The Genetic Diversity and Drug Resistance Patterns of HIV‐1 Pol Gene in East Africa

BackgroundThe first case of HIV infection in Sri Lanka was reported in 1987 and at the end of 2018 there were 3500 people living with HIV. There have been commendable efforts made towards the detection, treatment, and prevention of HIV in the country. Even though the genetic diversity of HIV has been shown to affect the parameters ranging from detection to vaccine development, there is no data available with respect to the molecular epidemiology of HIV-1 in Sri Lanka.MethodsIn this report we have performed the ancillary analysis of pol gene region sequences (n = 85) obtained primarily for the purpose of HIV-1 drug resistance genotyping. Briefly, dried blood spot specimens (DBS) collected from HIV-1 infected individuals between December 2015 and August 2018 were subjected to pol gene amplification and sequencing. These pol gene sequences were used to interpret the drug resistance mutation profiles. Further, sequences were subjected to HIV-1 subtyping using REGA 3.0, COMET, jPHMM and, RIP online subtyping tools. Moreover, Bayesian phylogenetic analysis was employed to estimate the evolutionary history of HIV-1 subtype C in Sri Lanka.ResultsOur analysis revealed that the majority (51.8%) of pol gene sequences were subtype C. Other than subtype C, there were sequences categorized as subtypes A1, B, D and G. In addition to pure subtypes there were sequences which were observed to be circulating recombinant forms (CRFs) and a few of the recombinants were identified as potential unique recombinants (URFs). We also observed the presence of drug resistance mutations in 56 (65.9%) out of 85 sequences. Estimates of the Bayesian evolutionary analysis suggested that the HIV-1 subtype C was introduced to Sri Lanka during the early 1970s (1972.8).ConclusionThe findings presented here indicate the presence of multiple HIV-1 subtypes and the prevalence of drug resistance mutations in Sri Lanka. The majority of the sequences were subtype C, having their most recent common ancestor traced back to the early 1970s. Continuous molecular surveillance of HIV-1 molecular epidemiology will be crucial to keep track of drug resistance, genetic diversity, and evolutionary history of HIV-1 in Sri Lanka.

Background: Globally, Human immunodeficiency virus (HIV) is a leading cause of morbidity and mortality. The fundamental Antiretroviral Therapy (ART) goal is to curb the spread of HIV and enhance the survival of HIV infected patients. Despite the tremendous benefits of ART, HIV treatment and management failures among the youth have been attributed to non-adherence to drug regimens and viral mutations leading to the emergence of drug resistance. Therefore, this study aimed to determine the genetic diversity and HIV-1 drug resistance patterns among the youth aged 15-24 years with non-suppressed viral load in the South Rift Valley Region (SRV), Kenya. Methods: A cross-sectional study design was adopted to select a total of 120 plasma samples from HIV-1-positive youth who had been on different ART regimens for over six months. Remnant plasma samples with >1000 copies/ml from real-time PCR using the Abbott Real-Time HIV-1 m2000rt quantitative kit were sequenced using the HIV-1 genotyping kit with integrase between April 2024 and October 2024. The target genes were Reverse Transcriptase, Protease and Integrase of the pol gene. HIV-1 level of drug resistance was evaluated using the Exatype Sanger analysis tool. Mutation patterns were ascertained by analysing FASTA files using the drug resistance HIV Stanford database. The subtypes of HIV-1 were analysed by the REGA HIV subtyping tool, and Maximum-likelihood phylogenetic trees and annotations of the mutations were constructed using the integrated Tree of Life. Results: Sequencing was completed for 99 samples, and Tenofovir Disoproxil Fumarate + Lamivudine + Dolutegravir (TDF/3TC/DTG) was the most commonly prescribed antiretroviral regimen across all age groups. The predominant HIV subtype was A1 (83%). Drug resistance was attributed to mutation, M184V (31.4%) associated with resistance to Emtricitabine and Lamivudine, K103N (20.9%) and G190A (15.1%) resistance to efavirenz, nevirapine and rilpivirine, G118R (5.7%) to raltegravir, elvitegravir and bictegravir. Conclusion: There was high genetic diversity of HIV-1 among the youths aged between 15 and 24 years, and subtype A1 is the dominant circulating form of HIV-1 in the South Rift Valley region. Understanding the evolutionary relationships of these strains provides insights into their genetic diversity and transmission.

Objective To investigate the distribution of subtypes of human immunodeficiency virus type 1(HIV-1)epidemic strains and the prevalence of primary drug resistance in the HIV infected individuals among men who have sex with men(MSM)population in Harbin from 2016 to 2017. Methods Peripheral blood samples with the antiretroviral therapy(ART)-naive were collected from 60 newly diagnosed HIV-1 infected individuals in Harbin Infectious Diseases Hospital and the Fourth Affiliated Hospital of Harbin Medical University.RNA was extracted from the plasma.HIV-1 gag, pol, and int gene fragments were amplified by reverse transcription PCR and nested PCR, purified, and sequenced.Phylogenetic tree and subtype analysis were performed using Mega 6.0 software.The type and frequency of drug resistance mutations were analyzed using the Stanford HIV Drug Resistance Database. Results 50 gag gene sequences, 56 pol gene sequences, and 44 int gene sequences were successfully amplified.The subtype analysis showed that CRF01_AE, CRF07_BC, B subtypes, and unique recombinant forms (URF) accounted for 59.7% (34/57), 26.3% (15/57), 3.5% (2/57), and 10.5% (6/57), respectively.The drug resistance mutations were found in total of 7 samples (12.5%), among them the highest frequency of V179D/E/T was 8.75% (5/56) for non-nucleoside reverse transcription inhibitors.In addition, Q58E (1/56) and M46I (1/56) mutations which were resistance to protease inhibitors were also found.No resistance mutation sites to nucleoside reverse transcriptase inhibitors and integrase inhibitors were found. Conclusions Among the newly diagnosed HIV-1 infected individuals via MSM transmission route, the proportion of CRF01_AE subtypes is the highest, followed by CRF07_BC and other URF recombinant with CRF01_AE.The proportion of drug-resistant strains is higher and no drug resistance(DR) mutations to the integrase inhibitors was found. Key words: Men who have sex with men; Human immunodeficiency virus; Virus subtype; Drug resistance mutation

BackgroundLiangshan Yi Autonomous Prefecture is one of the areas that most severely affected by human immunodeficiency virus (HIV) in China, and virological failure on antiretroviral therapy (ART) is serious in this area. Analyses of prevalence and determinants of ART failure, the genetic diversity and drug resistance among people living with HIV (PLWH) helps improve HIV treatment efficiency and prevent HIV transmission.MethodsA total of 5157 PLWH were recruited from 2016 to 2017. The venous blood samples were subjected to RT-PCR, followed by sequencing of the HIV-1 pol gene, targeting the protease and reverse transcriptase fragments. HIV-1 diversity was analyzed using the DNAStar software and drug resistance mutations were analyzed using the Stanford University HIV Drug Resistance Database.ResultsA total of 2156 (41.81%) PLWH showed virological failure on ART. Males (ORm = 1.25), heterosexual behaviors and drug injection (ORm = 1.44) and mother to child transmission routes (ORm = 1.58), the clinical stage of AIDS (ORm = 1.35), having used illicit drugs and shared the needles (1–4 times: ORm = 1.34; more than 5 times: ORm = 1.52), having ever replaced ART regimen (ORm = 1.48) increased the risk of virological failure among PLWH, while higher education lever (ORm = 0.77) and ≥ 12 months on ART (12 ~ 36 months: ORm = 0.72; ≥36 months: ORm = 0.66) was associated with lower likelihood of virological failure. The data revealed that CRF07_BC (1508, 95.62%) were the most common strains, and the drug-resistant rate was 32.10% among PLWH with virological failure in this area. The high frequencies of drug resistance were found in EFV and NVP of NNRTIs, ABC, FTC and 3TC of NRTIs, and TPV/r in PIs. The most common mutations in NNRTIs, NRTIs and PIs were K103N/KN (64.69%), M184V/MV/I (36.29%) and Q58E/QE (4.93%), respectively.ConclusionWe concluded that surveillance of virological failure, HIV-1 subtypes, and drug resistance to understand HIV-1 epidemiology and guide modification of ART guidelines, and target prevention and control strategies should be formatted to reduce the virological failure and drug resistance to promote viral suppression and prevent HIV-1 transmission.

HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.

To examine the prevalence of drug resistance mutations among the treatment-naive HIV (human immunodeficiency virus) infectors living in Beijing so as to provide the basal information for clinical antiviral treatment. HIV pol genes from plasma samples of 150 treatment-naive HIV-infected patients were amplified, sequenced and phylogenetically analyzed. And the drug-resistance associated mutations in protease and reverse transcriptase regions were analyzed with Stanford University HIV Drug Resistance Database. A total of 111 pol gene sequences were obtained. The overall prevalence of drug resistance was 8.1% (9/111), corresponding to 3.6% (4/111) for protease inhibitors, 1.8% (2/111) for nucleoside reverse transcriptase inhibitors and 3.6% (4/111) for non-nucleoside reverse transcriptase inhibitors. No drug resistance mutation was identified in 17 intravenous drug users. The prevalence of drug resistance is relatively high in the newly confirmed HIV infectors in Beijing. Regular surveillance and monitoring of drug-resistant HIV should be implemented.

Drug resistance profiles of human immunodeficiency virus-1 (HIV-1) in treatment-naïve infections have been reported in developed countries. However, little is known in developing countries, including China, especially in treatment-naïve volunteer blood donors. Fifty-two HIV-1-positive samples of blood donors were collected from 2005 to 2006 in Yunnan, China. Recent and long-term infections were distinguished by the HIV-1 subtypes B, E, and D immunoglobulin G-capture enzyme immunoassay assay. The nucleotide sequences of pol genes were amplified and sequenced. Phylogenetic tree and drug resistance analyses were performed. Of 49 samples successfully analyzed, circulating strains were circulating recombinant form (CRF)08_BC (51.0%), CRF07_BC (24.5%), CRF01_AE (20.4%), and B (4.1%). No protease inhibitors (PI) major drug resistance mutation (DRM) was detected. Six samples (12.2%) displayed seven minor PI DRMs. Nine samples (18.4%) displayed 10 nucleoside reverse transcriptase inhibitor DRMs, and DRMs to nonnucleoside reverse transcriptase inhibitors were present in one sample (2.0%). There was only one sample of the 49 (2.0%) in which the DRMs were of sufficient magnitude to result in a clinical change to drug susceptibility, but even in this sample, the clinical effect of these DRMs was predicted to be low. Significant differences were not observed between the long-term and recent infected population. Differences in DRMs were not observed between peripheral blood mononuclear cells and plasma within an individual. CRF_BC was the dominant subtype circulating in HIV-1-infected donors in Yunnan. Prevalence of genotypic drug resistances among donors in Yunnan was low in this study. Surveillance on HIV-1 infections among blood donors should be continued in China.

To the Editor: One of the most significant biologic characteristics of HIV-1 is its broad genetic diversity, which is revealed by the existence of 3 groups (M, N, and O), various subtypes (A-D, F-H, J, and K) and sub-subtypes (A1-A4, F1, and F2), and numerous circulating recombinant forms (CRFs) or unique recombinant forms (URFs) within HIV-1 group M (Los Alamos HIV/AIDS Sequence Database, available at: http://hiv-web.lanl.gov). In areas where CRFs spread widely, second-generation recombinant viruses (SGRs) have been reported to contain the genetic material of at least 1 CRF. The extensive genetic variation, the heterogeneous geographic distribution of HIV-1, and, in particular, the continuous emergence of HIV-1 variants pose potential public health and clinical challenges. It is thus necessary to monitor the evolution of HIV-1 on an ongoing basis. In 2002, we initiated a serologic survey in Douala and Yaoundé, Cameroon, where the pandemic infection of HIV-1 with broad genetic diversity and the natural reservoir of HIV-1 groups M and N have been identified. A total of 240 unlinked plasma samples were collected from 2 blood centers from urban areas in Douala and Yaoundé, Cameroon, and 135 samples were confirmed to be HIV-1-positive by US Food and Drug Administration (FDA)-licensed HIV diagnostic tests (results are to be published elsewhere). Eighty-eight HIV-1-positive samples were successfully amplified by polymerase chain reaction (PCR) and sequenced in gag (p17) and env (gp41) genes. In addition, 3 samples were sequenced in the gag (p17) gene only, and another 36 samples were sequenced in the env (gp41) gene only. The nucleotide sequences have been deposited in the GenBank under the following accession numbers: DQ056863 through DQ056984 (gp41) and DQ056985 through DQ057075 (p17). Phylogenetic analysis based on HIV-1 gag (p17) and env (gp41) sequences indicated that all analyzed sequences were classified as HIV-1 group M. HIV-1 group N or group O viruses were not found in these samples. Table 1 summarizes the genotyping results and indicates that HIV-1 CRF02_AG was dominant (69% in gag, 72% in env, and 60% in gag/env, respectively) in our study, followed by HIV-1 subtypes (15% in gag, 10% in env, and 5.7% in gag/env, respectively) and CRFs or URFs (15% in gag, 18% in env, and 34% in gag/env, respectively). Aghokeng et al1 also reported that 74% of the HIV-1 strains collected from blood donors in 7 localities in Cameroon in 2001 were CRF02_AG based on the sequences of gp41 gene. The prevalence of HIV-1 CRF02_AG is much lower in the general population in Cameroon, however, where HIV-1 CRF02_AG was identified in 20% to 32% of HIV-1-infected persons.2,3 HIV-1 CRF02_AG is also less prevalent in the surrounding countries, such as Congo (2.7%) and Central African Republic (2.6%), although a relatively high prevalence of 26% has been reported in Gabon.4TABLE 1: Genetic Subtypes in the gag and env Regions of HIV-1 Isolates From 2 Cities in CameroonWe also included in our analysis the recently listed reference strains of CRF17 to CRF33 at the Web site of Los Alamos National Laboratory (available at: http://www.hiv.lanl.gov/content/hiv-db/CRFs/CRFs.html). We thus identified CRF19_cpx- and CRF22_01A1-like sequences in 2 and 7 samples in gag (p17) gene, 2 and 4 samples in env (gp41) gene, and 0 and 4 in gag/env genes, respectively. Within the phylogenetic trees, CRF19_cpx-like sequences clustered together to form a separate branch, which is close to the CRF02_AG cluster. The branch of CRF22_01A1-like sequences was closer to the CRF01_AE cluster, but the CRF22_01A1 and CRF01_AE clusters were within the subtype A group of HIV-1. The homology of these CRF22_01A1 sequences was 80% in gag (p17) and 85% in env (gp41), respectively. Until now, CRF22_01A1 has been fully sequenced in 1 isolate (01CM001BBY, accession number AY371159) from Cameroon5 and is reported to contain portions of subtype A1 and to share ancestry with CRF01_AE, but the detailed mosaic structure has not been published. In our study, 4 samples were assigned to CRF22_01A1 in the gag and env genes, suggesting that CRF22_01A1 most likely contains genetic material of subtype A in gag (p17) and the gp41 region and providing further evidence of the existence of the new CRF22_01A1 in Cameroon. Unlike CRF22_01A1, the CRF19_cpx sequence was only identified in gag or env gene in 4 samples analyzed in our study. All 4 of these samples seemed to be infected with HIV-1 recombinant forms of CRF02_AG/CRF19_cpx. It must be noted that the full genomic sequence of CRF19_cpx was first characterized in Cuba but exhibits homology to partial sequences of the viruses from Cameroon, Gabon, Senegal, Chad, Niger, Central African Republic, and Congo.6 These results support the viewpoint that CRF18_cpx and CRF19_cpx may originate in Africa. Parallel phylogenetic analyses in the gag (p17) and env (gp41) genes revealed that 26.1% (23 of 88) of the sequences showed discordant subtypes in the 2 genes analyzed and were considered as URFs. Among them, 22 were identified as containing genetic material of at least 1 CRF in at least 1 gene, and were therefore considered as SGRs. The other URF identified was Agag/Denv. For the 22 SGRs identified in our study, 13 (59%) were the recombinants of CRF02_AG with HIV-1 subtype (A, B, D, and F2) or CRFs (CRF06_cpx, CRF11_cpx, CRF19_cpx, and CRF22_01A1). The remaining were recombinants of CRF06_cpx, CRF11_cpx, CRF13_cpx, and CRF22_01A1 (Table 2). Similar findings have been reported in Burkina Faso and Niger, where CRF02_AG/CRF06_cpx accounts for 6% to 9% of HIV-1 infections.7,8 CRF02_AG/CRF06_cpx and CRF02_AG/CRF09_cpx have been found in Côte d'Ivoire, and CRF07_BC/CRF08_BC has been found in China. Even CRF18_cpx and CRF19_cpx have been found to form new recombinants CRF18/CRF19 in Cuba.6 Our results are in agreement with those of previous studies and indicate that like HIV-1 subtypes in areas in which HIV-1 CRFs are endemic, CRFs are also involved in recombination events. The most striking observation in our study was the extremely high proportion (94%) of HIV-1 recombinants (CRFs or URFs) in our samples. Most of the recombinant forms contain the genetic material of CRF02_AG. The recombinants of CRF02_AG and HIV-1 subtypes A, C, G, H, and J have been reported in rural villages in the center, south, east, and west provinces of Cameroon.2 Consistent with these findings, our study further identified recombinants between CRF02_AG and subtypes B, D, and F2. We could also identify recombinants of CRF02_AG/CRF06_cpx in our study as well as several new URFs containing different CRFs, such as CRF02_AG/CRF11_cpx, CRF02_AG/CRF19_cpx, CRF02_AG/CRF22_01A1, CRF11_cpx/CRF22_01A1, and CRF06_cpx/CRF13_cpx. These results indicate that a second generation of recombinant forms of HIV-1 is emerging as a dominant recombination event in HIV-1 infection and highlight the importance of recombination of HIV-1 subtypes, especially the recombinant CRF02_AG, in blood donors in Cameroon.TABLE 2: Genotype Assignments of Partially Characterized Strains in CameroonIn summary, the results of this study further reveal the complexity of HIV-1 infection in blood donors from urban Cameroon, a region that is characterized by broad genetic diversity, the presence of different HIV-1 subtypes and recombinants, and the continuing emergence of new recombinants of HIV-1 as reflected by the identification of new recombinant strains in our study. The variation of HIV-1 in a population within a limited geographic area suggests the future complexity of the HIV-1 epidemic worldwide and the importance of continually monitoring current HIV-1 assays for sensitivity for HIV variants. Future investigations of HIV-1 variants should include studies on rural populations in Cameroon to evaluate further the extent of viral diversity in blood donors and patient populations. Ana Machuca, PhD* Shixing Tang, MD, PhD* Jinjie Hu, PhD* Sherwin Lee, BS* Owen Wood, PhD* Christopher Vockley, BS* Suresh Gupta Vutukuri, MS† Ranjana Deshmukh, MD, PhD† Bih Awazi, BS‡ Indira Hewlett, PhD* *Laboratory of Molecular Virology Division of Emerging and Transfusion Transmitted Diseases Center for Biologics Evaluation and Research US Food and Drug Administration Bethesda, MD †Haffkine Institute Mumbai, India ‡Mobile Laboratory Sanitation and Hygiene Administration of Health Laboratoire de Santé Hygiène MobileYaounde, Cameroon

The Human Immunodeficiency Virus 1 (HIV-1) is characterized by high rates of genetic diversity, being classified into groups, subtypes and recombinant forms. To date, 15 Circulating Recombinant Forms (CRFs) of subtypes B and C have been identified, three of them in 2021: CRF108_BC in Spain, CRF110_BC and CRF118_BC in China and one in 2024: CRF146_BC in Brazil. This study investigated the genetic diversity among circulating BC recombinant viruses. Near-Full Length Genomes (NFLG) of 229 BC strains were retrieved from the Los Alamos database. Recombination and phylogenetic analysis were conducted using bioinformatics tools. Sequences were obtained from 17 countries between 1992 and 2022. Fifteen CRFs and 81 distinct Unique Recombinant Forms (URFs) recombination patterns were identified. Preferential recombination points were found in pol (66.7%) and env (62.5%) genes, while subtype C is the predominant genetic form in gag, vif, vpr, tat, rev, tat2, rev2, nef and 3'-LTR genomic regions. Specific positions in pol and env genes maintain the B subtype, which may be related to the acquisition of adaptive advantage over subtype C.

BackgroundSichuan province is one of the highest AIDS epidemic provinces in China, with a large number of floating population. The annual number of cases of HIV/AIDS reported in Sichuan has been the highest province in China for several successive years. There is a lack of widespread and representative data on the distribution of HIV genotypes in Sichuan. We aim to investigate the characteristics of HIV-1 molecular epidemiology and transmitted drug-resistance in newly diagnosed HIV-infected patients in Sichuan, China.MethodArchived plasma samples (n = 1524) from HIV-1 newly-diagnosed individuals in April 2019 were selected by cross-sectional investigation from all 21 cities in Sichuan province. Phylogenetic relationship, transmission cluster, and genotypic drug resistance analyses were performed using HIV-1 polymerase (pol) gene sequences. We also analysed the association of demographic and virological factors with transmitted drug-resistance (TDR) and transmission clusters.ResultsPartial pol gene sequences were obtained from 1297 cases. HIV-1 epidemic strains in Sichuan province: the majority of genotypes were circulating recombinant form (CRF) 07_BC (675, 52.04%), CRF01_AE (343, 26.45%), CRF08_BC (115, 8.87%), CRF85_BC (67, 5.17%), subtype B (33, 2.54%), the other genotypes only accounted for 4.93%, and unique recombinant forms (URFs) (23, 1.77%) were observed in the study, and the difference of age, ethnicity, education, occupation, region and transmission pathway of different genotypes were statistically significant. According to WHO HIVDR surveillance threshold, the level of TDR has reached a medium level, with 72 of 1297 (5.55%) cases carrying drug-resistance mutation sites, TDR mutation frequency to nonnucleoside reverse transcriptase inhibitors (NNRTIs, 3.85%) was much higher than nucleoside reverse transcriptase inhibitors (NRTIs, 0.31%) and protease inhibitors (PIs, 1.70%), and CRF08_BC was a risk factor for TDR (odds ratio, 8.32; 95% CI 4.38–15.80 for CRF07_BC, P < 0.05). The most common drug resistance HIV-1 mutation pattern for NNRTI was V106 (1.31%, 17/1297) and E138 (1.16%, 15/1297), and for PI was M46 (0.69%, 9/1297). A total of 205 (15.8%) pol sequences were involved in the genetic transmission network clusters, CRF01_AE (odds ratio, 2.369; 95% CI 1.659–3.382; P < 0.05), subtype B (odds ratio, 13.723; 95% CI 6.338–29.71; P < 0.05), drug resistance (odds ratio, 0.306; 95% CI 0.106–0.881; P < 0.05) and different levels of education (P < 0.05) were significantly associated to be in clusters.ConclusionThe distribution of HIV-1 genotypes in Sichuan is more diverse and complex, and the Men who have sex with men (MSM) is underrated, arguing for behavior scaling up intervention in this specific population besides the elderly people with heterosexual transmission risk groups. The risk of TDR mutation frequency increased in newly diagnosed patients highlights the significance of genotypic drug resistance monitoring and molecular surveillance of pretreatment HIV-1 drug resistance. The regimen composed of TDF, 3TC and EFV was still currently the preferred solution used free first-line therapy.

Objective. This study aims to characterize the 20-year trends in human immunodeficiency virus 1 (HIV-1) subtypes and circulating recombinant forms (CRFs) in China, as well as patterns of transmitted drug resistance (TDR) to antiretroviral therapies commonly used in clinical practice.Methods. We analysed HIV-1 sequences from 81,563 individuals living in China between 2003 and 2024. Subtypes and CRFs were classified using COMET V2.4. Among these, pol gene sequences from 41,486 treatment-naïve individuals were used to assess TDR via the Stanford HIVdb genotypic resistance interpretation program.Results. Over the past two decades, CRF01_AE (43.9%) was the most prevalent HIV-1 strain in China, followed by CRF07_BC (19.0%), subtype B (12.3%), subtype C (8.4%) and CRF08_B (4.9%). However, subtype and CRF distributions varied considerably across provinces. CRF01_AE predominated in provinces such as Liaoning (92.4%), Guangxi (58.7%), Beijing (47.7%) and Hainan (44.8%), while CRF07_BC was dominant in Sichuan (63.6%), Chongqing (53.2%) and Xinjiang (82.7%). TDR analysis revealed elevated resistance to non-nucleoside reverse transcriptase inhibitors in certain provinces, including Yunnan (12.4%), Xinjiang (8.2%), Anhui (7.6%) and Henan (6.7%). In contrast, resistance to nucleoside reverse transcriptase inhibitors and integrase inhibitors remained low (<1%) across all regions. Notably, the TDR rate exceeded 5% for several regimens freely provided in China, including AZT+3TC+NVP (6.8%), AZT+3TC+RPV (8.0%), AZT+3TC+EFV (6.4%), TDF+3TC+NVP (6.0%), TDF+3TC+RPV (7.2%) and TDF+3TC+EFV (5.7%).Conclusion. Continued surveillance of HIV-1 genotypes and CRFs is critical, particularly in regions where routine genotypic testing is not implemented. Personalized antiretroviral regimens are urgently needed in regions with high levels of TDR.

Drug resistance mutations (DRMs) may reduce the efficacy of antiviral therapy. However, the studies focused on naturally occurring, pre-existing DRMs among co-infected patients in China are limited. To investigate DRMs prevalence in treatment-naïve human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) mono- and co-infected patients in China, a total of 570 patients were recruited for this study. DRMs sequences were amplified and successfully sequenced in 481 of these patients, who were grouped into three cohorts: (i) The HBV cohort included 100 HIV/HBV co-infected and 110 HBV mono-infected patients who were sequenced for HBV; (ii) The HCV cohort included 91 patients who were HIV/HCV co-infected and 72 who were HCV mono-infected for HCV sequencing; and (iii) The HIV cohort included 39 HIV mono-infected, 22 HIV/HCV, and 47 HIV/HBV co-infected patients for HIV sequencing. Next-generation sequencing and Sanger sequencing were used in this study. The results showed that in the HCV cohort, HCV genotypes 6a (P < 0.001) and 3b (P = 0.004) were more prevalent in HIV/HCV co-infected patients, however, the prevalence of HBV and HIV genotypes were similar within the HBV and HIV cohorts. HBV DRMs prevalence was significantly higher in HIV/HBV co-infected than HBV mono-infected patients (8.0% vs 0.9%, P = 0.015), whereas HCV and HIV DRMs did not differ within the HCV and HIV cohort (P > 0.05). This study revealed that HBV DRMs were more prevalent in HIV/HBV co-infected patients in China, while DRMs in HCV and HIV patients did not differ. Further dynamic surveillance of DRMs may be needed.

Objective To investigate the genetic variations of gag-pol gene in human immunodeficiency virus-1(HIV-1) CRF07_BC strain in Guangdong Province. Methods From February to September in 2015, plasma samples of 78 cases with HIV-1 CRF07_BC infection in Guangdong were collected before antiretroviral treatment. Viral RNA was extracted from plasma. Gene (gag and pol) sequences were amplified by reverse transcriptase and nested-PCR using specific primers. Phylogenetic tree, genic dispersion rate, nucleotide polymorphism, selection pressure and variation characteristics were analyzed. Results The main transmission route of the enrolled patients was homosexual transmission (80.77%, 63/78). The gag-pol gene phylogenetic tree was divided into two sub-clusters. The strains from different transmission routes were not in cluster. The average genetic dispersion rate and average entropy of gag gene were both higher than those of pol gene. The average genetic dispersion and average entropy of p17 and p6 regions of gag gene were both higher than those of p24. The average genetic dispersion and average entropy of pol gene were higher than those of rt region. The average ds/dn values of gag and pol genes were greater than one. Compared with the common HIV-related antigenic epitopes (A2, A11, B39, B60, Cw1, Cw3, Cw8), the cytotoxic lymphocyte (CTL) epitope mutations in the P17 region were more in the consensus of GAG region than those in the P24 region. The epitope conserved rates were 26.92%, 0, 1.28%, 0, 96.15%, 82.05%, 84.62% and 98.72%, respectively. The drug resistance rate of pol gene was 2.56% (2/78). Conclusions The gag and pol genes of CRF07_BC strain in Guangdong are all mutated. Diversity of gag gene is greater than that of pol gene, and gag gene variation is mainly in p17 and p6 regions. gag and pol genes are both affected by negative selection pressure. P17 protein CTL epitope variability is greater than P24 protein epitope. The prevalence of drug resistance mutation is lower than the threshold. It’s important to monitor the spread of drug-resistant strains. Key words: HIV-1; Epidemiology, molecular; CRF07_BC; Drug resistant mutations

The genetic diversity of human immunodeficiency virus-1 (HIV-1) in China is characterized by multiple subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs) across the country. Through timely molecular surveillance, over 65 distinct CRFs have been identified in China to date. In this study, we identified five novel URFs among newly reported HIV-1 infected individuals in Anhui Province, China. Near-full length HIV genome sequences were obtained using two-half molecule amplification methods from five samples containing potential URFs. The sequences were subsequently subjected to phylogenetic and recombination analyses. Phylogenetic and recombination analyses of the five near-full length genome sequences confirmed their classification as novel URFs. Among these, three sequences were recombinants of CRF01_AE and CRF07_BC, one sequence was a recombinant of CRF01_AE, CRF07_BC and B, and one sequence resulted from CRF07_BC and CRF08_BC recombination. The identification of URFs in newly infected individuals indicates ongoing transmission of multiple HIV-1 clades in Anhui Province, with superinfection occurring at notable frequencies. These findings emphasize the importance of enhancing long-term surveillance of circulating HIV-1 clades using near-full length sequence analysis in Anhui, China.

Global and regional epidemiology of HIV-1 recombinants in 1990–2015: a systematic review and global survey