HBV and HCV Co-Infection in Chinese Newly Diagnosed HIV+ Subjects in 2015 and 2023: A Cross-Sectional Study.

With shared routes of transmission, HBV and HCV co-infection are estimated to occur more in subjects with HIV. This study aimed to characterize and describe the prevalence of HBV and HCV co-infections in a cohort of newly diagnosed HIV+ subjects living in China. We conducted a cross-sectional study among newly diagnosed HIV+ subjects aged 18-100 who participated in surveys on the national HIV molecular epidemiology in 2015 and 2023. (The epidemiological table survey is located in the national database alongside serologic testing). The chi-square test was used to identify changes in infections between the studying populations in 2015 and 2023, and conditional logistic regression models were fit to identify risk factors for each co-infection. Among the 11,024 newly diagnosed HIV+ subjects who were surveyed (n = 4501 in 2015; n = 6523 in 2023), the prevalence of HBV, HCV, and HBV/HCV in 2023 was lower than that in 2015, respectively. No decrease was observed in HCV co-infection in men who had sex with men (MSM) in North China, Northeast China, and East China. Increasing recognition among those at high risk of heterosexual transmission and those with low educational backgrounds is paramount to the prevention and control of HIV/HBV/HCV infections.

Modelling the impact of treatment adherence on the transmission of HIV drug resistance.

INTRODUCTION: A lower adherence rate (percentage of individuals taking drugs as prescribed) to ART may increase the risk of emergence and transmission of HIV drug resistance, decrease treatment efficacy, and increase mortality rate. Exploring the impact of ART adherence on the transmission of drug resistance could provide insights in controlling the HIV epidemic. METHODS: We proposed a dynamic transmission model incorporating the CD4 cell count-dependent rates of diagnosis, treatment and adherence with transmitted drug resistance (TDR) and acquired drug resistance. This model was calibrated and validated by 2008-2018 HIV/AIDS surveillance data and prevalence of TDR among newly diagnosed treatment-naive individuals from Guangxi, China, respectively. We aimed to identify the impact of adherence on drug resistance and deaths during expanding ART. RESULTS: In the base case (ART at 90% adherence and 79% coverage), we projected the cumulative total new infections, new drug-resistant infections, and HIV-related deaths between 2022 and 2050 would be 420 539, 34 751 and 321 671. Increasing coverage to 95% would reduce the above total new infections (deaths) by 18.85% (15.75%). Reducing adherence to below 57.08% (40.84%) would offset these benefits of increasing coverage to 95% in reducing infections (deaths). Every 10% decrease in adherence would need 5.07% (3.62%) increase in coverage to avoid an increase in infections (deaths). Increasing coverage to 95% with 90% (80%) adherence would increase the above drug-resistant infections by 11.66% (32.98%). CONCLUSIONS: A decrease in adherence might offset the benefits of ART expansion and exacerbate the transmission of drug resistance. Ensuring treated patients' adherence might be as important as expanding ART to untreated individuals.

The impact of attrition on the transmission of HIV and drug resistance.

BACKGROUND: Attrition due to loss to follow-up or termination of antiretroviral therapy (ART) among HIV-infected patients in care may increase the risk of emergence and transmission of drug resistance (TDR), diminish benefit of treatment, and increase morbidity and mortality. Understanding the impact of attrition on the epidemic is essential to provide interventions for improving retention in care. METHODS: We developed a comprehensive HIV transmission dynamics model by considering CD4 + cell count dependent diagnosis, treatment, and attrition involving TDR and acquired drug resistance. The model was calibrated by 11 groups HIV/AIDS surveillance data during 2008-2018 from Guangxi, China, and validated by the prevalence of TDR among diagnosed treatment-naive individuals. We aimed to investigate how attrition would affect the transmission of HIV and drug-resistance when expanding ART. RESULTS: In the base case with CD4 + cell count dependent per capita attrition rates 0.025∼0.15 and treatment rates 0.23∼0.42, we projected cumulative total new infections, new drug-resistant infections, and HIV-related deaths over 2022-2030 would be 145 391, 7637, and 51 965, respectively. Increasing treatment rates by 0.1∼0.2 can decrease the above total new infections (deaths) by 1.63∼2.93% (3.52∼6.16%). However, even 0.0114∼0.0220 (0.0352∼0.0695) increase in attrition rates would offset this benefit of decreasing infections (deaths). Increasing treatment rates (attrition rates) by 0.05∼0.1 would increase the above drug-resistant infections by 0.16∼0.30% (22.18∼41.15%). CONCLUSION: A minor increase in attrition can offset the benefit of treatment expansion and increase the transmission of HIV drug resistance. Reducing attrition rates for patients already in treatment may be as important as expanding treatment for untreated patients.

Co-evolution of compensatory mutation K43E with mutation M41L in long-term HIV antiretroviral treatment.

BACKGROUND: Compensatory mutations have been observed to emerge with drug resistance (DR) mutations, but their effects on virological response to treatment have not been fully examined. In this study, we characterized the emergence and depletion dynamics of a compensatory mutation K43E that correlated with primary nucleoside reverse transcriptase inhibitor (NRTI) drug resistance mutations in Chinese HIV patients on antiretroviral treatment. METHOD: Single Genome Amplification (SGA) was used to obtain the HIV-1 pol gene quasispecies in three patients over 6 years of Antiretroviral Therapy (ART) treatment. SGA sequences were analyzed by Markov Chain Monte Carlo (MCMC) phylogenetic trees with molecular clock to identify and track compensatory mutation K43E correlated with primary DR mutation M41L. We evaluated the relationship between potential compensatory mutation and DR mutations through Ka/Ks ratio, Jaccard similarity coefficient, and compared these with concurrent viral load data. CONCLUSION: We determined that a known compensatory mutation, K43E, frequently co-occurs with the drug resistance mutation M41L and may offer a significant advantage in the long-term survival of such drug resistant strains.

The development of drug resistance mutations K103N Y181C and G190A in long term Nevirapine-containing antiviral therapy.

OBJECTIVE: We built a cohort study of HIV patients taking long-term first-line Antiretroviral Therapy in 2003. In this assay, we focused on the development of primary drug resistance mutations against Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI), K103N, Y181C and G190A. METHOD: The cohort study was built in Henan province, China. We used Single Genome Amplification (SGA) to analyze the frequency of K103N, Y181C and G190A in serial plasma samples of three individual patients. We also performed standard genotype HIV drug resistance assay in 204 patients of this cohort study to analyze the frequency of these mutations. RESULT: In the SGA sequences, the K103N decreased and vanished, while the frequency of Y181C and G190A increased in individual patient receiving long-term Antiretroviral Therapy (ART). In the sequences of standard genotype HIV drug resistance assay, the frequency of K103N, Y181C and G190A had the similar pattern with that in SGA sequences. Among these patients, the viral suppression were still sufficient after receiving ART for 72 months, and 78.6% (160/204) patients could have their CD4 count over than 200cells/ul. CONCLUSION: In some patients, first-line ART had the possibility to provide sufficient treatment effect for over than 72 months, but in long-term treatment, the dominant NNRTI drug resistance mutation K103N could reduced, while the proportion of variants with mutation Y181C or G190A may increased. This result was not similar with that in vitro study, which state that variant with K103N or Y181C had an equal viral fitness with wild type.

Impact of HIV drug resistance on virologic and immunologic failure and mortality in a cohort of patients on antiretroviral therapy in China.

OBJECTIVES: To study the dynamics of HIV drug resistance (HIVDR) and its association with virologic and immunologic failure as well as mortality among patients on combination antiretroviral therapy (cART) in China. DESIGN: We recruited 365 patients on cART in two rural Chinese counties in 2003-2004 and followed them every 6 months until May 2010. METHODS: Virologic failure, HIVDR, immunologic failure and death were documented. We used Kaplan-Meier and the proportional hazards models to identify the timing of the events, and risk factors for mortality. RESULTS: At the end of study, patients had been followed for 1974.3 person-years, a median of 6.1 years. HIVDR mutations were found in 235 (64.4%) patients and 75 died (20.5%, 3.8/100 person-years). Median time from cART to detection of virologic failure was 17.5 months, to HIVDR 36.6 months and to immunologic failure 55.2 months (≈ 18-month median interval between each adverse milestone). Being male, having a baseline CD4 cell count of less than 50 cells/µl and HIVDR were associated with higher mortality. Patients who developed HIVDR in the first year of treatment had higher mortality than those developing HIVDR later (adjusted hazard ratio 1.90, 95% confidence interval 1.01-3.48). CONCLUSION: HIVDR was common and was associated with higher mortality among Chinese patients on cART, particular when HIVDR was detected early in therapy. Our study reinforces the importance of improving patient adherence to cART in order to delay the emergence of HIVDR and obviate the need to switch to costly second-line drug regimens too early.

[The study of an in-house method for drug resistance genotyping testing on HIV-1 strains prevailing in China].

OBJECTIVE: To evaluate the amplification rate and the lowestlower detection limit of an in-house HIV-1 Drug resistant (HIVDR) genotyping test. METHODS: A total of 30 plasma samples were selected, which covered all major HIV-1 subtypes predominating prevailing in China (B', CRF07_BC, CRF01 _AE). The viral loads of the 30 selected samples were detected in triplicate by Easy Q method and the average values were taken as the viral loads of the samples. Each sample was diluted to the concentration of > 1000 copies/ml, 401-1000 copies/ml, 101-400 copies/ml, 50-100 copies/ml and < 50 copies/ml with HIV-negative plasma. After extraction of nucleic acids, RT-PCR and nested PCR amplification were performed, the efficiency of amplification of each subtype and the minimum detection limit were determined statistically based on the PCR results. RESULTS: The viral loads of the selected samples ranged from 2.03 x 10(2)-5.92 x 10(4) copies/ml. The sample of 50-1000 copies/ml have a high amplification rate (86%). CONCLUSION: The In-house method for HIV-1 drug resistance genotyping has a high sensitivity with a high successful amplification rate, especially in the samples with low viral load. This method can be used to the detection of drug-resistant virus and to provide scientific data to treatment options for patients.

A new pattern-based method for identifying recent HIV-1 infections from the viral env sequence.

The long asymptomatic stage of HIV infection poses a great challenge in identifying recent HIV infections. This is a bottleneck for monitoring HIV epidemic trends and evaluating the effectiveness of national AIDS control programs. Several serological methods were used to address this issue with some success. Because of high false-positive rates in patients with advanced infection or in ART treatment, UNAIDS still hesitates to recommend their use in routine surveillance. We developed a new pattern-based method for measuring intra-patient viral genetic diversity for determination of recent infections and estimation of population incidence. This method is verified by using several datasets (424 subtype B and 77 CRF07_BC samples) with clearly identified HIV-1 infection times. Pattern-based diversities of recent infections are significantly lower than that of chronic ones. With larger window periods varying from 200 to 350 days, a higher accuracy (90%-95%) not affected by advanced disease nor ART treatment could be obtained. The pattern-based genetic method is supplementary to the existing serology-based assays, both of which could be suitable for use in low and high epidemic regions, respectively.

Preferential CTL targeting of Gag is associated with relative viral control in long-term surviving HIV-1 infected former plasma donors from China.

It is generally believed that CD8(+) cytotoxic T lymphocytes (CTLs) play a critical role in limiting the replication of human immunodeficiency virus type 1 (HIV-1) and in determining the outcome of the infection, and this effect may partly depend on which HIV product is preferentially targeted. To address the correlation between HIV-1-specific CTL responses and virus replication in a cohort of former plasma donors (FPDs), 143 antiretroviral therapy naive FPDs infected with HIV-1 clade B' strains were assessed for HIV-1-specific CTL responses with an IFN-γ Elispot assay at single peptide level by using overlapping peptides (OLPs) covering the whole consensus clade B proteome. By using a Spearman's rank correlation analysis, we found that the proportion of Gag-specific CTL responses among the total virus-specific CTL activity was inversely correlated with viral loads while being positively correlated to CD4 counts, as opposed to Pol- and Env-specific responses that were associated with increased viral loads and decreased CD4 counts. In addition, Vpr-specifc CTL responses showed a similar protective effect with Gag responses, but with a much lower frequency of recognition. Significantly, we also observed an association between HLA-A*30/B*13/Cw*06 haplotype and lower viral loads that was probably due to restricted Gag-specific CTL responses. Thus, our data demonstrate the prominent role of Gag-specific CTL responses in disease control. The advantage of HLA-A*30/B*13/Cw*06 haplotype in viral control may be associated with the contribution of Gag-specific CTL responses in the studied individuals.

[Feasibility of using dried blood spots to detect HIV drug resistance genotyping].

OBJECTIVE: This study aimed at exploring the feasibility of using dried blood spots (DBS) to detect HIV drug resistance genotyping in China by comparing the results of drug resistance from DBS, plasma and whole blood samples. METHODS: Blood samples were collected from 39 AIDS patients from Anhui (10), Yunnan (13), Hunan (6) and Xinjiang (10) provinces and autonomous regions. The HIV strains that infected these patients covered all the major HIV-1 subtypes prevailing in China (B, CRF01_AE, CRF07_BC). HIV drug resistance genotyping assay was performed on DBS as well as on the whole blood and plasma samples from the same patients simultaneously by using an in-house nest RT-PCR method. Drug resistance levels were determined based on Stanford University HIV drug resistance database, and the results from these three types of samples were compared. RESULTS: The percentages of successful amplification of protease and reverse transcriptase regions in the pol gene were 95% (37/39) from DBS, 92% (36/39) from whole blood and 100% (39/39) from plasma samples. The sequences from the three types of samples showed more than 99% identity.86% (31/36) of the DBS samples had the same set of drug resistance mutations as those which were detected from plasma samples. The differences probably resulted from mixed bases. CONCLUSIONS: There was no major difference in detecting HIV drug resistance genotyping among DBS, plasma and whole blood samples. Therefore, DBS is useful for detection of HIV drug resistance genotyping and is particularly valuable in developing countries like China, especially in remote rural regions.

CD8+ cell noncytotoxic antiviral response in long-term HIV-1 infected former blood donors in China.

Most of the HIV-infected long term survivors show strong CD8+ cell noncytotoxic antiviral response (CNAR) that plays as an important factor for maintaining the relative healthy state of infected individuals. HIV infected former blood donors (FBDs) in Anhui, China are the unique population that considered infected by the same or a related HIV strain by the same exposure route, and is better to be studied for viral and host immunological factors associated with disease progression, such as CNAR. We examined CNAR in 63 asymptomatic untreated HIV infected FBDs with different CD4+ cell counts and plasma viral loads. The average CD8+ : CD4+ cell ratio to reach 90% suppression of HIV replication in the groups with CD4+ cell counts of >500, 300-500 and <300 cells/microl were 0.85 : 1, 1.47 : 1 and 1.88 : 1 respectively (P<0.0001). The average CD8+ : CD4+ cell ratio to reach 90% suppression of HIV replication was 1.07 : 1 and 1.66 : 1 in the group with plasma viral load of <30,000 and >30,000 RNA copy/ml respectively (P=0.0002). The results indicated that CNAR activity in long-term HIV-1 infected FBDs correlates directly with CD4+ cell counts, and correlates reversely with plasma viral loads. Our findings in long term infected FBDs confirm the clinical relevancy of CNAR and suggest that CNAR could be an additional marker to help determine the optimal time for starting therapy in HIV infected person.

[CD8+ cell noncytotoxic antiviral response (CNAR) to HIV in nosocomial HIV-infected individuals].

OBJECTIVE: To study the CD8+ cell noncytotoxic antiviral response (CNAR) to HIV in nosocomial HIV infected individuals, and reveal the relationship between the CNAR and CD4+ cell count. METHOD: CD8+ cells from HIV-1 sero-positive individuals were separated by immunomagnetic beads and mixed with CD4+ cells at different CD8 CD4 cell input ratios (2:1, 1:1, 0.5:1 and 0.25:1). Reverse transcriptase (RT) activity of cocultured supernatant was tested and compared with negative control and the suppression rate of HIV-1 replication was measured. RESULT: The average CD8:CD4 cell input ratios to reach 80% suppression of HIV replication in the group with CD4 < 300/microl and CD4 > 300/microl were 2.4:1 and 1.3:1, respectively (P < 0.05). CONCLUSION: CNAR activity in HIV infected individuals is associated with CD4+ cell count. The ability to suppress HIV replication in subjects with CD4 > 300 is stronger than those with CD4 < 300.

A line immunoassay utilizing recombinant nucleocapsid proteins for detection of antibodies to human coronaviruses.

Most coronaviruses infecting humans cause mild diseases, whereas severe acute respiratory syndrome (SARS)-associated coronavirus is an extremely dangerous pathogen. Here, we report the development of a serologic assay for detection of antibodies to human coronaviruses (HCoVs) based on recombinant nucleocapsid (N) proteins of all known pathogenic strains (229E, NL63, OC43, HKU1, SARS). The novel immunoassay is highly useful for epidemiologic surveys, where use of nucleic acid diagnostics often is limited. Purified recombinant antigens were immobilized on nitrocellulose membranes and applied in a line immunoassay, which allows rapid detection of antibodies to 5 different HCoVs in a single experiment. For assay evaluation, serum samples from persons infected with 229E or OC43 (acute/convalescent), recovered SARS patients and healthy donors were analyzed. Screening for nucleocapsid (N)-specific immunoglobulin G (IgG) in convalescent sera reached 100% sensitivity. With this new technique, we found that recently identified NL63 and HKU1 contribute significantly to the overall spectrum of coronavirus infections. Possibly, cross-reactive antibody responses were observed using 229E and OC43 serum pairs. However, the potential of this assay could clearly be demonstrated employing SARS-positive serum samples, where nonspecific binding to nucleocapsids of other HCoVs was not observed. This coronavirus strain-specific line immunoassay represents a powerful tool for serologic diagnostics.

[Sequence analysis of gag and env genes of HIV type 1 circulating in former blood donors of Fuyang city, Anhui province].

OBJECTIVE: To determine the subtype and analyze the genetic characteristics of the HIV-1 predominantly circulating in the former blood donors of Fuyang city, Anhui province. METHODS: Whole blood samples were collected from 294 HIV-positive former blood donors of Fuyang city, 157 males and 137 females, aged 42 +/- 8. The fragments of HIV-1 env and gag genes were amplified by nested-PCR from the whole blood samples and thereafter sequenced. The env and gag sequences derived from 244 and 245 HIV infected individuals respectively were analyzed by using MEGA software, and related researches were also done according to the disease progression of the HIV infected individuals. RESULTS: Phylogenetic trees showed that both the env and gag strains were clustered with the Thailand B reference strains. The internal nucleotide distances of the env and gag genes were 9.11% and 3.59% respectively. The nucleotide distances of both env and gag genes significantly increased as the CD4 T-cell counts decreased or as the viral load rose (both P < 0.001). The V3 loop tip motifs were dramatically dominated by GPGQ in the long-time non-progressors, and by GPGR in the slow progressors (P = 0.038). CONCLUSION: The predominant strains circulating in the HIV-1 infected former blood donors of Fuyang city are of the Thailand B clade. Low CD4 T-cell count and high viral load are associated with the increase of genetic distances among viral isolates. The V3 loop tip motif changes from GPGQ to GPGR along with the progression of disease.

Epidemiology, clinical and laboratory characteristics of currently alive HIV-1 infected former blood donors naive to antiretroviral therapy in Anhui Province, China.

BACKGROUND: Unregulated commercial blood/plasma collection among farmers occurred between 1992 and 1995 in central China and caused the second major epidemic of human immunodeficiency virus type 1 (HIV-1) infection in China. It is important to characterize HIV-1-infected former blood donors and to study characteristics associated with disease progression for future clinical intervention and vaccine development. METHODS: A cross-sectional study was performed on HIV-1-infected former blood donors (FBDs) and age-matched HIV-seronegative local residents. Demographic, epidemiologic, clinical and key laboratory data were collected from all study participants. Both unadjusted and adjusted multivariate linear regressions were employed to analyze the association of the decrease of CD4(+) T-cell counts with other characteristics. RESULTS: Two hundred and ninety-four HIV-1-infected FBDs and 59 age-matched HIV-seronegative local residents were enrolled in this study. The unregulated blood/plasma collection occurred more than a decade (10.8 - 12.8 years) ago, which caused the rapid spread of HIV-1 infection and the high prevalence of co-infection with hepatitis C virus (HCV, 89.5%); hepatitis B virus (HBV) co-infection was observed in only 11 HIV(+)participants (3.7%). Deterioration in both clinical manifestation and laboratory parameters and increase of viral loads were observed in parallel with the decrease of CD4(+) T-cell counts. The decrease of total lymphocyte counts (P < 0.001) and hemoglobin levels (P < 0.001) and the appearance of dermatosis (P = 0.03) were observed in parallel with the decrease of CD4(+) T-cell counts whereas viral loads (P < 0.001) and CD8(+) T-cell counts (P = 0.01) were inversely associated with CD4(+) T-cell counts. CONCLUSIONS: Co-infection with HCV but not HBV is highly prevalent among HIV-1-infected FBDs. CD4(+) T-cell counts is a reliable indicator for disease progression among FBDs. Total lymphocyte counts, hemoglobin level and appearance of dermatosis were positively associated with CD8(+) T-cell counts and viral loads were inversely associated with the decreased CD4(+) T-cell counts.

Characterization of five nearly full-length genomes of early HIV type 1 strains in Ruili city: implications for the genesis of CRF07_BC and CRF08_BC circulating in China.

To trace the genesis of HIV-1 CRF07_BC and CRF08_BC, two predominant circulating recombinants among intravenous drug users in China, a retrospective molecular epidemiological investigation (1996-1998) was conducted in Ruili city of Yunnan, where the first AIDS epidemic among IDUs was reported in 1989. Fifty-four HIV-1 env C2V3 sequences were determined and genotyped with 49 subtype B and only 5 subtype C strains. The nearly full-length genome analyses of these five env-based subtype C samples revealed that four of them were actually BC recombinants and only one was pure subtype C. The first identified nonrecombinant HIV-1 subtype C, genetically close to Indian C representatives, provided direct evidence for the hypothesis that subtype C in China was introduced from India. Interestingly, three BC recombinants with subtype B as backbones were identified; one BC recombinant that precisely shared a common subtype B segment (nef region) with CRF07_BC and CRF08_BC was described, which indicated a close evolutionary relationship to these two CRFs. The sequences undoubtedly lead us to a better understanding of the emergence of CRF07_BC and CRF08_BC.

[Identification of signature amino acids in the env V3-V4 and flanking regions of human immunodeficiency virus type 1 predominant strains in China].

OBJECTIVE: To identify signature amino acids in the V3-V4 and flanking regions of the env gene from human immunodeficiency virus type 1 (HIV-1) predominant strains in China and to elucidate the role of these signature amino acids on epidemiologic tracking and the development of vaccine. METHODS: Fragments of the HIV-1 env gene were amplified by nested-PCR from the whole blood of HIV-1 infected individuals from 12 provinces in China. Then, the PCR products were directly sequenced by using ABI 377 DNA SEQUENCER. The sequences covering the env V3-V4 region of the strains were used for the analyses described here. Envelope sequence subtypes were assigned using BLAST (http://www.HIV-Web.lanl.gov). Phylogenetic analyses were performed using GCG and MEGA as well as signature amino acids were identified using VESPA. RESULTS: Subtype B' strains and two recombinants (B'/C and CRF01-AE) were discovered among 157 currently circulating strains in China. The most prevalent subtypes were B'/C (38.85%), followed by B' (34.40%), and CRF01-AE (26.75%). Phylogenetic tree analysis of env V3-V4 region showed that subtype B' strains were closely related to B.CN.RL42, while most of B'/C strains clustered with 97CN54A and 97CNGX6F, CRF01-AE strains clustered into two distinct subgroups, which were closely related to THCM240 and 97CNGX2F. Analysis of signature amino acids revealed that eight of positions were identified as conserved signature amino acid sites in the env V3-V4 and flanking regions of the subtype B' and B'/C strains and almost all signature amino acids were found in their reference strains. Interestingly, eleven signature amino acids were demonstrated in the same regions of the CRF01-AE strains, but nine out of 11 signature amino acid sites were distinct from the same positions of the reference strains 97CNGX2F and TH.CM240. It is noteworthy that these 9 signature amino acids were found in the strains from all of the selected provinces except those from Yunnan province. CONCLUSION: Analysis of the signature amino acids suggest that much of the current Chinese epidemics of subtype B' and B'/C strains are descended from a single introduction into China, while the epidemic caused by the CRF01-AE strain is caused by multiple introductions into China from Thailand. These results will contribute to the policy of AIDS prevention and control as well as the ongoing development of AIDS vaccine.

[Sequence variation in the env V3-V4 region of HIV type 1 predominant subtype B and C strains circulating in China].

OBJECTIVE: To identify genetic variation of HIV-1 predominant subtype B and C strains in China during rapid horizontal transmission and to elucidate the potential relationship between genetic variation and selective pressure. METHODS: After the fragments of HIV-1 env gene were amplified by nested-PCR from the whole blood of 258 HIV-1 infected individuals, PCR products were directly sequenced using ABI 377 DNA sequencer. The sequences covering env V3-V4 region of 72 HIV-1 subtype B(n=37) and C(n=35) strains were selected for phylogenetic analysis. In addition, the ratios of synonymous (Ks) substitutions per nonsynonymous (Ka) substitutions were calculated using DIVERGE. RESULTS: The genetic distances of the V3-V4 region of subtype B strains were higher than that of subtype C strains. Furthermore, sequence analysis revealed that the V4 region was more variable than the V3 region for both subtype B and C strains. What's more, the V3 loop was less variable compared with the V3 upstream region and C3 region for subtype C Ks/Ka ratios of the entire aligned sequence of the two subtypes were below 1 0, with the lowest values found in the V3 region of subtype B strain and the V4 region of subtype C strain. CONCLUSIONS: The majority of variation in both subtypes B and C strains occurred in the V4 rather than the V3 region. It is important that our study found for the first time the V3 loop was more conservative than the V3 upstream region and C3 region for subtype C. Calculations of the Ks/Ka ratios throughout the V3-V4 region demonstrate that significant selective pressures experienced during the rapid horizontal spread of the virus in the Chinese HIV-1 infected population may have directed change in the V3 loop for the subtype B strain and the V4 loop for the subtype C strain. These results will contribute to the policy of AIDS prevention and control and the ongoing development vaccine.