the amplified region consisted of the majority of the gp120 sub-unit and the extracellular portion (ectodomain) of the gp41 sub-unit. According to another embodiment, the amplified region consisted of the domains ranging from the V1 loop to the V3 loop of HIV-1. However, improvements had still to be done in order to increase sensitivity of the method for HIV-1 subtype non-B viruses, and to achieve more accurate and easier analysis of tropism.

More recently, the international patent application WO 03/070985 has described a co-receptor tropism assay which comprises transfecting a first host cell with two different vectors, one containing the cloned envelope of a patient's sample, the other one lacking a sequence encoding the envelope protein and carrying a gene producing a detectable signal; culturing the transfected host cell to produce viral particles; infecting a second host cell with the viral particles; and measuring the detectable signal. In particular, a co-receptor tropism screening assay is described wherein the second host cell is a cell line expressing either both CD4 and CCR5 or both CD4 and CXCR4. The assay is optionally performed in the presence of a drug inhibiting either R5 or X4 tropic viruses. The phenotypic tropism co-receptor assays described in the international patent applications WO 02/27321 and WO 03/070985 have been compared and were shown to give overall 85% of concordant results (Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model. Skrabal K, Low AJ, Dong W, Sing T, Cheung PK, Mammano F, Harrigan PR. J Clin Microbiol. 2007 Feb;45(2):279-84; Is there a Gold Standard for Determining HIV Coreceptor Usage in Clinical Samples? A Comparison of two Phenotypic Tropism Assays and a Bioinformatic Model" A. Low, K. Skrabal, W. Dong, F. Mammano, T. Sing, P. Cheung and P.R. Harrigan, 13 ^th Conference on Retroviruses and Opportunistic Infections, Denver, February 5-8, 2006).

However, there is still a need for a tropism test with higher sensibility for the detection of X4-tropic viruses, especially in mixtures of viruses harbouring a minority of viruses using CXCR4 in addition to or in the place of CCR5, where previous tests were unable to detect these quasispecies. Additionally the test should allow the determination of tropism of subtype B and non-B samples with

high specificity and sensitivity, the increasing prevalence of subtype non-B samples and circular recombinant forms being a major problem for analysis.

This goal is achieved by the present invention which provides a RVA assay enabling to test viral tropism with high sensitivity. The method of the invention tests HIV-1 group M, subtype B and non-B samples, using two different amplification cassettes: Env (gp120/gp41ec) which has the advantage to allow in parallel the determination of susceptibility of a virus to entry/fusion/co-receptor inhibitors, and V1V3 which may be more convenient for the amplification of non-B samples, when either PCR or RVA were not successful. More specifically, it is proposed to perform a first amplification using the Env cassette, followed - in case of a negative PCR or RVA result - by a second amplification attempt using the V1V3 cassette. The addition of CCR5- and CXCR4-inhibitors allows the increase of the sensitivity of the assay when values at the detection limit did not allow a reliable interpretation in previous tests. Thus, the precise analysis of OD ratios in presence and absence of inhibitors proves (> 5%) the usage of CCR5- and/or CXCR4-coreceptors for viral entry.

Furthermore, amplifying the whole envelope region (gp160) instead of, or in addition to, gp120/gp41ec may be useful to determine the impact of HIV-1 gp41 amino acid substitutions on co-receptor usage and/or susceptibility to co-receptor inhibitors.

Indeed, the HIV envelope region outside of the V1-V3 loops (Huang W. et al, J. Virol. 2007 81 : 7885-7893), and even outside the gp120-gp41ec region (Huang W. et al, XV International Drug Resistance Workshop, 2006, Sitges, Spain), seems to determine or at least to contribute to co-receptor usage as well as entry inhibitor susceptibility. As the majority of the genetic determinants of the HIV-1 envelope phenotype remain largely intractable due to the extreme genetic variability of the env gene, it is important in case of doubt that the entire env gene can be assayed.

Today new HIV entry inhibitors which target either viral envelope glycoproteins or cell receptors and/or co-receptors (CD4, CCR5, CXCR4) are in development. Even if resistance-associated mutations in HIV are expected to be located in the gp120-gp41ec envelope region, appearance of mutations outside this region cannot be excluded, thus requiring the use of the gp160 region.

Furthermore, the use of the gp160 region is of major interest because of the genetic diversity observed within the gp41 cytoplasmic tails (CT) of primary HIV-1 at the quasispecies or subtype level, which may have different influences on virus assembly and replication capacity (Lambele et al., J. Virol. 2007 Jan;81 (1):125- 40). This may be at least partly due to differences in the gp41 CT determinants interacting with effectors involved in intracellular trafficking pathways.

Thus, the invention further provides a method of determining co-receptor usage and/or susceptibility to co-receptor inhibitors, which involves amplification of the whole gp160 region of the envelope.

Definitions

"HIV-1" denotes the human immunodeficiency virus type 1. Phylogenetic analysis of many isolates of HIV-1 from Africa and from other regions of the world have revealed three major lineages of HIV-1 : viruses of group M (for main) are responsible for the majority of infections worldwide, group O (for outlier) is a relatively rare group currently found in Cameroon, Gabon, and France, and group N gathers non-M/non-0 viruses. Within group M, in addition to subtype B, at least eight distinct non-B subtypes (A through H) and circulating recombinant forms (CRFs) have been proposed. In the instant application, nucleotide positions are indicated by reference to the genomic sequence of HIV-1 (p)NL4-3 shown in SEQ ID No.10. Nucleotides 6171 to 9090 of (p)NL4-3 are shown on Figures 1 to 3.

The "pNL4-3" plasmid is the most widely used vector for in vitro manipulations of the HIV-1 proviral sequences. pNL4-3 is a recombinant (infectious) proviral clone that contains DNA from HIV isolates NY5 (5 ¹ half) and BRU (3' half). The site of recombination is the EcoRI site at positions 5743-5748. The construction of pNL4-3 has been described in Adachi et al. (1986, J. Virol., 59 (2), 284-291).

"Primers" which are used for PCR amplification are oligonucleotides, i.e. nucleic acids generally of at least 12, preferably at least 15, and more preferably at least 20 nucleotides, and preferably no more than 30, more preferably no more than 40, still preferably no more than 50 nucleotides, which are hybridisable under high stringency conditions, and preferably complementary, to a region of double

stranded HIV-1 cDNA molecule. Advantageously, the sequence of a primer is designed so that the primer binds to a region of double stranded HIV-1 cDNA molecule which is highly conserved among strains of HIV-1 group M, subtype B or non-B. High stringency hybridization conditions typically correspond to the highest Tm, e.g., 50 % formamide, 5x or 6x SCC where SCC is a 0.15 M NaCI, 0.015 M Na-citrate. Appropriate conditions of temperature and solution ionic strength may be selected by the one skilled in the art (see Molecular Cloning, A Laboratory Manual Joseph Sambrook and David W Russell, Cold Spring Harbor Laboratory Press, New York). In the context of the invention, an "entry inhibitor" denotes a molecule, for instance a protein-based, a peptide-based, a peptide-mimetic, a synthetic peptide analog or a non peptide molecule (e.g. a small molecule), which inhibits entry of HIV-1 into cells by inhibiting either (i) interaction between gp120 and CD4, or (ii) interaction between CD4 and a co-receptor ("co-receptor inhibitors"), or (iii) fusion of viral and cellular membranes ("fusion inhibitor").

As used herein, a "CCR5 co-receptor inhibitor" denotes a molecule which prevents utilisation of CCR5 in the process of HIV infection. A CCR5 co-receptor inhibitor may typically act by interfering with gp120 binding to CCR5 co-receptor, or by inducing CCR5 internalisation thereby removing the co-receptor from the membrane surface. Examples of CCR5 co-receptor inhibitors include, without limitation, macrophage inflammatory protein MIP-1α and MIP-1 β, RANTES (Alkhatib et al., 1996, Science; 272: 1955-1958), or synthetic an analogs thereof (AOP-RANTES (Simmons et al., 1997, Science; 276: 276-279), PSC-RANTES (Hartley et al., 2004, Proc Natl Acad Sci U S A; 101 : 16460-16465)), LD78b, MIP- 1α isoform (Menten et al., 1999, J Clin Invest; 104: R1-R5), Sch-C (Palani et al., 2001 , J Med Chem., 44(21 ):3339-42.), Sch-D (Vicriviroc), UK-427,857 (Maraviroc), GSK-873140 (Aplaviroc), TAK-779 (CAS registry number: 229005-80-5), and anti- CCR5 antibodies. In particular anti-CCR5 monoclonal antibodies may be used, such as antibodies 3A9, SD7, 45502.111 , 45549.111 , 45531.111 and 45523.111 (http://www.aidsreagent.org).

As used herein, a "CXCR4 co-receptor inhibitor" denotes a molecule, which prevents utilisation of CXCR4 in the process of HIV infection. A CXCR4 co- receptor inhibitor may typically act by interfering with gp120 binding to CXCR4 co-

receptor, or by inducing CXCR4 internalisation thereby removing the co-receptor from the membrane surface. Examples of CXCR4 co-receptor inhibitors include, without limitation, Stromal cell-derived factor-la (SDF-Ia) and SDF-1 β, N-α-acetyl- nona-D-arginine amide (ALX-40-4C), synthetic polyphemusins (T22) or analogs thereof (T140) (Kazmierski et al., 2006, Chemical Biology & Drug Design, 67:13), KRH 1636 (lchiyama et al., 2003, Proc Nat Acad Sci U S A, 100: 4185-4190), AMD3100 (De Clercq, 2003, Nat Rev Drug Discov;2: 581-587), and anti-CXCR4 antibodies, such as 12G5, 44717.111 , 44708.111 , and 44716.111 (http://www.aidsreagent.org). Examples of fusion inhibitors include T20 (also known as fuzeon or enfuvirtide) and T-1249.

A "saturating dose of an inhibitor" denotes a concentration of inhibitor at which cell infection by a virus having tropism for said cell is 100% blocked by the inhibitor, which is function of the inhibitor. For example, up to 2 μg/ml for AMD3100 inhibitor, more than 500 ng/ml for RANTES and more than 12 μg/ml for T20.

By "R5-tropic virus" is meant a HIV-1 virus which uses CCR5 co-receptor for entry into cells.

By "X4-tropic virus" is meant a HIV-1 virus which uses CXCR4 co-receptor for entry into cells. By "R5/X4-tropic virus" is meant a HIV-1 virus which may use any of CCR5 and CXCR4 co-receptors for entry into cells.

The term "U373-CCR5" denotes U373MG-CD4 cells stably transfected with the Escherichia coli β-galactosidase gene (lacZ) under transcriptional control of the HIV-1 long terminal repeat (LTR) which express the CCR5 co-receptor (Labrosse et al., 1998, J Virol., 72(8): 6381-6388).

The term "U373-CXCR4" denotes U373MG-CD4 cells stably transfected with the Escherichia coli β-galactosidase gene (lacZ) under transcriptional control of the HIV-1 long terminal repeat (LTR) which express the CXCR4 co-receptor (Labrosse et al., 1998, J Virol., 72(8): 6381-6388).

Recombinant Virus Assay ofR5 and/or X4 tropism

The invention provides a Recombinant Virus Assay (RVA) of tropism which allows the evaluation of viral tropism (i.e. the utilisation of co-receptors CCR5

and/or CXCR4 in addition to CD4 for entry into target cells) of HIV-1 group M viruses, subtype B and non-B, as well as CRF variants. To that end, after extraction of viral RNA from patients' plasma samples, a specific region of the viral envelope (gp160 and/or gp120 and the ectodomain of gp41 - "gp41ec") is amplified using an RT-PCR. The gp160 and/or gp120-gp41ec region, and optionally the region spanning the tropism determinant region V1-V3, is then amplified using a Nested PCR. Recombinant viruses, comprising the HIV envelope isolated from patients' samples, are produced by co-transfection of 293T producer cells using the PCR-product and the plasmid pNL4-3 deleted of the corresponding region in the envelope (pNL4-3δgp160, pNL4-3δenv or pNL4-3δV). Viral supernatants are used to infect U373MG-CD4 indicator cells expressing either the CCR5 or CXCR4 co-receptor (U373-CCR5 or U373-CXCR4), in presence or absence of co-receptor inhibitors at a saturating dose. The indicator cells contain the lacZ gene under control of the HIV-1 LTR which allows the determination of viral infection and thus of viral tropism using a colorimetric assay based on the expression of the β-galactosidase by Tat (see Figure 4).

In the RVA tropism, viral infection is detected independently for both co- receptors. A sample is considered positive when the ratio [OD sample/ OD control] reaches or exceeds 1.5 (the control being an R5-tropic virus on CXCR4+ cells or a X4-tropic virus on CCR5+ cells). The addition of co-receptor inhibitors at saturating dose allows to specifically block the interaction of X4 tropic viruses with the CXCR4 co-receptor or R5 tropic viruses with the CCR5 co-receptor, and thus to specifically inhibit viral entry at 100% via the corresponding co-receptor.

Accordingly, the invention provides a method of assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor, which method comprises the steps consisting of: a) subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with at least a pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160; b) optionally preparing a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a);

c) transfecting a producer cell with the amplified nucleic acids of step (a) and with a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a) to obtain a chimeric virus by homologous recombination; d) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); e) infecting an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor, with the viral particles obtained in step (d), wherein (e1) said infection is carried out in the presence and in the absence of a saturating dose of a CCR5 co-receptor inhibitor where said indicator cell expresses CCR5, or (e2) said infection is carried out in the presence and in the absence of a saturating dose of a CXCR4 co-receptor inhibitor where said indicator cell expresses CXCR4; f) separately, (f1) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a X4-tropic control virus in the presence and in the absence of said saturating dose of CCR5 co-receptor inhibitor, or (f2) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a R5-tropic control virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor; g) quantifying the level of marker expressed in steps (e1) and (f1), and/or in steps (e2) and (f2); and h) calculating the ratios

[sample/control]ccR5+ = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[sample/control]ccR5- = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the presence of said saturating dose of CCR5 co- receptor inhibitor; and/or

[sample/control]cxcR4+ = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[sample/control]cxcR4- = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the presence of said saturating dose of CXCR4 co-receptor inhibitor; wherein a ratio [sample/control]ccR5+ equal or above 1.5, while the ratio [sample/controlJccRs- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CCR5 co-receptor, and/or wherein a ratio [sample/control]cxcR4+ equal or above 1.5, while the ratio [sample/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CXC R4 co-receptor.

As used herein, a "region coding all or part of gp160" is meant for a sequence coding at least for essentially all the gp120 sub-unit and for the ectodomain of gp41 sub-unit (gp120-gp41ec). The sequence may encode the whole gp160 (nt 6305-8785; the sequence of the env gene starts at nucleotide 6221 (ATG) with the signal peptide which is removed during protein synthesis in the cell. So at the protein level, gp160 starts at nucleotide 6305). It also includes a region coding for essentially all gp160.

As used herein, a "region coding for essentially all gp160" denotes a sequence consisting of the sequence encoding gp160 (nt 6305-8785) in which no more than 100, preferably 50, more preferably 30, still preferably 15, consecutive nucleotides have been deleted from the 5' end.

In the methods of the invention, if the biological sample is plasma, a reverse transcription step precedes the PCR amplification.

Therefore, according to an embodiment of the above method, the pair of primers of step a) borders a region of HIV-1 group M genome coding for all, or essentially all, the gp160.

In particular, the pair of primers bordering a region of HIV-1 group M genome coding for all, or essentially all, the gp160 may be selected so that:

- the forward primer hybridises to a region upstream of gp120 coding sequence (for instance a region upstream env sequence), or to a region at the 5' end of gp120 coding sequence, for instance a region upstream of nt 6479 (preferably a region within the 100, preferably 50, nucleotides at the 5' end of gp120 coding sequence); and

- the reverse primer hybridizes to a region downstream of the sequence encoding gp41 (for instance downstream of position 8785).

For instance, the forward primer may comprise or consist of the sequence

EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1 ; nt 6197- 6224), the sequence EST: GAA GTA TCA GCA CTT GTG (SEQ ID NO:8; nt 6235-

6252), or a fragment thereof. The reverse primer may comprise or consist of the sequence E01-: TCC AGT CCC CCC TTT TCT TTT AAA AA (SEQ ID NO:2; nt

9079-9054), the sequence END : CCA AGC CCT GTC TTA TTC (SEQ ID NO:9; nt

8751 to 8768), or a fragment thereof. The said fragments are at least 12, preferably at least 15, and more preferably at least 20 nucleotide-long.

Preferably, the step (a) of PCR amplification of the region coding for gp160 is performed by RT-PCR followed by a nested PCR.

According to an embodiment, said RT-PCR of the extracted nucleic acids uses primers: EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1), and

E01-: TCC AGT CCC CCC TTTTCTTTTAAAAA (SEQ ID NO:2), leading to the amplification of a 2882 bp (c)DNA spanning nt 6197-9079, followed by a nested PCR with primers : EST: GAA GTA TCA GCA CTT GTG (SEQ ID NO:8), and

END : CCA AGC CCT GTC TTA TTC (SEQ ID NO:9). leading to the amplification of a 2533 bp (nested c)DNA spanning nt 6235- 8768.

The primers EOO and E01- have been described in the international patent application WO 02/38792.

The suitable cycling conditions RT-PCR and nested PCR may be readily determined by the one skilled in the art. The cycling conditions described in the following examples may be used, advantageously.

The vector used in step (b) is preferably "RVA-δgp160", i.e. a pNL4-3 plasmid, deleted of all or part the gp160 region which has been replaced by a linker containing a suitable restriction site for linearization of the plasmid (i.e. a restriction site which will be found only once in the modified plasmid RVA-δ gp160). The region to be deleted in the pNL4-3 plasmid is selected in such a way that the linearised vector contains sequences at its 5' and 3' ends which overlap the amplified nucleic acids, so that homologous recombination can occur between the vector and the amplified nucleic acids.

Still preferably, said vector is the pNL4-3 plasmid, deleted of nucleotides 6345-8690 and replaced by a linker and containing a Nhe\ restriction site. In particular, a linker of sequence ctag creates a Nhe\ restriction site (gctagc) with the adjacent G6344 and C8691. The linker sequence is not relevant, because once the plasmid is linearized at the artificial Nhe\ site, the recombination takes place several nucleotides away (5' and 3') from the deletion. So the sequence of the linker will not be part of the « chimeric » env sequence.

Alternatively to the above method of amplifying all, or essentially all, the gp160, or further to it if it fails to lead to PCR amplification of the extracted nucleic acids and/or if the result of the RVA tropism assay with the gp160 cassette is negative, a method of amplifying the gp120-gp41ec region of env may be performed.

Thus, according to another embodiment, the pair of primers of step a) borders a region coding for all, or essentially all the gp120 sub-unit, and for the ectodomain of gp41 sub-unit. Accordingly, the invention provides a method of assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor, which method comprises the steps consisting of: a) subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with at least a pair of primers bordering a region of HIV-1 group M genome coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit;

b) preparing a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a); c) transfecting a producer cell with the amplified nucleic acids of step (a) and the vector prepared in step (b) to obtain a chimeric virus by homologous recombination; d) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); e) infecting an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor, with the viral particles obtained in step (d), wherein (e1) said infection is carried out in the presence and in the absence of a saturating dose of a CCR5 co-receptor inhibitor where said indicator cell expresses CCR5, or (e2) said infection is carried out in the presence and in the absence of a saturating dose of a CXCR4 co-receptor inhibitor where said indicator cell expresses CXCR4; f) separately, (f1) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a X4-tropic control virus in the presence and in the absence of said saturating dose of CCR5 co-receptor inhibitor, or (f2) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a R5-tropic control virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor; g) quantifying the level of marker expressed in steps (e1) and (f1), and/or in steps (e2) and (f2); and h) calculating the ratios

[sample/control]ccR5+ = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[sample/control]ccR5- = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the presence of said saturating dose of CCR5 co- receptor inhibitor; and/or

[sample/control]cxcR4+ = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[sample/control]cxcR4- = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the presence of said saturating dose of CXCR4 co-receptor inhibitor; wherein a ratio [sample/control]ccR5+ equal or above 1.5, while the ratio [sample/control]ccR5- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CCR5 co-receptor, and/or wherein a ratio [sample/control]cxcR4+ equal or above 1.5, while the ratio [sample/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CXCR4 co-receptor.

As used herein, "a region coding for essentially all the gp120 sub-unit" denotes a sequence consisting of the sequence encoding gp120 (nt 6305-7744) in which no more than 100, preferably 50, more preferably 30, still preferably 15, consecutive nucleotides have been deleted from the 5' end. The sequence encoding gp41ec consists of nucleotides 7745-8329.

Therefore, the pair of primers bordering a region of HIV-1 group M genome coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit may be selected so that:

- the forward primer hybridises to a region upstream of gp120 coding sequence (for instance a region upstream env sequence), or to a region at the 5' end of gp120 coding sequence, for instance a region upstream of nt 6479 (preferably a region within the 100, preferably 50, nucleotides at the 5' end of gp120 coding sequence); and

- the reverse primer hybridizes to a region downstream of the sequence encoding the ectodomain of gp41 (for instance downstream of position 8264).

For instance, the forward primer may comprise or consist of the sequence EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1 ; nt 6197- 6224), or E10: TTG TGG GTC ACA GTC TAT TAT GGG GT (SEQ ID NO:3; nt

6320-6345), or a fragment thereof. The reverse primer may comprise or consist of the sequence E01-: TCC AGT CCC CCC TTT TCT TTT AAA AA (SEQ ID NO:2; nt 9079-9054), or FuB: GGT GGT AGC TGA AGA GGC ACA GG (SEQ ID NO:4; nt 8521-8500), or a fragment thereof. The said fragments are at least 12, preferably at least 15, and more preferably at least 20 nucleotide-long.

Preferably, the step (a) of PCR amplification of the region coding for gp120 sub-unit and ectodomain of gp41 sub-unit is performed by RT-PCR followed by a nested PCR.

According to an embodiment, said RT-PCR of the extracted nucleic acids uses primers:

EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1), and

E01-: TCC AGT CCC CCC TTT TCT TTTAAAAA (SEQ ID NO:2), leading to the amplification of a 2882 bp (c)DNA spanning nt 6197-9079, followed by a nested PCR with primers :

E10: TTG TGG GTC ACA GTC TAT TAT GGG GT (SEQ ID NO:3), and

FuB: GGT GGT AGC TGA AGA GGC ACA GG (SEQ ID NO:4), leading to the amplification of a 2202 bp (nested c)DNA spanning nt 6320-8521.

The primer FuB has also been described in the international patent application WO 02/38792.

The suitable cycling conditions RT-PCR and nested PCR may be readily determined by the one skilled in the art. The conditions cycling described in the following examples may be used, advantageously.

The vector used in step (b) is preferably "RVA-δenv", i.e. a pNL4-3 plasmid, deleted of all or part the gp120-gp41ec region of the envelope gene which has been replaced by a linker containing a suitable restriction site for linearization of the plasmid (i.e. a restriction site which will be found only once in the modified plasmid RVA-δenv). The region to be deleted in the pNL4-3 plasmid is selected in such a way that the linearised vector contains sequences at its 5' and 3' ends which overlap the amplified nucleic acids, so that homologous recombination can occur between the vector and the amplified nucleic acids. Still preferably, said vector is the pNL4-3 plasmid, deleted of nucleotides 6480-8263 and containing the

MIuI restriction site (in particular deleted nucleotides 6480-8263 may be replaced

by a linker ACGCG which, together with T8264, creates the MIuI restriction site) (Labrosse et al., J. Virol. 2003 77(2): 1610-3).

Where the above methods fail to lead to PCR amplification of the extracted nucleic acids and/or if the result of the RVA tropism assay with the gp160 and/or gp120-gp41ec cassettes is negative, and/or if the biological sample is likely to contain non-B subtypes of HIV-1 group M, the method of amplifying the V1-V3 region of gp120 may be used.

Thus, according to the invention, the method of assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor may be carried out by implementing the above "gp120- gp41ec" method followed by the "V1V3 method" which is detailed below.

Indeed, the invention also provides a method of assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor, which method comprises the steps consisting of: a) subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with at least a pair of primers bordering the entire region of HIV-1 group M genome coding for V1-V3 loops of gp120 sub-unit; b) optionally preparing a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for the region coding for V1-V3 loops of gp120 sub-unit; c) transfecting a producer cell with the amplified nucleic acids of step (a) and a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for the region coding for V1-V3 loops of gp120 sub-unit to obtain a chimeric virus by homologous recombination; d) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); e) infecting an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor, with the viral particles obtained in step (d), wherein (e1) said infection is carried out in the presence and in the absence of a saturating dose of CCR5 co-receptor inhibitor where said indicator expresses

CCR5, or (e2) said infection is carried out in the presence and in the absence of a saturating dose of CXCR4 co-receptor inhibitor where said indicator cell expresses CXCR4; f) separately, (f1) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a X4-tropic control virus in the presence and in the absence of said saturating dose of CCR5 co-receptor inhibitor, or (f2) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a R5-tropic control virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor; g) quantifying the level of marker expressed in steps (e1) and (f1), and/or in steps (e2) and (f2); and h) calculating the ratios

[sample/control]ccR5+ = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[sample/control]ccR5- = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the presence of the saturating dose of CCR5 co- receptor inhibitor; and/or [sample/control]cxcR4+ = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[sample/control]cxcR4- = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the presence of the saturating dose of CXCR4 co-receptor inhibitor, wherein a ratio [sample/control]ccR5+ equal or above 1.5, while the ratio [sample/controlJccRs- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses having tropism for CCR5 co- receptor in the biological sample from the patient, and/or wherein a ratio [sample/control]cxcR4+ equal or above 1.5, while the ratio

[sample/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses having tropism for CXCR4 co- receptor in the biological sample from the patient.

The primers bordering the entire region coding for V1-V3 loops of gp120 sub-unit may be selected so that:

- the forward primer hybridises to a region upstream of the sequence encoding the V1 loop of gp120 coding sequence (for instance a region of gp 120 coding sequence upstream of nucleotide 6612, i.e. position -1 from the first nucleotide of V1 coding sequence);

- the reverse primer hybridizes to a region downstream of the sequence encoding the V3 loop of gp120 coding sequence (for instance a region of gp 120 coding sequence downstream of nucleotide 7205, i.e. position +1 from the last nucleotide of V3 coding sequence).

For instance, the forward primer may comprise or consist of the sequence EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1 , nt 6197- 6224), or E20: GGG CCA CAC ATG CCT GTG TAC CCA CAG (SEQ ID NO:6; nt 6426-6452), or a fragment thereof. The reverse primer may comprise or consist of the sequence ES8B: CAC TTC TCC AAT TGT CCC TCA (SEQ ID NO:5; nt 7658- 7638), or E115 : AGA AAA ATT CCC CTC CAC AAT TAA (SEQ ID NO:7; nt 7364- 7341), or a fragment thereof. The said fragments are at least 12, preferably at least 15, and more preferably at least 20 nucleotide-long. Preferably, the step (a) of PCR amplification of the region coding for V1-V3 loops of gp120 sub-unit is performed by a RT-PCR followed by nested PCR.

According to a preferred embodiment, said PCR involves a RT-PCR of the extracted nucleic acids using primers :

EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1), and

ES8B: CAC TTC TCC AAT TGT CCC TCA (SEQ ID NO:5), leading to the amplification of a 1461 bp (c)DNA spanning nt 6197-7658, followed by a nested PCR with primers :

E20: GGG CCA CAC ATG CCT GTG TAC CCA CAG (SEQ ID NO:6), and E115 : AGA AAA ATT CCC CTC CAC AAT TAA (SEQ ID NO:7), leading to the amplification of a 938 bp (nested c)DNA spanning nt 6426-7364.

The primers EOO, ES8B, E20 and E115 have been described in the international patent application WO 02/38792.

The suitable cycling conditions RT-CPR and nested PCR may be readily determined by the one skilled in the art. The conditions cycling described in the following examples may be used, advantageously.

The vector used in step (b) is preferably "RVA-δV", i.e. a pNL4-3 plasmid deleted of all or part the V1-V3 region of the envelope gene, and using a suitable restriction site for linearization of the plasmid (i.e. a restriction site which will be found only once in the modified plasmid RVA-δV). The region to be deleted in the pNL4-3 plasmid is selected in such a way that the linearised vector contains sequences at its 5' and 3' ends which overlap the amplified nucleic acids, so that homologous recombination can occur between the vector and the amplified nucleic acids. Still preferably, said vector is the pNL4-3 plasmid deleted of nucleotides 6612-7249 which contains the natural Nhe\ restriction site for linearization of the plasmid. By "natural Nhe\ restriction site" it is meant the Nhe\ restriction site which is normally found downstream the V3 region of pNL4-3 plasmid at positions 7250-7255.

In step (f) of the gp160, gp120-gp41ec and V1-V3 RVA assays, by "another indicator cell of the same type", is meant another cell of the indicator cell line which was used in step (e). For instance, if in step (e), a U373-CCR5 cell has been infected with the viral particles prepared from the patient's nucleic acids, then, in step (f), the U373-CCR5 cell line will be used for infection with the X4- tropic control virus. Conversely, if in step (e), a U373-CXCR4 cell has been infected with the viral particles prepared from the patient's nucleic acids, then, in step (T), the U373-CXCR4 cell line will be used for infection with the R5-tropic control virus.

As used in the instant application, a "control virus" denotes a negative control for the RVA tropism assay. For instance, a "R5-tropic control virus" denotes a R5-tropic virus which is to be assayed for infection of an indicator cell expressing CXCR4 in the presence or in the absence of a saturating dose of a CXCR4 co- receptor inhibitor. Conversely, a "X4-tropic control virus" denotes a X4-tropic virus which is to be assayed for infection of an indicator cell expressing CCR5 in the presence or in the absence of a saturating dose of a CCR5 co-receptor inhibitor.

The level of marker expressed, which is associated with a control virus, represents the background level of quantification of marker expression.

Hence, theoretically if infection of the indicator cell with the viral particles prepared from the patient's nucleic acids has been 100% inhibited by the CCR5 (or CXCR4) co-receptor inhibitor, the ratio [sample/control]ccR5- (or [sample/control]cxcR4-) should be equal to 1. However an interval of ratio values ranging from 0.9 to 1.1 has been retained, in order to take into account experimental variability.

In the RVA gp160, gp120-gp41ec and V1-V3 tropism assays step (f) may optionally further comprise: (f3) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a R5-tropic reference virus in the presence and in the absence of said saturating dose of CCR5 co- receptor inhibitor, or (f4) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a X4-tropic reference virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor.

A "reference virus" denotes a positive control for the RVA tropism assay, i.e. a control which ensures that the RVA tropism assay has worked. For instance, a "R5-tropic reference virus" denotes a R5-tropic virus which is to be assayed for infection of an indicator cell expressing CCR5 in the presence or in the absence of a CCR5 co-receptor inhibitor. Conversely, a "X4-tropic reference virus" denotes a X4-tropic virus which is to be assayed for infection of an indicator cell expressing CXCR4 in the presence or in the absence of a CXCR4 co-receptor inhibitor. The use of reference viruses thus makes it possible to ensure (i) that infection of indicator cells has succeeded, hence that the RVA tropism assay should have worked if the extracted nucleic acids had been successfully amplified, and (ii) infection of the indicator cell was 100% inhibited by the saturating dose of CCR5 (or CXCR4, as appropriate) co-receptor inhibitor. Accordingly, in the RVA gp160, gp120-gp41ec and V1-V3 tropism assays, optionally step (g) further comprises quantifying the level of marker expressed in step (f3) or (f4); and step h) further comprises calculating the ratios

[reference/control]ccR5+ = [level of marker expressed in step (f3) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[reference/control]ccR5- = [level of marker expressed in step (f3) / level of marker expressed in step (f1)] in the presence of the saturating dose of CCR5 co- receptor inhibitor; and/or

[reference/control]cxcR4+ = [level of marker expressed in step (f4) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[reference /control]cxcR4- = [level of marker expressed in step (f4) / level of marker expressed in step (f2)] in the presence of the saturating dose of CXCR4 co-receptor inhibitor, wherein a ratio [reference/control] _C cR5+ equal or above 1.5, while the ratio [reference/control]ccR5- is comprised between 0.9 and 1.1 (limits included), indicates that all steps of the method have been successfully performed, and/or wherein a ratio [reference/control] _C χcR4+ equal or above 1.5, while the ratio [reference/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), indicates that all steps of the method have been successfully performed.

Therefore, in a typical RVA tropism assay according to the invention, the control virus, reference virus, indicator cell, and inhibitor to be used would be as shown in Table 1.

Table 1. controls, references, cells and inhibitors used for determination of viral R5 or X4 tropism

R5 tropism X4 tropism

control virus X4 tropic virus (e.g. EnvX4) R5 tropic virus (e.g. EnvR5)

reference virus R5 tropic virus (e.g. EnvR5) X4 tropic virus (e.g. EnvX4) indicator cells e.g. U373-CCR5 e.g. U373-CXCR4 coreceptor e.g. RANTES e.g. AMD-3100 inhibitor

The criteria for validation of the RVA tropism assay, as well as criteria used to conclude if the virus is able to use or not (tropic or non-tropic for) the co- receptor assayed are detailed in Tables 2 and 3.

Table 2. Validation criteria for R5 tropism determination

Table 3. Validation criteria for X4 tropism determination

In the above methods, the nucleic acids may be extracted from the patient's biological sample according to any method known in the art. The biological sample may be for instance blood, plasma, serum, saliva, sperm or any other secretion from a patient harbouring HIV-1 group M virus.

A "producer" cell is a cell which supports the production of viral particles but which is not permissive for HIV-1 infection. Typically, a suitable producer cell is

deprived of the CD4 receptor which is necessary for the virus entry into cells. The producer cells may be for instance HeLa cells, or 293 T cells.

An "indicator" cell is a cell which produces a detectable signal upon infection with HIV-1 virus. An indicator cell may be for instance a U373-CCR5 or U373-CXCR4 cell, a P4 cell (i.e CD4-positive, HeLa cell-derived cells in which transactivation by Tat induces expression of the Escherichia coli lacZ gene from the HIV long terminal repeat; Charneau et al., 1994, J. MoI. Biol., 241 :651-662) or a P4C5 cell (i.e P4 cells constitutively expressing the CCR5 HIV co-receptor and containing lacZ under control of the HIV-1 LTR (Amara et al., 1997, J. Exp. Med. 186:139-146). HeLa cells naturally express CXCR4.

Preferably said indicator cell is U373-CCR5 or U373-CXCR4. These cells comprise a system of expression of the gene encoding the β-galactosidase enzyme, which can only be activated by tat activation sequences expressed by the chimeric virus obtained by recombination of the vector and the amplified nucleic acids. In this case, the level of marker expressed is quantified by measuring the β-galactosidase activity by any suitable mean, for instance using a CPRG (chlorophenolred-β-D-galactopyranoside) substrate. Briefly, when cleaved by β- galactosidase, CPRG yields chlorophenolred, which is a water-soluble red product measurable by spectrophotometry. Examples of suitable R5-tropic (control or reference) virus that may be used in the above methods include, for instance, ADA, YU-2, JRCSF, EnvR5 (T28-R5- 2) and CAR5 (T28-R5-1) viruses (the two last ones as described in Skrabal et al. (2005, J. Virol., 79(18), 11848-11857; EMBL database accession numbers AJ810480.2 and AJ810481.2). Examples of suitable X4-tropic (control or reference) virus that may be used in the above methods include, for instance, HXB2, NL4-3, EnvX4 (T28-X4-3) and CAX4 (T28-X4-1) viruses (the two last ones as described in Skrabal et al., 2005, J. Virol., 79(18), 11848-11857; EMBL database accession numbers AJ810482.2 to AJ810483.2). A "dual-tropic" virus, i.e. a virus having dual tropism for CCR5 and CXCR4 co-receptors may also be used as reference virus. T5-R5X4-1 ("DUAL" in the following examples) and T5-R5X4-2 (Skrabal et al., 2005, J. Virol., 79(18), 11848-

11857; EMBL database accession numbers AJ810478.2) are examples of such dual tropic viruses.

Once tropism for CCR5 or CXCR4 co-receptor has be determined, the patient's viruses may be assayed for susceptibility to entry inhibitors, according to the method described below.

Recombinant Virus Assay of susceptibility to entry inhibitors. A method of assaying susceptibility of HIV-1 group M viruses present in a biological sample of a patient to an entry inhibitor, may comprise the steps consisting of: a) transfecting a producer cell with (i) nucleic acids from said biological sample of a patient which have been amplified with at least a pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160, in particular a region coding for all, or essentially all, gp160, or coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit, and (ii) a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified, to obtain a chimeric virus by homologous recombination; b) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); c) incubating an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CCR5, if the viruses have tropism for CCR5 co- receptor, and/or an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CXCR4, if the viruses have tropism for CXCR4 co- receptor, in the absence and in the presence of an entry inhibitor; d) infecting said indicator cells which have been incubated in the absence and in the presence of said entry inhibitor in step (c), with the viral particles obtained in step (b); and e) quantifying the level of marker expressed by said indicator cells which have been subjected to infection in step (d);

wherein if the level of marker expressed by indicator cells which have been incubated in the presence of the entry inhibitor is decreased by comparison with the level of marker expressed by indicator cells which have been incubated in the absence of the entry inhibitor, then the viruses present in the biological sample of the patient are susceptible to said entry inhibitor.

Where the patient's viruses are dual-tropic viruses, the analysis of susceptibility to entry inhibitors is carried out on both cell types, i.e. the incubation step (step c) is performed on both an indicator cell expressing CCR5 and an indicator cell expressing CXCR4.

According to an embodiment, in the method of assaying susceptibility to an entry inhibitor, in step (c), the indicator cells are incubated in the absence and in the presence of increasing concentrations of the entry inhibitor. Step (e) of the method then further comprises determination of an inhibitory concentration index from the quantified levels of marker expressed by the indicator cells.

Thus, the method of assaying susceptibility may be a method of determining the inhibitory concentration index of an entry inhibitor towards the HIV-1 group M viruses present in a biological sample of a patient, which method comprises: a) transfecting a producer cell with (i) nucleic acids from said biological sample of a patient which have been amplified with at least a pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160, in particular a region coding for all, or essentially all, gp160, or coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit, and (ii) a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified, to obtain a chimeric virus by homologous recombination; b) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); c) incubating an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CCR5, if the viruses have tropism for CCR5 co- receptor, and/or an indicator cell, which is liable to be infected by an HIV-1 group

M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CXCR4, if the viruses have tropism for CXCR4 co- receptor, in the absence and in the presence of increasing concentrations of an entry inhibitor; d) infecting said indicator cells, which have been incubated in the absence and in the presence of said increasing concentrations of entry inhibitor in step (c), with the viral particles obtained in step (b); and e) quantifying the level of marker expressed by said indicator cells which have been subjected to infection in step (d), and determining the inhibitory concentration index of said entry inhibitor.

Where the patient's viruses are dual-tropic viruses, the method of determining inhibitory concentration index is carried out on both cell types, i.e. the incubation step (step c) is performed on both an indicator cell expressing CCR5 and an indicator cell expressing CXCR4. The determination of an inhibitory index is within the ordinary skills of the one skilled in the art. For instance, the concentration of a drug that inhibits viral replication by 50% (inhibitory concentration 50, IC50) or 90% (IC90) is calculated by determining the percentage of infection in presence of inhibitor (at different concentrations), as compared to 100% of infection (viral infection in absence of inhibitor), which allows the design of a sigmoidal inhibition curve (% of infection vs concentration of inhibitor). Inhibitory concentration indexes may be deduced from this curve very simply by determining the x-coordinate (inhibitor concentration) of the point on the curve having y-coordinate equal to 50% (IC50) or 90% (IC90).

Accordingly the invention further provides a method of assaying tropism of

HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor and susceptibility of said viruses to an entry inhibitor, which method comprises the steps consisting of: a) subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with at least a pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160, in particular a region coding for all, or essentially all, gp160, or coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit;

b) optionally preparing a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a); c) transfecting a producer cell with the amplified nucleic acids of step (a) and a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a) to obtain a chimeric virus by homologous recombination; d) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); e) infecting an indicator cell, which is liable to be infected by an HIV-1 group

M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor, with the viral particles obtained in step (d), wherein (e1) said infection is carried out in the presence and in the absence of a saturating dose of a CCR5 co-receptor inhibitor where said indicator cell expresses CCR5, or (e2) said infection is carried out in the presence and in the absence of a saturating dose of a CXCR4 co-receptor inhibitor where said indicator cell expresses CXCR4; f) separately, (f1) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a X4-tropic control virus in the presence and in the absence of said saturating dose of CCR5 co-receptor inhibitor, or (f2) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a R5-tropic control virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor; g) quantifying the level of marker expressed in steps (e1) and (f1), and/or in steps (e2) and (f2); and h) calculating the ratios

[sample/control]ccR5+ = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[sample/controllccRδ- = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the presence of said saturating dose of CCR5 co- receptor inhibitor; and/or

[sample/control]cxcR4+ = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[sample/control]cxcR4- = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the presence of said saturating dose of CXCR4 co-receptor inhibitor; wherein a ratio [sample/control] _C cR5+ equal or above 1.5, while the ratio

[sample/controlfccRδ- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CCR5 co-receptor, and/or wherein a ratio [sample/control]cxcR4+ equal or above 1.5, while the ratio [sample/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CXCR4 co-receptor; and i) transfecting a producer cell with the amplified nucleic acids of step (a) and the vector prepared in step (b) to obtain a chimeric virus by homologous recombination; j) culturing said producer cell of step (j) under conditions enabling the production of viral particles during a single replication cycle; k) incubating an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CCR5, if the viruses have tropism for CCR5 co- receptor, and/or an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CXCR4, if the viruses have tropism for CXCR4 co- receptor, in the absence and in the presence of an entry inhibitor; I) infecting said indicator cells which have been incubated in the absence and in the presence of said entry inhibitor in step (k), with the viral particles obtained in step (j); and

m) quantifying the level of marker expressed by said indicator cells which have been subjected to infection in step (I); wherein if the level of marker expressed by indicator cells which have been incubated in the presence of the entry inhibitor is decreased by comparison with the level of marker expressed by indicator cells which have been incubated in the absence of the entry inhibitor, then the viruses present in the biological sample of the patient are susceptible to said entry inhibitor.

Where the viruses have been identified as dual-tropic viruses, the analysis of susceptibility to entry inhibitors is carried out on both cell types, i.e. the incubation step (step k) is performed on both an indicator cell expressing CCR5 and an indicator cell expressing CXCR4.

In the method of assaying tropism for CCR5 and/or CXCR4 co-receptor and susceptibility to an entry inhibitor, step (k) may be performed by incubating the indicator cells in the absence and in the presence of increasing concentrations of the entry inhibitor, and step (m) may further comprise determining an inhibitory concentration index of said entry inhibitor.

Thus, the method may be a method of assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co- receptor and of determining inhibitory concentration index of said HIV-1 group M viruses present in the biological sample of a patient towards an entry inhibitor, which method comprises the steps consisting of: a) subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with at least a pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160, in particular a region coding for all, or essentially all, gp160, or coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit; b) optionally preparing a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a); c) transfecting a producer cell with the amplified nucleic acids of step (a) and a vector comprising the parts of an HIV-1 group M virus genome required for

viral replication except for all or part of the region amplified in step (a) to obtain a chimeric virus by homologous recombination; d) culturing said producer cell under conditions enabling the production of viral particles (during a single replication cycle); e) infecting an indicator cell, which is liable to be infected by an HIV-1 group

M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor, with the viral particles obtained in step (d), wherein (e1) said infection is carried out in the presence and in the absence of a saturating dose of a CCR5 co-receptor inhibitor where said indicator cell expresses CCR5, or (e2) said infection is carried out in the presence and in the absence of a saturating dose of a CXCR4 co-receptor inhibitor where said indicator cell expresses CXCR4;

¹ f) separately, (f1) where said indicator cell expresses CCR5, infecting at least another indicator cell of the same type with a X4-tropic control virus in the presence and in the absence of said saturating dose of CCR5 co-receptor inhibitor, or (f2) where said indicator cell expresses CXCR4, infecting at least another indicator cell of the same type with a R5-tropic control virus in the presence and in the absence of said saturating dose of CXCR4 co-receptor inhibitor; g) quantifying the level of marker expressed in steps (e1) and (f1), and/or in steps (e2) and (f2); and h) calculating the ratios

[sample/control]ccR5+ = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the absence of the CCR5 co-receptor inhibitor, and

[sample/control]ccR5- = [level of marker expressed in step (e1) / level of marker expressed in step (f1)] in the presence of said saturating dose of CCR5 co- receptor inhibitor; and/or [sample/control]cxcR4+ = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the absence of the CXCR4 co-receptor inhibitor, and

[sample/controlJcxcFM- = [level of marker expressed in step (e2) / level of marker expressed in step (f2)] in the presence of said saturating dose of CXCR4 co-receptor inhibitor; wherein a ratio [sample/control]ccR5+ equal or above 1.5, while the ratio [sample/controlJccRs- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CCR5 co-receptor, and/or wherein a ratio [sample/control]cxcR4+ equal or above 1.5, while the ratio [sample/control]cxcR4- is comprised between 0.9 and 1.1 (limits included), is indicative of the presence of HIV-1 group M viruses, in the biological sample from the patient, having tropism for CXCR4 co-receptor; and i) transfecting a producer cell with the amplified nucleic acids of step (a) and the vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified in step (a) to obtain a chimeric virus by homologous recombination; j) culturing said producer cell of step (j) under conditions enabling the production of viral particles during a single replication cycle; k) incubating an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CCR5, if the viruses have tropism for CCR5 co- receptor, and/or an indicator cell, which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses CXCR4, if the viruses have tropism for CXCR4 co- receptor, in the absence and in the presence of increasing concentrations of an entry inhibitor;

I) infecting said indicator cells, which have been incubated in the absence and in the presence of said increasing concentrations of entry inhibitor in step (k), with the viral particles obtained in step (i); and m) quantifying the level of marker expressed by said indicator cells which have been subjected to infection in step (I), and determining the inhibitory concentration index of said entry inhibitor.

Where the patient's viruses are dual-tropic viruses, the method of determining inhibitory concentration index is carried out on both cell types, i.e. the

incubation step (step c) is performed on both an indicator cell expressing CCR5 and an indicator cell expressing CXCR4.

In the above methods of assaying tropism for CCR5 and/or CXCR4 co- receptor and susceptibility to an entry inhibitor (in particular of determining inhibitory concentration index), advantageously:

- the producer cells of steps (c) and (i) are cells from a same cell line; and/or

- the indicator cells of steps (e) and (k) are cells from a same cell line. All definitions, embodiments, etc, described in the Section "Recombinant

Virus Assay of R5 and/or X4 tropism" also apply to the instant methods of assaying tropism for CCR5 and/or CXCR4 co-receptor and susceptibility to an entry inhibitor (in particular of determining inhibitory concentration index).

The entry inhibitor to be assayed may be an inhibitor interacting between gp120 and CD4, or a co-receptor inhibitor, or a fusion inhibitor.

The range of concentrations of inhibitor which may be used in the assay can be readily determined by the one skilled in the art. The one skilled in the art would typically determine first the concentration at which toxicity starts to be observed on the indicator cells of step (k). The inhibitor would then be assayed with non-toxic concentrations.

The methods of assaying tropism for CCR5, and/or CXCR4, co-receptor and/or susceptibility to an entry inhibitor according to the invention should help the clinician to define an appropriate therapeutic treatment (in particular a treatment including a co-receptor inhibitor), and/or to determine whether such a treatment is appropriate for the patient. Indeed, if the viruses of the patient show a dual tropism pattern (R5/X4), administration of a CCR5 inhibitor might induce mutations towards a marked X4-tropic pattern with a risk of disease progression.

The methods of assaying tropism for CCR5 and/or CXCR4, co-receptor also make it possible to monitor efficacy of a treatment. Actually, analysis of the pattern of R5-tropic and X4-tropic viruses in the course of a therapeutic treatment is valuable for the clinician who can ensure him(her)self that a switch from R5- tropic to X4-tropic viruses does not occur.

Kits

The invention further provides kits for implementing the above described methods.

In particular, a kit for assaying susceptibility of HIV-1 group M viruses present in a biological sample of a patient to CCR5 and/or CXCR4 co-receptor inhibitors, and/or of assaying tropism of said HIV-1 group M viruses for CCR5 and/or CXCR4 co-receptor, may comprise: a) at least one pair of primers bordering a region of HIV-1 group M genome coding for all or part of gp160, in particular a region coding for all, or essentially all, gp160; b) a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified with the pair of primers defined in (a); c) a producer cell which is suitable to support the production of HIV-1 viral particles, and which is preferably not permissive for HIV-1 infection; d) an indicator cell which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor; e) a R5-tropic virus and a CCR5 co-receptor inhibitor, and/or a X4-tropic virus and a CXCR4 co-receptor inhibitor; f) optionally, reagents required to carry out PCR amplification; and g) optionally, reagents required to quantify the level of marker expressed. Said kit may comprise the following primer pairs:

- a pair of primers having sequences SEQ ID NO:1 and SEQ ID NO:2, and - a pair of primers having sequences SEQ ID NO:8 and SEQ ID NO:9.

Said kit may also comprise a pNL4-3 plasmid deleted of nucleotides 6345- 8690 and replaced by a linker containing the Nhe\ restriction site.

According to an embodiment, the kit for assaying susceptibility of HIV-1 group M viruses present in a biological sample of a patient to CCR5 and/or CXCR4 co-receptor inhibitors, and/or of assaying tropism of said HIV-1 group M viruses for CCR5 and/or CXCR4 co-receptor, may comprise:

a) at least one pair of primers bordering a region of HIV-1 group M genome coding for all, or essentially all, the gp120 sub-unit and for the ectodomain of gp41 sub-unit; b) a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified with the pair of primers defined in (a); c) a producer cell which is suitable to support the production of HIV-1 viral particles, and which is preferably not permissive for HIV-1 infection; d) an indicator cell which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor; e) a R5-tropic virus and a CCR5 co-receptor inhibitor, and/or a X4-tropic virus and a CXCR4 co-receptor inhibitor; f) optionally, reagents required to carry out PCR amplification; and g) optionally, reagents required to quantify the level of marker expressed.

Said kit may comprise the following primer pairs:

- a pair of primers having sequences SEQ ID NO:1 and SEQ ID NO:2, and

- a pair of primers having sequences SEQ ID NO:3 and SEQ ID NO:4. Said kit may also comprise a pNL4-3 plasmid deleted of nucleotides 6480- 8263 and replaced by a linker containing the MIuI restriction site.

It is further provided a kit for assaying tropism of HIV-1 group M viruses present in a biological sample of a patient for CCR5 and/or CXCR4 co-receptor, which comprises: a) a least one pair of primers bordering the entire region of HIV-1 group M genome coding for V1-V3 loops of gp120 sub-unit; b) a vector comprising the parts of an HIV-1 group M virus genome required for viral replication except for all or part of the region amplified with the pair of primers defined in (a); c) a producer cell which is suitable to support the production of HIV-1 viral particles, and which is preferably not permissive for HIV-1 infection;

d) an indicator cell which is liable to be infected by an HIV-1 group M virus, which comprises a marker gene which is only activated upon viral infection and which expresses either CCR5 or CXCR4 co-receptor; e) a R5-tropic virus and a CCR5 co-receptor inhibitor, and/or a X4-tropic virus and a CXCR4 co-receptor inhibitor;

T) optionally, reagents required to carry out PCR amplification; and g) optionally, reagents required to quantify the level of marker expressed. Said kit may comprise the following primer pairs:

- a pair of primers having sequences SEQ ID NO:1 and SEQ ID NO:5, and - a pair of primers having sequences SEQ ID NO:6 and SEQ ID NO:7.

Said kit may also comprise a pNL4-3 plasmid deleted of nucleotides 6612- 7249, containing the natural Nhel restriction site for linearization of the plasmid.

In the kits of the invention, a reagent required to quantify the level of marker expressed may be for instance the CPRG substrate.

The R5-tropic control/reference virus may be, for instance, EnvR5, CAR5, ADA, YU-2, or JR-CSF.

The X4-tropic reference virus may be, for instance, EnvX4, CAX4, HXB2. A CCR5 co-receptor inhibitor may be, for instance, RANTES, or antibodies. 3A9, SD7, 45502.111 , 45549.111 , 45531.111 and 45523.111 (http://www.aidsreagent.org)

A CXCR4 co-receptor inhibitor may be, for instance, AMD3100, antibodies or natural ligands of CXCR4.

The invention will be further illustrated in view of the following figures and examples.

gp160 cassette

The invention further relates to a pair of primers consisting of primers of sequences EST: GAA GTA TCA GCA CTT GTG (SEQ ID NO:8), and END: CCA AGC CCT GTC TTA TTC (SEQ ID NO:9).

This pair may be used in a method of assaying viral tropism for CXCR4 and/or CCR5 co-receptors and/or for assaying susceptibility to entry inhibitors. The pair of primers enables to provide a 2533 bp amplicon ("gp160 cassette") which

may be inserted in vector RVA-δgp160, i.e. pNL4-3 deleted of the gp160 region of the envelope gene (nt 6345-8690) and replaced by a linker containing the Nhe\ restriction site for linearization of the plasmid.

The invention also provides a method of amplifying all or essentially all gp160 region of HIV-1 group M viruses present in a biological sample of a patient, which method comprises subjecting nucleic acids extracted from said biological sample of a patient to a PCR amplification with a pair of primers consisting of EST: GAA GTA TCA GCA CTT GTG (SEQ ID NO:8), and END: CCA AGC CCT GTC TTA TTC (SEQ ID NO:9). The invention also relates to amplicons of HIV-1 group M viruses which are obtainable by the above method of amplification.

FIGURES

Figures 1-3 display the genomic sequence of HIV-1 strain NL43 from nucleotide 6171 to nucleotide 9090.

Figure 4 is a diagrammatic representation of the principle of the RVA assay.

Figure 5 shows the results of RVA assays (gp120-gp41ec) performed on a mixture of viral envelopes from reference viruses NL4-3 and JR-CSF, with increasing percentages of X4 tropic virus (NL43). Figure 6 shows the results of RVA assays (gp120-gp41ec) performed on a mixture of viral envelopes from primary viruses CAX4 and EnvR5, with increasing percentages of the X4 tropic virus (CAX4).

Figure 7 shows the results of RVA assays (gp120-gp41ec) performed on a mixture of viral envelopes from primary viruses CAX4 and DAR5, with increasing percentages of the X4 tropic virus (CAX4).

Figure 8 shows the results of RVA assays (gp120-gp41ec) performed on a mixture of viral envelopes from primary viruses CAX4 and EnvR5, with increasing percentages of the R5 tropic virus (EnvR5). Figure 9 shows the results of RVA assays (V1-V3) performed on a mixture of primary envelopes CAX4 and EnvR5, and with increasing percentages of X4 tropic virus (CAX4).

Figure 10 shows the results of RVA assays (V1-V3) performed on a mixture of primary envelopes CAX4 and DAR5, and with increasing percentages of X4 tropic virus (CAX4).

Figure 11 shows the results of RVA assays (gp160) performed on a mixture of viral envelopes from primary viruses CAX4 and EnvR5, with increasing percentages of the X4 tropic virus (CAX4).

Figure 12 shows the results of RVA assays (gp160) performed on a mixture of viral envelopes from primary viruses CAX4 and EnvR5, with increasing percentages of the R5 tropic virus (EnvR5).

EXAMPLES

Example 1 : amplification of gp120/gp41ec by RT-PCR and nested PCR The SuperScriptTM III One-Step RT-PCR System with Platinum® Taq DNA

Polymerase (Invitrogen Life Technologies Cat. No. 12574-018 or 12574-026) has been used for performing RT-PCR.

A RT-PCR mix is prepared as follows: 2X Reaction mix 25 μl primer EOO (10 μM) 1 μl primer E01 (10 μM) 1 μl

SuperscriptTM III RT/Platinum® Taq Mix 2 μl water ad 45 μ I where the primers EOO and E01 have the following sequences: EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1), and E01-: TCC AGT CCC CCC TTT TCT TTT AAA AA (SEQ ID NO:2).

45 μl of this mix are put in each PCR tube, then 5 μl of viral RNA are added, with pipette tips and the pipette reserved for RNA. Viral RNA has been prepared with QIAamp Viral RNA Mini Kit (Qiagen 52904 (x50) or 52906 (x250)) according to the manufacturer's instructions.

EnvR5, EnvX4, CAR5, CAX4 and DUAL are used as reference and control viruses to amplify.

The RT-PCR tubes are placed in the thermocycler Hybaid PCR Express or the icycler Biorad, and amplification is carried out as follows: 1 cycle: 45 ⁰ C 30 min

94 ⁰ C 2 min

40 cycles: 94°C 15 sec 55 ⁰ C 30 sec

68°C 3 min

1 cycle: 68°C 10 min 4°C

For nested PCR, Accuprime™ Pfx SuperMix (Invitrogen Life Technologies

Cat. No. 12344-040) was used.

A mix for the nested PCR is prepared as follows: AccuPrimeTM Pfx SuperMix 22.5 μl Primer E10 (10μM) 0.5 μl Primer FuB (10μM) 0.5 μl where the primers E10 and FuB have the following sequences: E10: TTG TGG GTC ACA GTC TAT TAT GGG GT (SEQ ID NO:3), and FuB: GGT GGT AGC TGA AGA GGC ACA GG (SEQ ID NO:4).

23.5 μl of this mix are placed in PCR tubes. Under a molecular biology hood, 3 μl of the RT-PCR reaction mixture are added in the PCR tubes. The nested PCR is carried out by placing the tubes in the thermocycler Hybaid PCR Express or the icycler Biorad, with the following program: 1 cycle: 95°C 5 min 35 cycles: 95°C 15 sec 55°C 30 sec

68°C 2 min 30 sec 1 cycle: 68°C 10 min 15°C

Example 2: amplification of V1 V3 by RT-PCR and nested PCR

A RT-PCR mix is prepared as follows 2X Reaction mix 25 μl primer EOO (10 μM) 1 μl primer ES8B (10 μM) 1 μl SuperscriptTM III RT/Platinum® Taq Mix 2 μl water ad 45 μl where the primers EOO and ES8B have the following sequences: EOO: TAG AAA GAG CAG AAG ACA GTG GCA ATG A (SEQ ID NO:1), and

ES8B: CAC TTC TCC AATTGT CCC TCA (SEQ ID NO:5).

45 μl of this mix are put in each PCR tube, then 5 μl of viral RNA, with pipette tips and the pipette reserved for RNA.

EnvR5, EnvX4, CAR5, CAX4 and DUAL are used as reference and control viruses to amplify.

The RT-PCR tubes are placed in the thermocycler Hybaid PCR Express or the icycler Biorad, and amplification is carried out as follows: 1 cycle: 45°C 30 min

94°C 2 min 40 cycles: 94 ⁰ C 15 sec

52°C 30 sec 68°C 1 min 45 sec 1 cycle: 68 ⁰ C 10 min 4°C

A mix for the nested PCR is prepared as follows:

AccuPrimeTM Pfx SuperMix 22.5 μl

Primer E20 (10μM) 0.5 μl

Primer E115 (10μM) 0.5 μl where the primer E20 and E115 have the following sequences:

E20: GGG CCA CAC ATG CCT GTG TAC CCA CAG (SEQ ID NO:6), and E115 : AGAAAA ATT CCC CTC CAC AATTAA (SEQ ID NO:7).

23.5 μl of this mix are placed in PCR tubes. Under a molecular biology hood, 3 μl of the RT-PCR reaction mixture are added in the PCR tubes. The nested PCR is carried out by placing the tubes in the thermocycler Hybaid PCR Express or the icycler Biorad, with the following program: 1 cycle: 95°C 5 min 35 cycles: 95°C 15 sec 54°C 30 sec

68°C 1 min

1 cycle: 68°C 10 min 15°C

Example 3: amplification of gp160 by RT-PCR and nested PCR

A RT-PCR mix is prepared as follows 2X Reaction mix 25 μl primer EOO (10 μM) 1 μl primer E01- (10 μM) 1 μl

SuperscriptTM III RT/Platinum® Taq Mix 2 μl water ad 45 μl where the primers EOO (SEQ ID NO:1) and E01- (SEQ ID NO:2) are as defined above.

45 μl of this mix are put in each PCR tube, then 5 μl of viral RNA, with pipette tips and the pipette reserved for RNA.

EnvR5, EnvX4, CAR5, CAX4 and DUAL are used as reference and control viruses to amplify. The RT-PCR tubes are placed in the thermocycler Hybaid PCR Express or the icycler Biorad, and amplification is carried out as follows: 1 cycle: 45 ⁰ C 30 min

94°C 2 min

40 cycles: 94°C 15 sec 55°C 30 sec

68°C 3 min

1 cycle: 68°C 10 min 4 ⁰ C

A mix for the nested PCR is prepared as follows:

AccuPrimeTM Pfx SuperMix 22.5 μl

Primer EST (10μM) 0.5 μl

Primer END (10μM) 0.5 μl where the primer EST and END have the following sequences: EST: GAA GTA TCA GCA CTT GTG (SEQ ID NO:8), and END : CCA AGC CCT GTC TTA TTC (SEQ ID NO:9).

23.5 μl of this mix are placed in PCR tubes. Under a molecular biology hood, 3 μl of the RT-PCR reaction mixture are added in the PCR tubes. The nested PCR is carried out by placing the tubes in the thermocycler Hybaid PCR Express or the icycler Biorad, with the following program: 1 cycle: 95°C 5 min

35 cycles: 95°C 15 sec 52°C 30 sec 68°C 3 min

1 cycle: 68°C 10 min 15°C

Example 4: verification of PCR products

The PCR products are controlled on an agarose gel at 1 %. The expected size of the PCR product is 2533 nt for gp160, 2202 nt for gp120/gp41ec, and 938 nt for V1V3.

The RT-PCR tubes of positive samples are stored in a clean room at 4°C. The RT-PCR tubes for samples giving negative, weak or non-specific products are discarded, unless they represent the best result obtained for the sample.

The nested PCR tubes for positive samples are stored at 4°C, until purification. The nested PCR tubes for samples giving negative, weak or nonspecific products are also kept until the result of the next PCR is available.

Example 5: transfection of producer cells (293T cells)

One T25 flask of 293T cells is prepared for each sample to be tested and for the 2 references and the 3 controls. Cells are added in sufficient number to give a confluence of 70 to 80% on the transfection day. The complete medium for 293T cells is 500 ml DMEM (Dulbecco's Modified Eagles Medium with Glutamax- I), with 50 ml Foetal calf serum (FCS), 2.5 ml P/S (Penicillin (10000 IU/ml) and Streptomycin (10000 μg/ml)). The flasks are incubated at 37°C, 5% CO2. On the day of transfection, the condition of cells in the T25 flasks is verified and the medium changed at least 3 to 4 hours before transfection (4 ml/ T25).

The plasmid used for transfection is either RVA-δenv, pNL4-3 deleted of the gp120-gp41ec region of the envelope gene (nt 6480-8263) and replaced by a

linker containing the Mlu\ restriction site for linearization of the plasmid, or RVA- δV, pNL4-3δ deleted of the V1-V3 region of the envelope gene (nt 6612-7249), wherein the natural and unique Nhe\ restriction site downstream of the deletion is used for linearization of the plasmid.

A RVA-δgp160 plasmid is also used for transfecting the gp160 cassette. RVA-δgp160 is pNL4-3 deleted of the gp160 region of the envelope gene (nt 6345-8690) and replaced by a linker containing the Nhe\ restriction site for linearization of the plasmid.

In a labelled sterile microtube, a transfection mix is prepared for each sample using the volumes given in the table below:

Then 15 μl of the appropriate PCR product (approximately 0.8 μg of DNA) are added.

For each sample, 500 μl of HBS 2X (280 mM NaCI, 10 mM KCI, 1 ,5 mM Na ₂ HPO4, 50 mM Hepes) are placed into a second labelled sterile microtube.

The mixture of the transfection mix and PCR product is added, drop by drop, into the tube containing the HBS 2X, while lightly vortexing. This transfection precipitate is added to the flasks of 293T cells. The presence of a precipitate on the cells is verified and the flasks are incubated 16-18 hours at 37°C, 5% CO2.

All the medium is aspirated using a pipette and the cells are washed once with sterile PBS 1X. 4 ml of fresh medium per sample are added and the flasks are incubated 24 hours at 37°C, 5% CO2.

Example 6: infection of indicator cells The condition, confluence and mortality of the transfected 293T cells are verified. The entire medium is removed from each flask and transferred into a 15 ml conical tube to be clarified. The tubes are centrifuged at 1800 rpm for 10 to 15 minutes. The supematants are kept at +4°C until the test is completed.

The indicator cells U373-CCR5 and U373-CXCR4 have been prepared by passing in T75 flasks (1 T75 flask for 8 plates to be prepared on the transfection day) and incubating the flasks at 37°C, 5% CO2. The complete medium for U373-

CCR5 and U373-CXCR4 cells is 500 ml DMEM with 50 ml FCS, 2.5 ml P/S, 0.5 ml puromycine (10 mg/ml), 1 ml hygromycine (50 mg/ml).

On the day of infection, the condition of the indicator U373-CCR5 and U373-CXCR4 cells is verified. CXCR4- and CCR5-inhibitors are prepared at 4x their final concentrations used in the test (e.g. 4x AMD-3100 at 8 μg/ml, 4x RANTES at 500 ng/ml). The medium of plates of U373-CCR5 and U373-CXCR4 cells is aspirated and 50 μl of medium containing DEAE dextran (4X, for a final concentration of 2 μg/ml per well/ 200 μl) are distributed simultaneously to avoid drying of the cells, and 50 μl of medium or of the co-receptor inhibitor on half of the plate.

50 and 100 μl of virus are transferred and medium is added up to 200 μl in each well of the U373-CCR5 and U373-CXCR4 plates. Each plate includes one

R5-tropic control/reference virus (EnvR5 or CAR5), as well as one X4-tropic control/reference virus (EnvX4 or CAX4) which will allow the analysis of data : The presence of all references (EnvR5, EnvX4, CAR5, CAX4 and DUAL) on at least one plate per cell-line and per batch allows the general validation of the experiment. The reference serves thus as positive control for the validation of the test (e.g., EnvR5 on U373-CCR5 or EnvX4 on U373-CXCR4). The controls

(EnvR5 on U373-CXCR4 or EnvX4 on U373-CCR5) serve for the calculation of the ratio [OD sample/OD control].

Infection is carried out using two different doses of viral input (50 and 100 μl) in triplicates, with replica plates in presence of co-receptor inhibitors (RANTES (Sigma Aldrich R6267) or AMD-3100 (Sigma Aldrich A5602)).

The plates are incubated for 40 h at 37°C, 5% CO2.

Example 7: CPRG test The β-galactosidase produced by the infected U373-CCR5 or U373-CXCR4 cells is quantified: the level of marker expressed is quantified by measuring the β-galactosidase activity by using a CPRG (chlorophenolred-β-D- galactopyranoside) substrate. Briefly, when cleaved by β-galactosidase, CPRG

yields chlorophenolred, which is a water-soluble red product measurable by spectrophotometry. Briefly, cells are lysed and the substrate (CPRG diluted in lysis buffer) is added before OD measurement.

A sample is considered positive, when the ratio [OD sample/OD control] reaches or exceeds 1.5, and when specific inhibition is observed in presence of the corresponding co-receptor inhibitor at saturating dose (e.g. RANTES, AMD- 3100).

Example 8: RVA tropism assay with the cassette Env (gp120-gp41ec) The RVA tropism test has been realized on PCR products obtained from mixtures of proviral plasmids of different tropism (characterized reference viruses NL4-3/JR-CSF and mixtures of plasmids carrying cloned envelopes from patients' plasma samples: CAX4/EnvR5 or CAX4/DAR5 at different percentages (0%, 2.5%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 100% of X4 tropic virus). The PCR products of independent PCR reactions have been tested in independent tropism tests.

Results representative of 3 independent recombinant virus assays, realized with PCR products obtained in independent PCR reactions, are shown on Figures 5 and 6. The gp120-gp41ec fragment was amplified on mixtures of plasmids NL43 and JR-CSF for reference, and CAX4/EnvR5 mixtures for primary viruses.

When mixing viral envelopes from reference viruses NL4-3 and JR-CSF, 5% of X4 tropic virus were detectable, and the infection was inhibited (100% of inhibition) using AMD3100 (Figure 5). This inhibition proves the specificity of the CPRG signal and hence of the infection via CXCR4. In a mixture of primary viruses of comparable infectivity (i.e. production of infectious viral particles induces comparable CPRG signals on U373-CCR5 and U373-CXCR4 cells), X4 tropic viruses are specifically detectable at a percentage of 5% (3 experiments) (Figure 6).

Detection of X4 tropic viruses was also assayed in a mixture of primary viruses (CAX4 and DAR5) which relative infectivity is unknown. X4 tropic viruses are specifically detectable at a percentage of 2.5% (Figure 7).

In a mixture of primary viruses of comparable infectivity, R5 tropic viruses are specifically detectable at a percentage of 1-2.5% (1 experiment), and the

infection was inhibited using RANTES (Figure 8). This inhibition proves the specificity of the CPRG signal and hence of the infection via CCR5.

Example 9: RVA tropism assay with the cassette V1V3 The inventors presumed that sensitivity of the test for non-B subtypes might increase when using a smaller fragment of the envelope, the V1V3 or tropism- determinant region: due to amplification of the smaller fragment, not only PCR, but also recombination, viral production and hence infection of indicator cells might be more sensitive. PCR products spanning the V1V3 region (~900 nt) were obtained on plasmid mixtures of reference and primary envelopes.

Using this V1V3 cassette, detection of primary X4 tropic virus in a mixture of viruses with comparable infectivity was 2.5% (Figure 9).

Detection of X4 tropic viruses was also assayed in a mixture of primary viruses (CAX4 and DAR5) which relative infectivity is unknown. X4 tropic viruses are specifically detectable at a percentage of 2.5% (Figure 10).

Example 10: RVA tropism assay with the cassette gp160

PCR products spanning the full length env gene (2533 nt) were obtained on plasmid mixtures of primary envelopes (CAX4/ENVR5). Using this gp160 region, in a mixture of primary viruses of comparable infectivity (CAX4/EnvR5), X4 tropic viruses are specifically detectable at a percentage of 20% (one experiment, Figure 11), whereas R5 tropic viruses are detectable at a percentage of 10% (one experiment, Figure 12).

Example 11 : PCR and RVA success rate for group M non-B samples

The test of the invention allows the amplification of subtype B as well as non-B samples, with high specificity and sensitivity.

The PCR success rate for most prevalent European non-B subtypes with the 2 different cassettes was comparable, ranging from 57 to 100% for gp120- gp41ec, and from 67 to 96% for the V1V3 cassette.

The overall RVA success rate for tropism determination using one or the other cassette ranged from 42 to 98%, depending on the subtype.

Table - 4: PCR success rate

Subtype Prevalence Tested in PCR PCR Tested in PCR in Europe gp120-gp41ec success PCR success rate V1V3 rate

C 37.5% 55 95% 95 75%

G 15.5% 38 87% 32 81%

CRF02 AG 12.5% 30 87% 45 96%

A 11.0% 21 57% 24 67%

CRF01 AE 9.0% 19 89% 32 88%

D 3.5% 12 83% 14 71%

F 3.5% 8 63% 20 70%

J 2.5% 4 100% 6 83%

The use of the V1V3 region of the envelope slightly increased the PCR success rate for subtypes CRF02_AG, A and F, whereas it did not increase the PCR success rate for other subtypes. The use of the V1V3 cassette is thus a valuable alternative for samples that tested negative using the gp120-gp41 extracellular region.

Thus, a strategy for samples of unknown subtype is to amplify in a first step the gp160 or gp120-gp41ec region which would allow not only to determine viral tropism, but also the sensitivity of a viral plasma population to entry inhibitors. In case of a negative PCR result or a negative RVA using the gp160 or gp120-gp41 extracellular region, the V1V3 region can be amplified to determine viral tropism, only.

Table 5 summarizes the RVA success rate in non-B subtypes using one or the other amplification region (gp120-gp41ec or V1V3). As for PCR, the RVA success rate is subtype-dependent: for the most prevalent subtype (subtype C), the success rate was 98%, again comparable to subtype B, whereas for the other subtypes the success rate ranged from 42% to 87% and was subtype dependent.

Table 5: RVA tropism assay rate of success

In order to confirm the viral tropism with the two different envelope regions, each sample was tested twice, once for the gp120-gp41ec and once for the V1V3 region. For samples which were negative for the amplification of one region (V1V3 or gp120/gp41ec), viral tropism was determined in two independent experiments for the available PCR product.

The assay allowed determining R5, R5/X4 mixed tropic and X4 tropic viruses for these subtypes (Table 5). For subtype C samples, the predominance of R5 tropic viruses corresponds to the percentage previously described (Cilliers et al, 2003; Johnston et al, 2003; Monteiro et al, 2007). For the other subtypes, due to the low number of recombinant viruses analyzed, the indicated proportions of viruses using CXCR4 may not be representative. Nevertheless, the higher percentage of X4 tropic viruses as observed for subtype D is in accordance with previous observations (Huang et al, 2007 and 2nd Workshop Targeting HIV entry, Boston, 2006).