Human immunodeficiency virus type 1 (HIV-1) enters CD4-expressing cells using one or both of the chemokine receptors cysteine-cysteine receptor 5 (CCR5) and cysteine-X-cysteine receptor 4 (CXCR4). CCR5-using viruses are classified as R5 variants, CXCR4-using viruses are classified as X4 variants, and viruses using both coreceptors are classified as R5X4 dualtropic variants . A virus population may use both coreceptors because it contains R5X4 dualtropic clones and/or a mixture of pure R5 and X4 virus clones (dual/mixed R5X4 phenotype). R5 viruses usually predominate early in a HIV-1 infection, whereas R5X4 or X4 viruses emerge in half the patients at late stages [2,3]. The X4 variants present late in the infection are associated with the accelerated decline of CD4+ T lymphocytes and progression to AIDS [2,4,5]. HIV-1 tropism in recent seroconverters seems to be restricted to R5 variants whatever the transmission route and the tropism of the variants in the source . The mechanisms underlying the selective advantage of CCR5-tropic viruses in establishing an HIV-1 infection are poorly understood. It may be that target cells and tissues important for establishing the initial infection preferentially express CCR5 and/or there is an immune response preferentially directed against CXCR4-using viruses. The classic view that CCR5-tropic viruses massively predominate during primary HIV-1 infection has been challenged by recent finding that X4/R5X4 viruses are not necessarily rare during HIV-1 primary infection. Frequencies of 3–17.2% have been reported depending on the assay used to measure HIV-1 tropism [7–10].
HIV-1 coreceptor usage can be assessed by phenotypic assays, mainly using recombinant virus assays, or by culturing the HIV-1 isolate on MT-2 cells [11–13]. Genotypic assays that analyze the V3 region of env have also been developed for predicting HIV-1 tropism [14–16]. Phenotypic methods indicated that the plasma of patients with recent seroconversion contained about 3% of CXCR4-using viruses [9,10]. By contrast, genotypic methods found 13.4–17.2% of CXCR4-using viruses in the plasma of primary infected patients [7,17]. Another recent study using genotypic methods found 15.9% of CXCR4-using viruses in the peripheral blood mononuclear cells (PBMCs) of recently infected patients . Cases of rapid disease progression after the transmission of CXCR4-using variants have been reported [5,19,20]. But the impact of the tropism of transmitted virus on the subsequent clinical evolution has rarely been studied in cohorts . Moreover, characterization of HIV-1 tropism in primary infection is now of therapeutic interest because CCR5 antagonists have been developed.
The aim of this study was to determine the HIV-1 coreceptor usage in the plasma and PBMCs of patients with a primary HIV-1 infection using both phenotypic and genotypic approaches. We also monitored the biological and clinical outcomes of these patients to evaluate the impact of HIV-1 tropism on disease progression.
Study population and samples
We studied 133 consecutive patients with a primary HIV-1 infection treated at Toulouse University Hospital, France, between 1995 and 2008. They all gave their informed consent for virological studies. Plasma samples were collected from each patient and stored at −80°C. Samples of peripheral whole blood were also collected after 2000, and the Ficoll-separated PBMCs were stored at −80°C. Recent HIV-1 seroconversion was defined as patients with a negative anti-HIV-1 antibody test and positive plasma HIV-1 RNA; a positive HIV-1 antibody test and a negative or indeterminate immunoblot, confirmed positive later; HIV-1 seropositivity that was seronegative when tested within the previous 6 months. Plasma HIV-1 RNA was measured by Amplicor HIV-1 Monitor until June 2004 and by COBAS Ampliprep/COBAS Taqman HIV test (Roche) thereafter. Genotypic resistance analyses were performed by the consensus method of the AC11 ANRS Resistance Group (http://www.hivfrenchresistance.org). CD4+ T cells were counted by flow cytometry.
We studied the impact of R5X4/X4 virus transmission on subsequent disease progression. Patients who were given antiretroviral treatment during the first 6 months following primary infection were excluded from this analysis. Each patient infected with an R5X4/X4 virus was matched with five control patients infected with an R5 virus for age (± 5 years) and HIV-1 RNA load at the time of primary infection (± 0.5 log copies/ml) because these two factors are associated with disease progression. Patients' follow-up was censored when antiretroviral therapy was started.
Phenotypic characterization of HIV-1 coreceptor usage
Phenotypic characterization of HIV-1 tropism was performed using the Toulouse Tropism Test assay . Briefly, a fragment encompassing the gp120 and the ectodomain of gp41 was amplified by RT-PCR using HIV-1 RNA isolated from the plasma or by PCR from HIV-1 DNA taken from PBMCs. The PCR products then underwent nested PCR. Two amplifications were performed in parallel from each sample and pooled to prevent sampling bias of the assessed virus population.
The phenotype of HIV-1 coreceptor usage was determined using a recombinant virus entry assay with the pNL43-Δenv-Luc2 vector. 293T cells were cotransfected with NheI-linearized pNL43-Δenv-Luc2 vector DNA and the product of the nested PCR obtained from the challenged HIV-1-containing sample. The chimeric recombinant virus particles released into the supernatant were used to infect U87 indicator cells bearing CD4 and either CCR5 or CXCR4. Virus entry was assessed by measuring the luciferase activity in lyzed cells [as relative light units (RLUs)]. Minor X4 variants were detectable when present at 0.5% or higher. The reproducibility of the assay was assessed by 35 repeated experiments with the reference strains HXB2 and BaL; the coefficient of variation was 3.4–6.2% in both U87 indicator cell lines.
Genotypic prediction of HIV-1 coreceptor usage
The V3 region was directly sequenced from bulk env PCR products in both directions by the dideoxy chain termination method (BigDye Terminator v.3.1, Applied Biosystems) on an ABI 3130 DNA sequencer. Results were analyzed with Sequencher (Genecodes), blinded to the phenotype. Minor species were detected when the automated sequencer electrophoregram showed a second base peak. Multiple alignments were performed with CLUSTALW 1.83 (Conway Institute UCD Dublin), and sequence alignments were manually edited using BioEdit software. Phylogenetic analyses of the PCR product sequences excluded any possibility of sample contamination (see supplementary figure, http://links.lww.com/QAD/A72).
We used a combination of criteria from the 11/25 and net charge rules to predict HIV-1 tropism from the V3 genotype . One of the following criteria is required for predicting CXCR4 coreceptor usage: 11R/K and/or 25K; 25R and a net charge of at least +5; a net charge of at least +6. The V3 net charge was calculated by subtracting the number of negatively charged amino acids (D and E) from the number of positively charged ones (K and R). All possible permutations were assessed when amino acid mixtures were found at some codons of V3. The combination resulting in the highest net charge was used to predict the tropism. We also compared the performances of these combined criteria for detecting CXCR4-using viruses with that of the bioinformatic tool Geno2pheno with false-positive rates of 10 and 5.75% . Geno2pheno is available at http://coreceptor.bioinf.mpi-sb.mpg.de/cgi-bin/coreceptor.pl (January 2010).
We used STATA 8.0 (Stata Corporation, Grand Forks, North Dakota, USA) software for statistical analysis. Continuous variables were tested with the Mann–Whitney test. Categorical variables were tested by the chi-squared test or the Fisher's test. A statistically significant difference was defined as a P value of less than 0.05. Kaplan–Meier curves were used to provide a graphic representation of the time to disease progression according to virus tropism. Events were defined as a CD4+ T-cell count dropping below 350 cells/μl, or the initiation of antiretroviral therapy. The log rank test was used to compare groups.
Nucleotide sequence accession numbers
The sequences reported here were given Genbank accession numbers HM239515 to HM239639 for plasma RNA sequences and HM246186 to 246241 for cellular DNA sequences.
We identified and prospectively monitored 133 patients who were at the stage of primary infection during the 13-year study. The median follow-up time was 31 months [interquartile range (IQR) 12–68]. The clinical, virological, and immunological characteristics of the patients are shown in Table 1. Their median age was 35 years and 83.5% were men. Most (85%) were infected with HIV-1 subtype B, but 15% had non-B subtypes (CRF01, CRF02, A, C, D, F1 and G). The median HIV-1 virus load was 5.5 log copies/ml; (IQR 4.5–6.5). The median CD4 cell count was 479 cells/μl (IQR 325–653) and the percentage of CD4 cells was 24% (IQR 16–32). Ten per cent of the patients harbored HIV-1 viruses resistant to at least one class among the nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors or protease inhibitors of HIV-1.
Entry phenotype of HIV-1 at the time of primary infection
Phenotypic characterization of coreceptor usage from plasma HIV-1 RNA
The env gene was successfully amplified from plasma of 126 of the 133 patients. The phenotype was then determined for 125 of these 126 patients (94% of samples) and recombination failed for one sample. Amplification failed for three non-B subtype viruses and four subtype B viruses, probably because of mismatches in the priming site due to HIV-1 polymorphisms. We found 117 virus populations with an R5 phenotype and eight with a dual/mixed R5X4 phenotype. No virus had a pure X4 phenotype. There was thus 6.4% of CXCR4-using HIV-1 at the time of primary infection. We performed a phylogenetic analysis to exclude the possibility that the R5X4 variants belonged to a single transmission cluster; only two patients had related R5X4 viruses. The patients harboring subtype B viruses (7/109 subtype B, 6.4%) and those harboring non-B viruses (1/16 non-B subtypes, 6.2%) had similar percentages of CXCR4-using HIV-1. The only CRF01 strain was R5X4 and there was no R5X4 viruses among nine CRF02, one subtype A, one subtype C, one subtype D, one subtype F, one subtype G and one undetermined subtype. Five patients harbored dual/mixed R5X4 virus populations able to use both coreceptors with similar entry efficiencies (Table 2). In contrast, two patients (patients 95 and 106) harbored a dual/mixed R5X4 virus population that infected CXCR4+ cells less efficiently than CCR5+ cells; whereas one patient (patient 23) harbored a dual/mixed R5X4 virus population that infected CXCR4+ cells more efficiently than CCR5+ cells.
Phenotypic characterization of coreceptor usage from cellular HIV-1 DNA
Peripheral blood mononuclear cells were available for 74 patients, recruited after 2000, and gp140 was successfully amplified for 56 of them. The failure rate of amplification may be explained by mismatches in the priming site due to HIV-1 polymorphism and by the virus DNA load in cell samples being lower than the virus RNA load in the plasma. The phenotype was determined for 54 of the 56 amplified samples with 51 virus populations using exclusively CCR5, two dual/mixed R5X4 virus populations (patients 93 and 111) and one virus population using exclusively CXCR4 (patient 23). Thus the prevalence of CXCR4-using HIV-1 in PBMCs was 5.6%.
The 51 R5 and the two dual/mixed R5X4 virus populations identified in the PBMCs were concordant with the results for the plasma. Patient 23 harbored a virus population phenotyped as purely X4 in his PBMCs but dual/mixed R5X4 in his plasma. HIV-1 tropism in the plasma and PBMCs from patients at the stage of primary infection was thus 98% concordant.
Genotypic prediction of HIV-1 tropism during primary infection
Genotypic prediction of tropism from plasma HIV-1 RNA
We obtained the V3 genotype of plasma HIV-1 by direct sequencing from bulk env PCR products from 125 of the 126 patients for whom the env gene had successfully been amplified. The combined criteria from the 11/25 and net charge rules predicted 117 CCR5 and eight CXCR4-using virus populations (predicted prevalence of CXCR4-using viruses in plasma of 6.4%), whereas Geno2pheno10 predicted 110 CCR5 and 15 CXCR4-using virus populations (predicted prevalence of CXCR4-using viruses in plasma of 12%). The capacity of the genotype to predict the observed phenotype was determined for 124 plasma samples that had been characterized by both assays (Table 3). The combined criteria from the 11/25 and net charge rules accurately predicted the entry phenotype of 113/116 CCR5-using viruses and 5/8 CXCR4-using viruses (concordance with observed phenotype 95.2%). Geno2pheno10 accurately predicted 107 CCR5-using viruses and six CXCR4-using viruses (concordance 91.1%). Geno2pheno with an optimized cut-off at 5.75% accurately predicted 114/116 CCR5-using viruses and 5/8 CXCR4-using viruses (concordance 96%).
Genotypic prediction of tropism from cellular HIV-1 DNA
The V3 genotype was also characterized for the 56 patients whose HIV-1 DNA had been amplified successfully. The combined rule classified 53 CCR5 and three CXCR4-using virus populations (predicted prevalence of CXCR4-using viruses in PBMCs of 5.4%), whereas Geno2pheno10 predicted 51 CCR5 and five CXCR4-using viruses (predicted prevalence of CXCR4-using viruses in PBMCs of 8.9%). The observed phenotype for 54 samples and the genotype determined with the combined rule or with Geno2pheno5.75 were in complete agreement (100%), whereas the genotype determined with Geno2pheno10 was almost as good (96.3%) (Table 3).
The V3 genotype predicted from HIV-1 DNA in the PBMCs correlated well with the tropism predicted from HIV-1 RNA in the plasma. Fifty-five viruses were concordant in the plasma and PBMCs using the combined rule or Geno2pheno to predict HIV-1 tropism. There was only one discordance between a plasma sequence predicted as CXCR4-using and the sequence of virus DNA predicted as CCR5-using. This difference is explained by a double population S/R at position 11 of V3 on the plasma virus, thus predicting a CXCR4-using virus, whereas there was only an S residue on the viral DNA at this position.
Relationships between HIV-1 tropism and characteristics of the patients at the time of primary infection
The characteristics of patients according to their plasma HIV-1 tropism are shown in Table 4. R5X4-infected patients were younger (median age 29 years), with fewer men (50%), than the R5-infected patients (37 years) and mostly men (88%). The HIV-1 transmission route was similar in both groups. But more of the R5X4 group were intravenous drug users (IDUs) (2/8 patients) than the R5 group (2 of 97 patients with known risk factors) (P = 0.028) (Table 4). In agreement with the higher frequency of IDUs among the patients harboring R5X4 viruses, more of these patients were infected with hepatitis C virus (HCV) than in the R5 group. The HIV-1 viral load, CD4+ T-cell count and the frequency of drug-resistant viruses at the time of the primary infection were similar in the two groups. We also analyzed a subgroup of patients diagnosed at an early stage of infection, when the HIV-1 antibody test was negative or the immunoblot was indeterminate. The four R5X4-infected patients and the 65 R5-infected patients had similar HIV-1 virus loads and CD4+ T-cell counts. The prevalence of CXCR4-using viruses during primary infection did not vary throughout the study period.
Impact of HIV-1 tropism during primary infection on the course of the subsequent infection
We studied the patients who were not given any antiretroviral treatment at the stage of primary infection to compare the natural evolution of the CD4+ T-cell count and the delay before the first antiretroviral treatment in the patients infected with R5 and R5X4 viruses. Five R5X4-infected patients were analyzed and each of them was matched with five R5-infected control patients for age and baseline HIV-1 RNA load. We assessed HIV-1 coreceptor usage one year after the first characterization in four patients initially infected with dual/mixed R5X4 viruses. All four patients were persistently infected with R5X4 viruses (data not shown). Age and HIV-1 RNA load were similar in both groups, with medians of 30 years (IQR 22–39) in the R5X4 group and of 31 years (IQR 25–36) in the R5 group (P = 0.8), and medians of 5.0 log copies/ml (IQR 4.0–6.1) in the R5X4 group and of 4.9 log copies/ml (IQR 4.3–5.5) in the R5 group (P = 0.9). The CD4 cell counts at baseline were also similar, with medians of 477 cells/μl (IQR 386–850) in the R5X4 group and of 599 cells/μl (IQR 432–725) in the R5 group (P = 0.88). Kaplan–Meier estimate of the proportion of patients who progressed to CD4+ T-cell count under 350 cells/μl, stratified according to HIV-1 tropism, revealed that infection with R5X4 viruses was associated with an accelerated rate of disease progression (log rank test P < 0.001) (Fig. 1a). Infection with R5X4 viruses was also associated with a reduced delay in initiating a first antiretroviral treatment (log rank test P = 0.01) (Fig. 1b).
The determination of HIV-1 coreceptor usage is now of therapeutic interest as CCR5 antagonists have recently been developed. Conflicting results have recently been reported regarding the frequency of CXCR4-using viruses during HIV-1 primary infection. Previous studies have suggested that CCR5-using viruses overwhelmingly predominate during primary HIV-1 infection [2,3]. But recent studies using genotypic methods have found a prevalence of about 15% CXCR4-using viruses at this stage [7,17,18], particularly in PBMCs. We therefore investigated HIV-1 tropism during primary infection using an ultrasensitive phenotypic assay to examine the virus in both the plasma and PBMCs.
Phenotypic characterization of HIV-1 in the plasma indicated that dual-mixed R5X4 virus populations accounted for 6.4% of the total in patients with recent seroconversion, with the prevalence being similar in subtype B and non-B HIV-1 subtypes. These results are close to the 3% of CXCR4-using viruses in the plasma of recent seroconverters previously estimated with phenotypic methods [9,10]. More of the patients infected with dual-mixed R5X4 viruses were intravenous drug users than were those infected with R5 viruses. Phylogenetic analysis excluded a cluster of transmission with a unique strain of R5X4 viruses among the intravenous drug users. The increased frequency of R5X4 virus among the patients infected via the parenteral route could be linked to the CXCR4+ CD4+ T cells being more abundant than CCR5+ CD4+ T cells in the blood . By contrast, CCR5-expressing target cells are abundant in genital and rectal mucosae. Nevertheless, counterselection of CXCR4-using viruses following their transmission via the parenteral route had been reported [24,25], suggesting that the global advantage of R5 viruses in establishing primary HIV-1 infection is not only related to the mucosal transmission step. The transmitted R5X4 viruses were not counterselected in our study and remained predominant after the acute phase of the infection in all four patients whose longitudinal samples were analyzed. Others have reported similar findings [7,26] but larger studies are required to explore viral tropism in this transmission group. In addition, the patients infected with R5X4 viruses were younger and more often female than those harboring R5 viruses. This was not related to any specific characteristics of the intravenous drug user population, as women and young people were not over-represented in this particular group. We have determined HIV-1 tropism using phenotypic methods in both plasma and PBMC samples taken from recently infected patients. HIV-1 tropism in the two compartments was 98% concordant. A recent study suggested that CXCR4-using viruses were more frequent in PBMCs than in the plasma of patients with advanced disease . However, the virus population during the first few months of HIV-1 infection is more homogenous than later in the disease evolution. This may explain why the HIV-1 tropism in the cellular and plasma compartments are similar at this stage. Thus, data for the plasma compartment during primary infection do not underestimate the prevalence of CXCR4-using viruses.
Several studies have shown that genotypic methods can be used to accurately determine HIV-1 tropism in chronically infected patients [14,16,17,28]. But little is known about how they perform during primary infection. We sequenced the V3 region of env from plasma HIV-1 RNA and used the combination of the 11/25 and net charge rules to predict coreceptor usage . The concordance between the observed phenotype and the combined rule was better than 95% using both plasma and PBMC samples. The Geno2pheno10 bioinformatic algorithm also performed well with a concordance better than 91% using samples from both compartments.
Genotypic methods predicted the prevalence of CXCR4-using viruses in the plasma to be 6.4% with the combined rule, and 12% with Geno2pheno10. The unexpected high prevalence of CXCR4-using viruses during primary infection found by others [7,17,18] may be due to the use of genotypic algorithms that overestimated the number of CXCR4-using viruses. We found that the Geno2pheno10 positive predictive value was only 40% for plasma samples (six samples well predicted X4 divided by a total of 15 samples predicted X4 by Geno2pheno10). Specificity was also significantly reduced by combining several genotypic algorithms in order to increase the sensitivity of detecting CXCR4-using viruses [7,8,18], and prevalence of CXCR4-using viruses was thus overestimated. Geno2pheno algorithm is now available with an optimized cut-off at 5.75% (false-positive rate). Using this new algorithm estimated better the prevalence of CXCR4-using viruses in this set of samples (5.6%).
CXCR4-using viruses are considered to be more pathogenic than R5 viruses, including at the time of primary infection in a few studies [7,19]. Previous studies have not agreed on the correlation between the CD4+ T-cell count and HIV-1 tropism at the stage of primary infection [8,18]. HIV-1 coreceptor usage could influence the clinical evolution of these patients, as observed in other groups of patients [29,30]. We find that the CD4+ T-cell counts in patients infected with R5 viruses and in those infected with R5X4 viruses are similar at the time of primary infection. We compared the clinical evolution of patients infected with CCR5 or CXCR4-using viruses in a case-control study. The patients infected with CXCR4-using viruses at the time of primary infection had an increased risk of disease progression, estimated by a CD4+ T lymphocyte count under 350 cells/μl or by initiation of a first antiretroviral treatment.
In conclusion, the prevalence of CXCR4-using viruses at the time of primary infection was only of 6.4% in the plasma using an ultrasensitive phenotypic method. HIV-1 tropism in paired plasma and PBMC samples was essentially the same (concordance 98%) at the time of primary infection. The capacity of genotypic algorithms to predict CXCR4 usage by viruses identified during HIV-1 primary infection was similar to that previously described for viruses identified at a later stage of the disease. However, the use of low-specificity genotypic algorithms, or their combination to increase their sensitivity can lead to overestimation of the prevalence of CXCR4-using viruses. Finally, larger studies are required to confirm the negative impact of the transmitted CXCR4-using viruses on the subsequent evolution of HIV-1 disease.
Author contributions: S.R., P.D., and J.I. designed the study, analyzed the data, and wrote the manuscript. M.C., S.E., C.S. and P.B. performed the experiments. M.M., B.M. and P.M. contributed substantially to study conception and provided clinical samples. K.S.-S. performed statistical analysis.
The English text was checked by Owen Parkes.
Financial support: INSERM U563
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