Characterization of the polyproline region of the hepatitis E virus in immunocompromised patients.

Little is known about virus adaptation in immunocompromised patients with chronic genotype 3 hepatitis E virus (HEV3) infections. Virus-host recombinant strains have been isolated recently from chronically infected patients. The nature and incidence of such recombinant events occurring during infections of solid-organ transplant (SOT) recipients are essentially unknown. The polyproline region (PPR) of strains isolated from SOT patients was sequenced during the acute-infection phase (n = 59) and during follow-up of patients whose infections became chronic (n = 27). These 27 HEV strains included 3 (11%) that showed recombinant events 12, 34, 48, or 88 months after infection. In one strain, parts of the PPR and the RNA-dependent RNA polymerase were concomitantly inserted. In the second, a fragment of a human tyrosine aminotransferase (TAT) gene was inserted first, followed by a fragment of PPR. A fragment of the human inter-α-trypsin inhibitor (ITI) gene was inserted in the third. All the inserted sequences were rich in aliphatic and basic amino acids. In vitro growth experiments suggest that the ITI insertion promoted more vigorous virus growth. In silico studies showed that the inserted sequences could provide potential acetylation, ubiquitination, and phosphorylation sites. We found that recombinant events had occurred in the HEV PPR in approximately 11% of the strains isolated from chronically infected transplant patients followed up in Toulouse University Hospital. These inserted fragments came from the HEV genome or a human gene and could enhance virus replication. Importance: Hepatitis E virus (HEV) can cause chronic infections in immunocompromised patients, including solid-organ transplant (SOT) recipients. Two strains that had undergone recombination with human ribosomal genes were described recently. The strains with inserted sequences replicated better in vitro. Little is known about the frequency of such recombinant events or how such an insertion enhances replication. We therefore investigated 59 SOT patients infected with HEV and found 3 strains with 4 recombinant events in 27 of these patients whose infection became chronic. The 4 inserted sequences were of different origins (human gene or HEV genome), but all were enriched in aliphatic and basic amino acids and provided potential regulation sites. Our data indicate that recombinant events occur in approximately 11% of strains isolated from chronically infected patients. The structures of the inserted sequences provide new clues as to how the inserted sequences could foster virus replication.

Genotypic prediction of HIV-1 CRF01-AE tropism.

HIV-1 subtype CRF01-AE predominates in south Asia and has spread throughout the world. The virus tropism must be determined before using CCR5 antagonists. Genotypic methods could be used, but the prediction algorithms may be inaccurate for non-B subtypes like CRF01-AE and the correlation with the phenotypic approach has not been assessed. We analyzed 61 CRF01-AE V3 clonal sequences of known phenotype from the GenBank database. The sensitivity of the Geno2pheno10 genotypic algorithm was 91%, but its specificity was poor (54%). In contrast, the combined 11/25 and net charge rule was highly specific (98%) but rather insensitive (64%). We thus identified subtype CRF01-AE determinants in the V3 region that are associated with CXCR4 use and developed a new simple rule for optimizing the genotypic prediction of CRF01-AE tropism. The concordance between the predicted CRF01-AE genotype and the phenotype was 95% for the clonal data set. We then validated this algorithm by analyzing the data from 44 patients infected with subtype CRF01-AE, whose tropism was determined using a recombinant phenotypic entry assay and V3-loop bulk sequencing. The CRF01-AE genotypic tool was 70% sensitive and 96% specific for predicting CXCR4 use, and the concordance between genotype and phenotype was 84%, approaching the concordance obtained for predicting the tropism of HIV-1 subtype B. Genotypic predictions that use a subtype CRF01-AE-specific algorithm appear to be preferable for characterizing coreceptor usage both in pathophysiological studies and for ensuring the appropriate use of CCR5 antagonists.

Hepatitis E virus quasispecies and the outcome of acute hepatitis E in solid-organ transplant patients.

Hepatitis E virus (HEV) infections are responsible for chronic hepatitis in immunocompromised patients, and this can evolve to cirrhosis. Like all RNA viruses, HEV exists as a mixture of heterogeneous viruses defining quasispecies. The relationship between the genetic heterogeneity described as a quasispecies, cytokine secretion, and the outcome of acute hepatitis in immunocompromised patients remains to be elucidated. We cloned and sequenced the region encoding the M and P capsid domains of HEV from eight solid-organ transplant (SOT) patients with acute HEV infection who subsequently cleared the virus and from eight SOT patients whose infection became chronic. We analyzed the cytokines and chemokines in the sera of these SOT patients by multianalyte profiling. The nucleotide sequence entropy and genetic distances were greater in patients whose infections became chronic. A lower K(a)/K(s) ratio was associated with the persistence of HEV. The patients who developed chronic infection had lower serum concentrations of interleukin-1 (IL-1) receptor antagonist and soluble IL-2 receptor. Increased concentrations of the chemokines implicated in leukocyte recruitment to the liver were associated with persistent infection. Those patients with chronic HEV infection and progressing liver fibrosis had less quasispecies diversification during the first year than patients without liver fibrosis progression. Great quasispecies heterogeneity, a weak inflammatory response, and high serum concentrations of the chemokines involved in leukocyte recruitment to the liver in the acute phase were associated with persistent HEV infection. Slow quasispecies diversification during the first year was associated with rapidly developing liver fibrosis.

Genotype 3 diversity and quantification of hepatitis E virus RNA.

Genotype 3 hepatitis E viruses (HEVs) are distributed across the world and are now considered to be an emerging public health concern in industrialized countries. At least 10 genotype 3 subtypes have been identified in humans and animals worldwide. It was recently reported that the sensitivities of HEV RNA assays differ greatly. We have assessed the influence of genotype 3 diversity on the performances of two HEV RNA assays: one targeting the ORF3 gene and the other targeting the ORF2 gene. We tested a panel of 5 HEV-positive reference samples of genotypes 3a, 3b, 3c, 3e, and 3f at 10-fold serial dilutions. The HEV RNA concentrations obtained with both reverse transcription (RT)-PCRs were correlated, but the RT-PCR based on ORF2 underestimated the HEV RNA concentrations. The mean [ORF3 - ORF2] difference was 1.41 log copies/ml. We also tested 34 clinical specimens of genotypes 3c (n = 15), 3e (n = 4), and 3f (n = 15), representing the most prevalent subtypes in Europe. The mean [ORF3 - ORF2] differences were 1.41 log copies/ml for genotype 3c, 0.96 log copies/ml for genotype 3e, and 0.70 log copies/ml for genotype 3f. The bias between the 2 RT-PCR assays was significantly greater for genotype 3c than for genotype 3f (P = 0.007). We therefore recommend the use of an RT-PCR protocol based on ORF3 to quantify HEV RNA of genotype 3 strains.

Hepatitis E virus infection without reactivation in solid-organ transplant recipients, France.

Infections with hepatitis E virus (HEV) in solid-organ transplant recipients can lead to chronic hepatitis. However, the incidence of de novo HEV infections after transplantation and risk for reactivation in patients with antibodies against HEV before transplantation are unknown. Pretransplant prevalence of these antibodies in 700 solid-organ transplant recipients at Toulouse University Hospital in France was 14.1%. We found no HEV reactivation among patients with antibodies against HEV at the first annual checkup or by measuring liver enzyme activities and HEV RNA. In contrast, we found 34 locally acquired HEV infections among patients with no antibodies against HEV, 47% of whom had a chronic infection, resulting in an incidence of 3.2/100 person-years. Independent risk factors for HEV infection were an age <52 years at transplantation and receiving a liver transplant. Effective prophylactic measures that include those for potential zoonotic infections should reduce the risk for HEV transmission in this population.

Genotypic prediction of HIV-1 subtype D tropism.

BACKGROUND: HIV-1 subtype D infections have been associated with rapid disease progression and phenotypic assays have shown that CXCR4-using viruses are very prevalent. Recent studies indicate that the genotypic algorithms used routinely to assess HIV-1 tropism may lack accuracy for non-B subtypes. Little is known about the genotypic determinants of HIV-1 subtype D tropism. RESULTS: We determined the HIV-1 coreceptor usage for 32 patients infected with subtype D by both a recombinant virus phenotypic entry assay and V3-loop sequencing to determine the correlation between them. The sensitivity of the Geno2pheno10 genotypic algorithm was 75% and that of the combined 11/25 and net charge rule was 100% for predicting subtype D CXCR4 usage, but their specificities were poor (54% and 68%). We have identified subtype D determinants in the V3 region associated with CXCR4 use and built a new simple genotypic rule for optimizing the genotypic prediction of HIV-1 subtype D tropism. We validated this algorithm using an independent GenBank data set of 67 subtype D V3 sequences of viruses of known phenotype. The subtype D genotypic algorithm was 68% sensitive and 95% specific for predicting X4 viruses in this data set, approaching the performance of genotypic prediction of HIV-1 subtype B tropism. CONCLUSION: The genotypic determinants of HIV-1 subtype D coreceptor usage are slightly different from those for subtype B viruses. Genotypic predictions based on a subtype D-specific algorithm appear to be preferable for characterizing coreceptor usage in epidemiological and pathophysiological studies.

Characteristics of autochthonous hepatitis E virus infection in solid-organ transplant recipients in France.

BACKGROUND: Hepatitis E virus (HEV) infections can lead to chronic hepatitis in immunocompromised patients. We have investigated the risk factors for HEV infection among solid-organ transplant recipients and the characteristics of these infections. METHODS: We performed serological tests, quantified the virus, and genotyped the virus in plasma samples. We performed a case-control study with HEV-infected patients and control participants matched for sex and age who were recruited from a population of solid-organ transplant recipients with no markers of HEV infection. RESULTS: We investigated 38 consecutive cases of HEV genotype 3 infection. Twenty-two (58%) of these 38 patients developed a chronic infection. The acute-phase aminotransferase levels were higher in the patients who cleared the virus than in those who developed chronic infections. The anti-HEV immunoglobulin G and immunoglobulin M profiles and HEV RNA concentration in patients who cleared the virus were similar to those in patients who developed a chronic infection. A logistic regression analysis of 37 case patients and 148 control participants indicated that the only factor independently associated with HEV infection was the consumption of game meat (68% of case patients vs 47% of control participants; odds ratio, 2.32; 95% confidence interval, 1.04-5.15). CONCLUSION: Immunocompromised patients should avoid eating insufficiently cooked game meat or pork products so as to reduce the risk of HEV infection and chronic liver disease.

Genotypic prediction of human immunodeficiency virus type 1 CRF02-AG tropism.

We assessed the performance of genotypic algorithms for predicting the tropism of human immunodeficiency virus type 1 coreceptor usage in 52 patients infected with the CRF02-AG subtype. The combined criteria of the 11/25 and net charge rules accurately detected CXCR4-using CRF02-AG viruses, whereas the Geno2pheno tool lacked sensitivity and the position-specific scoring matrix (PSSM) tool WebPSSM lacked specificity.

Pegylation of IFN-alpha and antiviral activity.

The development of pegylated interferons (PEG-IFN) has significantly improved the eradication rates in patients with chronic hepatitis C. Two forms of PEG-IFN have been developed, based on two pegylation chemistries: the 12-kDa linear PEG-IFN-alpha2b and the 40-kDa branched PEG-IFN-alpha2a. We compared the in vitro antiviral activity of linear and branched PEG-IFN using the vesicular stomatitis virus (VSV) cytopathic effect (CPE) reduction assay. The specific antiviral activity of branched PEG-IFN was 7% of that of linear PEG-IFN. A given quantity of linear and of branched PEG-IFN does not represent the same biologic activity. A bioassay could give new insights to compare the pharmacokinetic profile of linear PEG-IFN and of branched PEG-IFN.

Analysis of CCR5, CCR2, CX3CR1, and SDF1 polymorphisms in HIV-positive treated patients: impact on response to HAART and on peripheral T lymphocyte counts.

Although polymorphisms of chemokine genes (SDF1, stromal cell-derived factor-1 and RANTES, regulated on activation, normal T cell expressed and secreted) and chemokine-receptor genes (CCR5, CCR2, CX(3)CR1) were shown to be associated with sensitivity to HIV infection and untreated HIV disease progression, their association with the response to highly active antiretroviral therapy (HAART) remains unclear. To explore the possible influence of such polymorphisms on the evolution of AIDS in treated patients, we have studied SDF1-3'A, CCR5Delta32, CCR2-64I, CX(3)CR1-249I, and CX(3)CR1-280M polymorphisms in HIV-infected patients under HAART (n = 169). We studied the evolution of plasma virus load and peripheral T lymphocyte counts in these patients up to 3 years after the initiation of HAART. We observed that some of the genetic polymorphisms studied had an impact on the evolution of these two parameters. After 1 year of HAART, patients with a virological response (undetectable plasma HIV-1 RNA) have a higher frequency of the homozygous SDF1-3'A genotype than other patients (p = 0.005). Similarly, patients with a CD4 increase of over 200/mm(3) from baseline after 1 year of HAART display higher frequencies of homozygous SDF1-3'A (p = 0.035) and homozygous CX(3)CR1-280M genotypes (p = 0.04) than other patients. Moreover, we showed that the CX(3)CR1- 280M allele was associated with higher peripheral CD4+ T cell counts not only in HIV+ patients but also in healthy controls (p = 0.003).

Persistence of distinct HIV-1 populations in blood monocytes and naive and memory CD4 T cells during prolonged suppressive HAART.

OBJECTIVE: Reservoirs of HIV-1 are a major obstacle to virus eradication. There is therefore a need to clearly understand the molecular nature of the virus populations that persist in patients with sustained suppression of plasma viraemia on highly active antiretroviral therapy (HAART). DESIGN: We performed a detailed analysis of the genotypes of HIV-1 quasispecies isolated from highly purified blood cell types taken from three selected patients with sustained undetectable viral loads on HAART for 7 years. METHODS: We used polychromatic flow cytometry to sort naive and memory CD4 T cells, CD14 monocytes, and CD56+CD3- natural killer (NK) cells from the total peripheral blood mononuclear cells after 7 years of HAART. Clonal analysis was used to determine coreceptor use and drug-resistance genotypes of HIV-1 quasispecies in the sorted blood cell types. RESULTS: We detected HIV-1 DNA in memory and naive CD4 T cells and in CD14 monocytes, but not in the CD56+CD3- NK cells. Phylogenetic analysis demonstrated that the various blood cells types of two of the three patients harboured genetically distinct HIV-1 quasispecies. Drug-resistance mutations were also distributed differently from one cell type to another. This compartmentalization suggests a minimal virus trafficking between blood cell types during suppressive HAART. CONCLUSIONS: We observed a cell-specific compartmentalization of the residual virus populations during prolonged suppressive HAART. The coexistence of numerous HIV-1 quasispecies with different resistance genotypes and coreceptor use in cellular reservoirs may be relevant for future antiretroviral treatment strategies.

Evolution of hepatitis C virus quasispecies during therapy with IL2 combinated to alpha interferon and ribavirin.

This study analyses the impact of interleukin 2 (IL2) combined with alpha interferon (IFN-alpha) and ribavirin on the heterogeneity of hepatitis C virus (HCV). We studied 10 patients who took part in a clinical trial that assessed the effects of retreatment with IL2, IFN-alpha and ribavirin in patients who failed to clear the virus after a previous bitherapy. The heterogeneity of HCV quasispecies was assessed by cloning and sequencing the hypervariable region 1 (HVR1) in samples obtained at baseline (W0), after 12 weeks of treatment with IFN-alpha and ribavirin (W12), after a cycle of administration of IL2 in combination with the classical bitherapy (W21 and W24) in the eight patients who failed to clear the virus under treatment. The mean viral load at W21 and at W24 was not different from that at W12. The heterogeneity of HVR1 quasispecies after the administration of IL2 was not different from that at baseline or after 12 weeks of bitherapy. Furthermore, the proportion of nonsynonymous substitutions was unchanged after the IL2 cycles. Thus, the efficacy of the tritherapy with IL2, IFN-alpha and ribavirin is similar to that of the classical bitherapy. Treatment with IL2 in combination with IFN-alpha and ribavirin had no effect on the selective pressure on HCV quasispecies. IL2 is not the best option to treat hepatitis C.

Follow-up of 28 HCMV seropositive renal-transplant recipients: comparison of clinical, biological and virological parameters in the groups of treated versus untreated infected patients.

BACKGROUND: A pre-emptive strategy for prevention of Human Cytomegalovirus (HCMV) disease depends on accurate detection of HCMV infection and clinical and/or biological abnormalities. OBJECTIVES: The aim of our study was to evaluate a therapeutic strategy based on the presence of either minimal clinical and/or biological symptoms or high HCMV viral load assessed by quantitative real-time PCR from whole blood as previously described. STUDY DESIGN: Between June 2002 and July 2003, 70 HCMV seropositive patients underwent a renal transplantation. Virological monitoring was performed every 2 weeks until day 90 then every 3-4 weeks until day 180. Biochemical and haematological parameters were also prospectively monitored. RESULTS: Twenty-eight patients (40%) showed at least one positive HCMV DNA in whole blood. Based on the following criteria: HCMV viral load greater than 4log(10)/ml, or the persistence of a HCMV DNAemia in two consecutive blood samples, or fever, or leucopenia or neutropenia, or increase in alanine aminotransferase level, 14 of the 28 patients received IV ganciclovir as a pre-emptive treatment. Immunosuppressive therapy and demographical data were comparable in both groups. As far as virological, haematological and biochemical parameters are concerned, no statistical significant difference was observed between treated and untreated patients. Moreover no adverse outcome was observed among untreated patients always having a HCMV viral load below 4log(10)/ml. CONCLUSIONS: This study reinforces the need of monitoring of HCMV seropositive renal-transplant recipients based on HCMV diagnosis and quantification by real-time PCR. The results showed that HCMV viraemic patients may benefit of absence of antiviral treatment when they have a low viral load (below 4log(10)/ml) and absence of clinical and/or biological abnormalities. Further studies are required now to validate the threshold value at which we should begin pre-emptive therapy.

[The evolution of the hypervariable region-1 of hepatitis C virus may predict liver fibrosis outcome after renal transplantation]. / La diversification de la région hypervariable-1 du virus de l'hépatite C pourrait prédire l'évolution de la fibrose hépatique après transplantation rénale.

The aim of our study was to assess hepatitis C virus (HCV) evolution and long term liver histology outcome in anti-HCV(+)/RNA(+) renal-transplant (RT) patients. Fifty-five anti-HCV(+)/RNA(+) RT patients underwent every 3-4 years after transplantation liver biopsies (LB) (2 LBs, N = 55; 3 LBs, N = 44; 4 LBs, N = 10). The hypervariable region (HVR)-1 of the HCV genome from all patients was characterized over time. Overall, the rate of liver fibrosis progression was 0.07 +/- 0.03 Metavir units/year. We identified three groups of patients: those in whom liver fibrosis remained stable (group I, N = 21), those with progressing liver fibrosis (group II, N = 21), and those with a regression in liver fibrosis (group III, N = 13). Initial fibrosis stage and high diversification of the HVR-1 of HCV genome between the transplantation and the first liver biopsy were independent factors associated with liver fibrosis regression. In conclusion, in this study, after renal transplantation, HCV infection is not harmful upon liver histology in more than fifty percent of the patients. The diversification of the HVR-1 of the HCV genome might be used to predict liver fibrosis outcome.

Temporal evolution of the distribution of hepatitis E virus genotypes in Southwestern France.

Southwest France is a highly endemic region for hepatitis E virus (HEV). This study examined the circulation of HEV strains between 2003 and 2014 in the Midi-Pyrénées, and compared these data with those from the rest of France. The polyproline region (PPR) of the ORF1 region of the HEV genome was also analyzed. HEV genotype was determined by sequencing a 348-nt fragment within the ORF2 gene for 333 strains in the Midi-Pyrénées and for 571 strains from the rest of France. PPR region was characterized for 56 strains. The frequency of subgenotype 3f decreased over time, whereas subgenotype 3c increased in the Midi-Pyrénées. Repartition of strains did not differ in the Midi-Pyrénées compared to the rest of France. HEV3i and HEV4 have been recently detected throughout France. PPR lengths showed that two major groups of HEV3f exist. Our study shows that HEV3 distribution in the Midi-Pyrénées was similar to the whole of France. Local dietary habits could explain the higher seroprevalence in the Midi-Pyrénées rather the circulation of a particular variant in this region.

Long-term ribavirin therapy in hepatitis C virus-positive renal transplant patients: effects on renal function and liver histology.

BACKGROUND: Long-term renal transplant (RT) recipient mortality and graft loss increase significantly in hepatitis C virus positive (HCV-[+]ve) patients. Treatment with alpha-interferon in this population is associated with a high rate of acute rejection. The aims of this study were the evaluation of the efficacy and the safety of ribavirin monotherapy in 16 HCV-(+) RT patients (group A) matched to 32 HCV-(+) RT patients (group B) who did not receive ribavirin. METHODS: Ribavirin was started at a daily dose of 1,000 mg and then adapted to hemoglobin level. The study was scheduled for 1 year. RESULTS: Ribavirin monotherapy was associated with a decrease in liver enzymes and serum creatinine levels. When proteinuria was present, this decreased or disappeared. There were no significant changes in HCV viremia. There was a significant progression in liver fibrosis with no improvement in inflammation scores. Hemoglobin levels fall dramatically, despite an important support by recombinant erythropoeitin (median, 20,000 IU/wk). In 3 cases, ribavirin therapy had to be stopped. In the control group, after 1 year of follow-up, there was a significant increase in serum alanine aminotransferase and creatinine values. Proteinuria decreased in only 2 of 12 patients (P = 0.03 as compared with group A). CONCLUSION: One year of ribavirin monotherapy seems to have, at best, no beneficial effect on liver histology, although it improves liver enzyme levels. Despite its efficiency to dramatically decrease proteinuria, its impact on renal function remains unknown.

Amantadine therapy in renal transplant patients with hepatitis C virus infection.

BACKGROUND: To date, there is no safe and efficient treatment of hepatitis C virus (HCV) infection after renal transplantation. Recently, there were encouraging reports after using amantadine in HCV-positive immunocompetent patients. OBJECTIVES: In an open pilot study, we evaluated the efficacy and the safety of amantadine monotherapy in 8 HCV positive renal-transplant patients with chronic active hepatitis and increased alanine aminotransferase (ALT) levels. RESULTS: After 6 months of amantadine therapy (200 mg per day), there were no decrease in HCV viremia (5.87 +/- 0.37 log copies/ml at M6 versus 5.71 +/- 0.5 log copies/ml at baseline; P > 0.05). However, we found a significant decrease in ALT activity (71 +/- 17 IU/l at M6 versus 100 +/- 9 IU/l at baseline; P = 0.04), whereas the decrease in aspartate aminotransferase activity did not reach statistical significance. There were no significant changes in liver histology. The clinical and biological tolerance was very good. Finally, there were a significant decrease in cyclosporine A whole blood trough levels during therapy. CONCLUSIONS: Our study is the first one to demonstrate that amantadine monotherapy lack of efficacy in HCV renal-transplant patients. It is able to improve liver enzymes but it has no impact neither upon HCV viremia nor upon liver histology.

Effects of long-term lamivudine therapy in renal-transplant patients.

BACKGROUND: Following renal transplantation (RT), chronic immunosuppression is associated in hepatitis B virus (HBV) (+) patients with a flare-up of the disease, which might be harmful in the long term. OBJECTIVES: We report on the effect of long-term lamivudine therapy given at an initial daily dose of 100mg in 18 HBV (+) RT patients. RESULTS: When lamivudine therapy was commenced, 14 patients (77%) had an increase in their aspartate (AST) and alanine (ALT) aminotransferase levels. During a mean follow-up, under treatment, of 36.5 +/- 3.5 months (up to 66 months), 10 patients (55%) had a sustained partial (HBV DNA < 4 x 10(5)copies/ml) (n = 4) or complete (HBV DNA < 400 copies/ml) (n = 6) virological response. Overall, 12 virological breakthroughs were observed. Of those who were HBe Ag(+) prior to lamivudine therapy (n = 4), one seroconverted to HBe Ab during therapy. At the last follow-up, AST and ALT levels were normal in 13 patients. When liver biopsy was repeated during treatment (n = 15), the virological responders showed a significant decrease in total Knodell score from 10 +/- 0.6 to 7 +/- 1 (P = 0.04), but no significant change in the stage of fibrosis. Conversely, in those patients with high HBV DNA titers, there were no significant changes in the total Knodell score or in the grade of fibrosis. CONCLUSION: In conclusion, lamivudine therapy is safe in HBV(+)ve renal-transplant patients. However, even if the full and partial virological response rates are still high (55%) in the long term, relapse or primary non-responses occur. The implementation of alternative efficient strategies is warranted.

Assessment of HIV-1 subtyping for Cameroon strains using phylogenetic analysis of pol gene sequences.

Phylogenetic analysis of human immunodeficiency virus type 1 (HIV-1) pol gene is a useful method for subtyping European strains of HIV-1. The suitability of this method for genetically diverse African strains was evaluated by comparing HIV-1 subtyping of Cameroon strains using a long fragment of the pol gene sequence to the findings obtained using env gene sequences. When the pol gene could not be amplified, the reverse transcriptase (RT) or the protease (PR) genes were used. Phylogenetic analysis of the env C2/V3 gene sequences of 60 HIV-1 isolates showed 52 to be subtype A, 2 subtype G, plus one each of subtypes C, F2 and H, with 3 subtypes not determined. A long fragment of the pol gene was amplified successfully and sequenced in 23% of cases. The RT region was amplified for 42% of the samples that could not be typed by analysing the long fragment, and the PR gene was amplified for 40% of them. Thus, 63% of samples were typable. Env and pol gene subtypings were in agreement in 86% of cases. It is concluded that the phylogenetic analysis of pol gene sequences is not a practical method for HIV-1 subtyping in areas of high subtype diversity, despite the good agreement between the env and pol gene subtypings. However, it can be a useful method for HIV-1 subtyping, provided that the gene is amplifiable.

Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing.

We used ultra-deep pyrosequencing and the Toulouse Tropism Test phenotypic assay to determine the prevalence of CXCR4-using viruses in 21 patients with primary HIV-1 infections. We found X4-containing virus populations in 9% of patients by ultra-deep pyrosequencing using position-specific scoring matrices (PSSM(X4/R5)) or geno2pheno(5.75) and in 14% using the combined 11/25 and net charge rule. The phenotypic assay identified 9% of CXCR4-using viruses. This confirms that R5 viruses are predominant in primary HIV-1 infections.