The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s

Analysis of the Driving Factors of Active and Rapid Growth Clusters Among CRF07_BC-Infected Patients in a Developed Area in Eastern China

Background

The purpose of this study was to research the molecular transmission and genetic evolutionary characteristics among CRF07_BC-infected patients in a developed area in Eastern China.

Methods

Plasma samples from newly diagnosed HIV-1-positive patients from 2015–2018 and basic demographic and epidemiological information were obtained. Pol sequences from CRF07_BC-infected patients were selected for phylogenetic, molecular transmission network, and Bayesian evolutionary analyses.

Results

Pol sequences were successfully obtained from 258 samples of CRF07_BC. Phylogenetic analysis revealed 2 distinct lineages: lineage 1 (66.3%, 171/258), primarily from men who have sex with men (MSM) and some heterosexual individuals, and lineage 2 (33.7%, 87/258), primarily from heterosexual individuals. Under an optimal genetic distance of 0.01 substitutions/site, 163 individuals (63.2%, 163/258) formed 23 groups comprising 6 clusters and 17 dyads in the networks. A distinctly large and rapidly growing cluster (C1) containing 105 individuals was identified, in which MSM with ≥4 links had quite a high transmission risk (low educational background, active sexual behavior, low sexual protection awareness, etc.). According to Bayesian analyses, most C1 clades formed from 2005 to 2009, most of which were closely geographically related to CRF07_BC epidemic strains from Anhui province.

Conclusions

Here, we elucidated the local transmission characteristics and epidemic pattern of HIV-1 CRF07_BC, revealing that MSM (especially with ≥4 links) may be a significant driver in the formation of active and rapid growth networks in regional CRF07_BC epidemics. Thus, unique region– and risk group–specific transmission network analysis based on a molecular approach can provide critical and insightful information for more effective intervention strategies to limit future HIV-1 transmission.

Intrapatient Evolutionary Dynamics in an Individual Infected with HIV-1 CRF01_AE Who Experienced Periods of Treatment Failure

Although previous studies have analyzed cross-level CRF01_AE viral genomic data in populations, less is known about intrapatient viral evolutionary dynamics during antiretroviral therapy (ART) failure. We longitudinally sampled plasma and peripheral blood mononuclear cells (PBMC) at different time points from one human immunodeficiency virus type 1 infected patient. The evolution of viral quasispecies was inferred from viral phylogenies. Before treatment, no drug-resistant mutations were found in this patient's plasma, and all viruses had C-C chemokine receptor type 5 (CCR5) tropism. Two months after treatment, the majority of the virus population in plasma and PBMC were drug resistant and X4-tropic. By 5 months after treatment, the viral load increased significantly, and viruses reversed tropism from X4 to R5 in plasma and PBMC. During treatment failure, the effective population of the pol DNA reservoir in PBMC remained stable, whereas the env DNA reservoir increased. The effective population of the R5 tropism virus increased more rapidly than that of the X4 tropism virus. The ratio of non-synonymous to synonymous substitutions in the env gene of R5 tropism virus (0.43) was lower than X4 tropism (0.52). However, four env positive selection sites were identified in R5 tropism viruses (HXB2: 364, 398, 399, and 400) but none were identified in X4 tropism viruses. Our data demonstrated the different intrapatient evolutionary dynamics patterns of env and pol genes in an individual who experienced periods of ART failure. Our findings also suggest the importance of the R5 tropism virus in the DNA reservoir during ART failure.

Increase in HIV-1-transmitted drug resistance among ART-naïve youths at the China-Myanmar border during 2009 ~ 2017

Background

HIV-transmitted drug resistance (TDR) is found in antiretroviral therapy (ART)-naïve populations infected with HIV-1 with TDR mutations and is important for guiding future first- and second-line ART regimens. We investigated TDR and its effect on CD4 count in ART-naïve youths from the China-Myanmar border near the Golden Triangle to better understand TDR and effectively guide ART.

Methods

From 2009 to 2017, 10,832 HIV-1 infected individuals were newly reported along the Dehong border of China, 573 ART-naïve youths (16 ~ 25 y) were enrolled. CD4 counts were obtained from whole blood samples. HIV pol gene sequences were amplified from RNA extracted from plasma. The Stanford REGA program and jpHMM recombination prediction tool were used to determine genotypes. TDR mutations (TDRMs) were analyzed using the Stanford Calibrated Population Resistance tool.

Results

The most common infection route was heterosexuals (70.51%), followed by people who inject drugs (PWID, 19.20%) and men who have sex with men (MSM) (8.90%). The distribution of HIV genotypes mainly included the unique recombinant form (URF) (44.08%), 38.68% were CRFs, 13.24% were subtype C and 4.04% were subtype B. The prevalence of TDR increased significantly from 2009 to 2017 (3.48 to 9.48%) in ART-naïve youths (4.00 to 13.16% in Burmese subjects, 3.33 to 5.93% in Chinese subjects), and the resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) were 3.49, 2.62, and 0.52%, respectively. Most (94.40%, n = 34) of HIV-1-infected patients with TDRM had mutation that conferred resistance to a single drug class. The most common mutations Y181I/C and K103N, were found in 7 and 9 youths, respectively. The mean CD4 count was significantly lower among individuals with TDRMs (373/mm³ vs. 496/mm³, p = 0.013).

Conclusions

The increase in the prevalence of HIV-1 TDR increase and a low CD4 count of patients with TDRMs in the China-Myanmar border suggests the need for considering drug resistance before initiating ART in HIV recombination hotspots.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05794-5.

Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria

HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little is known about the molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1995 and 2019. Using network analyses at a 1.5% genetic distance threshold (d), we found a large 154-member outbreak cluster composed mostly of persons who inject drugs (PWID) that were predominantly men. At d = 0.5%, which was used to identify more recent transmission, the large cluster dissociated into three clusters of 18, 12, and 7 members, respectively, five dyads, and 107 singletons. Phylogenetic analysis of the Bulgarian sequences with publicly available global sequences showed that CRF01_AE likely originated from multiple Asian countries, with Vietnam as the likely source of the outbreak cluster between 1988 and 1990. Our findings indicate that CRF01_AE was introduced into Bulgaria multiple times since 1988, and infections then rapidly spread among PWID locally with bridging to other risk groups and countries. CRF01_AE continues to spread in Bulgaria as evidenced by the more recent large clusters identified at d = 0.5%, highlighting the importance of public health prevention efforts in the PWID communities.

Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China

The CRF01_AE and CRF07_BC clades dominate the human immunodeficiency virus (HIV) epidemics in China. Both clades have been identified in the men who have sex with men (MSM) population in Guangdong province, raising a serious concern of possible complex recombination events ahead. Here, we report the first case of CRF01_AE/CRF07_BC recombinant sampled from a MSM patient in southern China. The genomic structure of this case is a mosaic with some regions resembling the CRF01_AE and CRF07_BC clades. Our phylogenetic analyses show that the two parental lineages of this recombinant virus were mainly found in the MSM population. This case has a different genomic composition compared with other recombinants descended from the same parental clades CRF01_AE and CRF07_BC. Our finding suggests that the MSM populations have become a hotspot for expanding viral diversity through the viral recombination mechanism. Therefore, further epidemiologic surveillance and monitoring should be conducted within the MSM populations to help advance our knowledge of viral transmission mechanisms. Additionally, these measures will serve to enhance the control and prevention of HIV/acquired immunodeficiency syndrome in China.

Characterization of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Strain Among Men Who Have Sex with Men in Liaoning, China

CRF01_AE and CRF07_BC are two widespread human immunodeficiency virus type 1 (HIV-1) strains among different high-risk populations, including men who have sex with men (MSM), in China. This co-epidemic of various HIV strains enables the production of second-generation recombinants. In this study, we detected a novel HIV-1 CRF01_AE/CRF07_BC recombinant from LN321945, an MSM lived in Liaoning province, northeast China. The phylogenetic and recombination analyses indicated the near full-length genome (NFLG) sequence of LN321945 had six recombination breakpoints, with three CRF07_BC fragments inserted into a CRF01_AE backbone. Further subregion trees analysis revealed that both CRF01_AE and CRF07_BC fragments were derived from two predominant HIV-1 strains among MSM. In addition, the NFLG of LN321945 was revealed to be clustered closely to another CRF01_AE/CRF07_BC recombinant previously identified in Shaanxi province, northwest China, but these two recombinants had distinct recombination structure and origin of CRF01_AE fragments. Hence, this study identified a second-generation recombinant between the main strains circulating among MSM, indicating more complicated trend of HIV-1 epidemic in China.

Complicated genotypes circulating among treatment naïve HIV-1 patients in Guangzhou, China

Guangzhou city is the political, economic, and cultural center of the Guangdong Province, China. The molecular epidemiological characteristics of HIV-1 in Guangzhou are not widely known. The aim of this study was to explore the characteristics of HIV-1 genotypes among treatment naïve HIV/AIDS patients living in Guangzhou. HIV-1 RNA was extracted from serum specimens. The partial pol gene of the HIV-1 genome was amplified and sequenced. The genotypes were screened using the subtyping tool COMET and further confirmed by phylogenetic analysis, with the exception of the URFs that were analyzed by jpHMM and RIP. The distributions of HIV genotypes in different risk populations were analyzed. Subsequently, pol sequences were used to construct transmission networks and analyze drug resistance. Twelve HIV-1 genotypes including 3 subtypes and 9 CRFs, with several URFs were identified from 1388 HIV-1 sequences, which were derived from 1490 patients. The main genotypes circulating in Guangzhou were CRF07_BC (38.3%), CRF01_AE (32.3%), and CRF55_01B (10.7%). CRF01_AE was the secondary dominant strain and multiple lineages of CRF01_AE had been identified in Guangzhou. The 01B recombinant forms, including CRF55_01B, CRF59_01B and CRF68_01B, have circulated widely in Guangzhou. 42.22% (586/1388) of the study sequences fell into 143 transmission networks, and the three main clusters revealed that sequences from MSM and HET populations were intermixed. 5.40% (75/1388) of patients had pre-treatment drug resistance. The HIV-1 strains that were present in Guangzhou have demonstrated complex genotypes. Particular attention should be given on these genotypes for the further strategy of prevention and intervention of HIV transmission.

HIV-1 Genetic Diversity and High Prevalence of Pretreatment Drug Resistance in Tianjin, China

Diversity of genotypes and prevalence of pretreatment drug resistance (PDR) are challenges for the epidemic control and vaccine development of HIV-1. However, little is known about the situation in Tianjin. Blood samples were collected from newly diagnosed, antiretroviral treatment (ART)-naive HIV/AIDS patients from January 2016 to November 2019. The target fragment in the pol gene was sequenced after RNA extraction and gene amplification. The HIV-1 genotype was identified by phylogenetic analysis. Drug resistance was carried out using the Stanford University HIVdb algorithm. A total of 305 pol sequences from 279 non-PDR individuals and 35 PDR individuals were successfully amplified. The most prevalent genotype was CRF01_AE (65.6%, 200/305), followed by CRF07_BC (22.0%, 67/305) and B (3.0%, 9/305). A variety of circulating recombinant forms (CRFs) and unique recombinant forms were found. The overall incidence of PDR was 11.5% (35/305), with 9.8% (30/305) to non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs). The most frequent mutation pattern against NNRTIs was V179D/E/T (6.9%, 21/305), with M184V (1.0%, 3/305) and K65R (1.0%, 3/305) against nucleoside RT inhibitors (NRTIs). M64L (0.1%, 1/305) was the sole mutation found against protease inhibitors (PIs). Eight variants generated at least low-level resistance to NNRTIs (2.6%, 8/305), which was much higher than that to NRTIs (1.6%, 5/305) and PIs (0/305) (p < .05). Genotypic drug resistance testing before initiating ART in newly diagnosed HIV/AIDS patients may be necessary in Tianjin, China. The non-NNRTI-based regimen may be preferred as initial therapy in Tianjin.

Effects of HIV-1 genotype on baseline CD4+ cell count and mortality before and after antiretroviral therapy

To assess whether human immunodeficiency virus type 1 (HIV-1) genotype influences baseline CD4+ T lymphocyte (CD4+) cell count and mortality of patients. The study was conducted from 2014 to 2019 in Guangxi, China, and included 2845 newly diagnosed HIV patients. We used a median regression model to compare CD4+ cell counts in patients newly diagnosed with different HIV-1 genotypes, and a Cox regression model to analyze the associations between HIV-1 genotypes and mortality before and after antiretroviral treatment (ART). In newly diagnosed HIV patients, the baseline CD4+ cell counts of patients with CRF01_AE were significantly lower than those of patients with CRF07_BC, CRF08_BC, and other genotypes. Compared with CRF01_AE, patients infected with CRF07_BC (hazard ratio, 0.55; 95% CI 0.36–0.85), CRF08_BC (hazard ratio, 0.67; 95% CI 0.52–0.85), or other genotypes (hazard ratio, 0.52; 95% CI 0.29–0.94) had significantly lower mortality rates before ART. There were no significant associations between different HIV-1 genotypes and mortality after ART. HIV-1 genotype significantly influences baseline CD4+ cell count and mortality before ART in newly diagnosed HIV patients. We find no significant difference in the outcome of death after ART in patients with different HIV-1 genotypes.

First Detection of a Circulating Recombinant Form of HIV-1 CRF01_AE/08_BC (CRF105_0108) with Drug-Resistant Mutations in Sichuan, China

In this study, we identified a novel circulating recombinant form (CRF) of HIV (CRF105_0108) in a total of five patients with no obvious epidemiological linkage in Sichuan, China. Four strains were found in this study, and another strain (XC2014EU01) was reported in a previous study. The phylogenetic analysis of the five near full-length genomes showed that a CRF08_BC segment was inserted into the CRF01_AE backbone with one recombinant breakpoint in the pol region, which is the first HIV-1 CRF of CRF01_AE and CRF08_BC. Three genetic sequences had drug-resistant mutations, E138Q and V179D, indicating that there were low resistance levels to efavirenz (EFV) and nevirapine (NVP) in Liangshan Yi Autonomous Prefecture. CRF105_0108 increases the diversity and complexity of the prevalent HIV-1 CRFs in Sichuan. Simultaneously, drug-resistant mutations in this CRF may influence the efficacy of highly active antiretroviral treatments (ARTs) in Liangshan Yi Autonomous Prefecture.

New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination

Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important strain, we sequenced near complete genomes from HIV samples with subgenomic CRF01_AE regions collected in Cameroon and the Democratic Republic of the Congo from 2001 to 2006. HIV genomes were generated from N = 13 plasma specimens by next-generation sequencing of metagenomic libraries prepared with spiked primers targeting HIV, followed by Sanger gap-filling. Genome sequences were aligned to reference strains, including Asian and African CRF01_AE sequences, and evaluated by phylogenetic and recombinant analysis to identify four CRF01_AE strains from Cameroon. We also identified two CRF02, one CRF27, and six unique recombinant form genomes (01|A1|G, 01|02|F|U, F|G|01, A1|D|01, F|G|01, and A1|G|01). Phylogenetic analysis, including the four new African CRF01_AE genomes, placed these samples as a bridge between basal Central African Republic CRF01_AE strains and all Asian, European, and American CRF01_AE strains. Molecular dating confirmed previous estimates indicating that the most recent common CRF01_AE ancestor emerged in the early 1970s (1968–1970) and spread beyond Africa around 1980 to Asia. The new sequences and analysis presented in this study expand the molecular history of the CRF01_AE clade, and are illustrated in an interactive Next Strain phylogenetic tree, map, and timeline at (https://nextstrain.org/community/EduanWilkinson/hiv-1_crf01).

Impact of the expression system on the immune responses to self-assembling protein nanoparticles (SAPNs) displaying HIV-1 V1V2 loop

The V1V2 loop of the Env protein is a major target for HIV-1 vaccine development because in multiple studies antibodies to this region correlated with protection. Although SAPNs expressed in E. coli elicited anti-V1V2 antibodies, the Env protein is heavily glycosylated. In this study the technology has been adapted for expression in mammalian cells. SAPNs containing a V1V2 loop from a B-subtype transmitter/founder virus were expressed in E. coli, ExpiCHO, and Expi293 cells. Independent of the expression host, particles were well-formed. All SAPNs raised high titers of V1V2-specific antibodies, however, SAPN_E.coli induced a mainly anti-V1 response, while SAPN_ExpiCHO and SAPN_Expi293 induced a predominantly anti-V2 response. In an ADCP assay, sera from animals immunized with the SAPN_ExpiCHO or SAPN_Expi293 induced a significant increase in phagocytic activity. This novel way of producing SAPNs displaying glycosylated epitopes could increase the antibody titer, functional activity, and shift the immune response towards the desired pathway.

Near Full-Length Genomic Characterization of a Novel Unique Recombinant (CRF01_AE/CRF07_BC) in Fuyang City of China

Recombinant forms contribute substantially to the genetic diversity of HIV-1. Recent studies have also revealed that three major viral strains (CRF07_BC, CRF01_AE, and subtype B) have been cocirculating among men who have sex with men (MSM) in Anhui, suggesting a high probability of generating new recombinants. In this study, we reported a novel CRF01_AE and CRF07_BC HIV-1 recombinant form in MSM in Fuyang city of China. Two near full-length genome (NFLG) named FY184 and FY208 were successfully obtained. The genomic composition analysis of the NFLG reveals that it was divided into four segments by three breakpoints, with two regions of CRF07_BC inserted into a CRF01_AE backbone's gag and pol regions. The CRF01_AE regions were originated from a subcluster lineage of CRF01_AE, which is mainly circulating among MSM in China. The emergence of a novel recombinant of CRF01_AE/CRF07_BC is indicative of the increasing genetic diversity of the HIV epidemic in MSM in Anhui.

The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals

HIV has remarkable genetic diversity among populations. The diversity has critical impacts on transmission, immune escape, pathogenesis, and clinical management. HIV-1 diversity originates from frequent mutation and recombination during reverse transcription. This work focuses on the quasispecies genetic dynamics within individuals with primary infections. Eleven men who have sex with men from the Beijing PRIMO Clinical Cohort were identified as primary infection and had three or four series of their anticoagulant blood samples collected. Viral RNA was extracted and amplified using single-genome amplification. Products of the gp120 gene that met single-genome amplification requirements were sequenced. Subtype assortment of all collected sequences was performed using both the jumping profile hidden Markov model (jpHMM) and REGA. Quasispecies diversity at each time was estimated using Mega 6. Intrapatient recombination was analyzed using RDP4. According to the Fiebig classification system, YA-81 belongs to stage III and YA-113 belongs to stage IV. The other samples are all associated with the infection stage of V/VI. YA113 had a dual infection with subtype B and a new unique recombinant form involving CRF01_AE and C. The other eight were infected with CRF01_AE, one was infected with B/C recombinant, and the last one with B. Of the 10 single infections, 8 were caused by 1 founder virus. They all displayed a sharp increase of quasispecies diversity during the sampling times. Two were caused by at least two founder viruses. The diversity of these strains starts at a significantly high level and is followed by a relatively steady trend. Critically, the separate subtypes YA113-B and YA113-CRF01_AE/C both showed a similar trend to those infected by a single founder virus. Recombination analysis revealed that 5 of 11 cases underwent detectable intrapatient recombination. These findings indicate that tracing the dynamics of HIV-1 quasispecies during early infection may be relevant and valuable for understanding pathways of viral diversification and immune escape.

Prevalence of HIV-1 Drug-Resistance Genotypes Among Unique Recombinant Forms from Yunnan Province, China in 2016-2017

To investigate the prevalence and characteristics of drug-resistance genotypes among unique recombinant forms (URFs) in HIV-1 infected people under long-term antiretroviral treatment failure from Yunnan Province. The plasma samples were collected from antiretroviral therapy (ART)-failure experienced individuals from 2016 to 2017 in Yunnan Province, China. The genotyping drug resistance of HIV-1 pol gene fragments was implemented using in-house assay. According to the analysis of RIP and MEGA 7.0, the HIV-1 strains related to URFs were screened for recombinant identification and drug resistance analysis. A total of 130 pol sequences of HIV-1 URF strains were obtained from 1,121 samples. The proportion of HIV-1 URF strains was 11.6% among the ART-failure individuals from 2016 to 2017 in Yunnan. The overall drug-resistance rate of HIV-1 URF strains was 56.9%. Meanwhile, the percentage of protease inhibitors, nucleoside reverse transcriptase inhibitors (NRTIs), and non-nucleoside reverse transcriptase inhibitors (NNRTIs) resistance was 3.8% (5/130), 36.2% (47/130), and 53.8% (70/130), respectively. Mutations such as M184V/I (35.4%) in NRTIs and K103N/R/S/T (25.4%), V179D/E/T/Y (18.9%), G190A/E/R/S (13.8%), and Y181C (9.2%) in NNRTIs were common among the HIV-1 URF strains relative to other mutations. Factors such as male, sexual transmission pathway, and source of the year 2017 were significantly correlated with the development of HIV-1 URF drug resistance. The emergence of the multiple recombinant forms identified in Yunnan indicates active transmission networks of HIV-1 of different HIV-1 subtype/circulating recombinant forms cross-infection in this region. Therefore, it is necessary to further monitor the molecular epidemiology and drug resistance of HIV-1 in Yunnan.

Natural presence of the V179D and K103R/V179D mutations associated with resistance to nonnucleoside reverse transcriptase inhibitors in HIV-1 CRF65_cpx strains

BACKGROUND

There is increasing evidence that HIV-1 genetic diversity can have an impact on drug resistance. The aim of this study is to investigate the epidemiological situation of CRF65_cpx and the impact of natural polymorphisms of this variant on genotypic resistance.

METHODS

We used the BLAST search program followed by phylogenetic analysis to identify additional CRF65_cpx pol sequences from the Los Alamos HIV Sequence Database. Maximum likelihood phylogeny was estimated to clarify the epidemiological relationship of CRF65_cpx strains. Genotypic resistance was determined by submitting sequences to the Stanford HIV Drug Resistance Database.

RESULTS

A total of 32 CRF65_cpx pol sequences were obtained. The CRF65_cpx strains were detected in seven provinces with large geographic distance. Yunnan CRF65_cpx sequences were mainly derived from a heterosexual risk group, whereas the CRF65_cpx sequences in other provinces were almost exclusively derived from an MSM population. With one exception of V179E, the other 31 strains harbored V179D mutation. The combination of V179D and K103R, conferring intermediate resistance to EFV and NVP, was detected in seven treatment-naive MSM patients.

CONCLUSIONS

This study confirmed the expansion CRF65_cpx in China. Furthermore, we found the natural presence of the V179D and K103R/V179D mutations associated with resistance to NNRTIs in HIV-1 CRF65_cpx. Our findings highlight the contribution of polymorphic mutations to drug resistance and underscore the challenges in treating patients harboring CRF65_cpx strains.

HIV-1 Drug Resistance, Distribution of Subtypes, and Drug Resistance-Associated Mutations in Virologic Failure Individuals in Chengdu, Southwest China, 2014-2016

The National Free Antiretroviral Therapy (ART) Program in China has initiated to provide ART to HIV-1 patients, which has acted as an efficient method to suppress viral replication and helps prevent onward transmissions. But the problems of HIV drug resistance (HIVDR) may also come along. There is little data on the prevalence of HIVDR in Chengdu, where the number of HIV/AIDS patients ranks first among provincial capitals. Therefore, epidemiological surveillance was conducted in this area. From 2014 to 2016, HIV/AIDS patients (15 years and older) who had received first-line ART for at least six months were enrolled. Demographic, behavioral information and medical history were recorded, and blood samples were collected for viral loads and immune cell count analyses. HIV-1 pol was obtained for HIV-1 subtypes and drug resistance-associated mutations (DRMs) among virologic failure patients. A total of 13,782 individuals were enrolled, and 481 samples were sequenced for subtypes and drug resistance analysis. Six subtypes were identified, among which CRF01_AE (54.3%) and CRF07_BC (41.6%) were the dominant subtypes, and CRF55_01B (0.4%) was detected in Chengdu for the first time. The prevalence of HIVDR in treatment-experienced patients was 1.8%, with 1.2% to nucleoside reverse transcriptase inhibitors (NRTIs), 1.7% to non-NRTIs (NNRTIs), and 0.14% to protease inhibitors (PIs). The leading DRMs observed in the study were M184I/V (59.59%) against NRTIs and K103N (37.55%) against NNRTIs. This study focused on the HIVDR surveillance among patients receiving treatment in Chengdu. The overall prevalence of HIVDR was relatively low among treated patients. These findings were believed to be contributed to an understanding of HIV-1 subtypes, HIVDR prevalence, and DRMs in Chengdu and thereby optimizing clinical management, prevention, and control of HIV.

Genome Sequence of a Novel HIV-1 Circulating Recombinant Form (CRF103_01B) Identified from Hebei Province, China

We reported a novel HIV-1 circulating recombinant form (CRF) among three epidemiologically unlinked patients through men having sex with men in Hebei Province, China. It was named CRF103_01B (this is temporary as we have not received the CRF number from HIV databases). A near full-length genome phylogenetic tree showed that CRF103_01B was generated by three B (Western origin) segments and CRF01_AE that was described as cluster 5 lineage of CRF01_AE (CRF01-5). The emergence of CRF103_01B increased the complexity of the HIV-1 epidemic in China.

Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China

BACKGROUND

The impacts of genetic polymorphisms on drug resistance mutations (DRMs) among various HIV-1 subtypes have long been debated. In this study, we aimed to analyze the natural polymorphisms and acquired DRM profile in HIV-1 CRF01_AE-infected patients in a large first-line antiretroviral therapy (ART) cohort in northeastern China.

METHODS

The natural polymorphisms of CRF01_AE were analyzed in 2034 patients from a long-term ART cohort in northeastern China. The polymorphisms in 105 treatment failure (TF) patients were compared with those in 1148 treatment success (TS) patients. The acquired DRM profile of 42 patients who experienced TF with tenofovir/lamivudine/efavirenz (TDF/3TC/EFV) treatment was analyzed by comparing the mutations at TF time point to those at baseline. The Stanford HIVdb algorithm was used to interpret the DRMs. Binomial distribution, McNemar test, Wilcoxon test and CorMut package were used to analyze the mutation rates and co-variation. Deep sequencing was used to analyze the evolutionary dynamics of co-variation.

RESULTS

Before ART, there were significantly more natural polymorphisms of 31 sites on reverse transcriptase (RT) in CRF01_AE than subtype B HIV-1 (|Z value| ≥ 3), including five known drug resistance-associated sites (238, 118, 179, 103, and 40). However, only the polymorphism at site 75 was associated with TF (|Z value| ≥ 3). The mutation rate at 14 sites increased significantly at TF time point compared to baseline, with the most common DRMs comprising G190S/C, K65R, K101E/N/Q, M184 V/I, and V179D/I/A/T/E, ranging from 66.7 to 45.2%. Moreover, two unknown mutations (V75 L and L228R) increased by 19.0 and 11.9% respectively, and they were under positive selection (Ka/Ks > 1, log odds ratio [LOD] > 2) and were associated with several other DRMs (cKa/Ks > 1, LOD > 2). Deep sequencing of longitudinal plasma samples showed that L228R occurred simultaneously or followed the appearance of Y181C.

CONCLUSION

The high levels of natural polymorphisms in CRF01_AE had little impact on treatment outcomes. The findings regarding potential new CRF01_AE-specific minor DRMs indicate the need for more studies on the drug resistance phenotype of CRF01_AE.

HIV-1 genetic diversity and recombinant forms among men who have sex with men at a sentinel surveillance site in Xi'an City, China

HIV-1 genetic distribution and recombinant patterns are important in understanding the HIV epidemic among men who have sex with men (MSM). In this study, 83 HIV-positive MSM infections were confirmed at a sentinel surveillance site in Xi'an city, China in 2018. HIV-1 genotypes were determined by phylogenetic analyses of HIV-1 gag, pol and env gene fragments, including CRF07_BC (51.8%), CRF01_AE (30.1%), subtype B (3.6%), CRF55_01B (3.6%), CRF104_0107 (1.2%) and unique recombinant forms (URFs) (9.6%). Transmitted drug resistance mutations were detected in 2.4% (2/82) of HIV-infected MSM individuals. The phylogenetic analyses of near full-length genome (NFLG) of HIV-1 URFs were performed. A new circulating recombinant form (CRF), designated as CRF104_0107, was found in three epidemiologically unlinked individuals in Shaanxi province, China. The CRF104_0107 is composed of genomes CRF01_AE and CRF07_BC, with six recombinant breakpoints in the gag, pol, vif and vpr genes. This second-generation CRF has a breakpoint (HXB2 nt 3011) in common with CRF07_BC. The emergence of novel CRF and multiple URFs reflected HIV-1 genetic complexity among the local key populations in Xi'an city, China.

Characterization of a Novel HIV-1 Recombinant Form (CRF01_AE/CRF07_BC/CRF08_BC) Identified from Guangxi, China

Recently, more and more kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in the population in China. A novel HIV-1 recombinant virus (2016GXNNIDU016) was identified in this study, which was isolated from an HIV-1 infected intravenous drug user in Nanning, the capital of Guangxi, China. Phylogenetic analysis of the near full-length genome (NFLG) indicated that the sequence (2016GXNNIDU016) was a monophyletic branch that did not cluster with any previously identified genotype. Recombinant analysis showed that the NFLG of 2016GXNNIDU016 is composed of CRF07_BC, CRF01_AE, and CRF08_BC, including nine mosaic segments. Differing from previously documented CRF01_AE and CRF07/08_BC recombinant forms, 2016GXNNIDU016 increases the genetic complexity of HIV-1 in Guangxi. The constant emergence of novel recombinant forms should draw our attention to make more efforts in supervising and preventing the spread of HIV infection.

Genomic Characterization of a Novel HIV Type 1 Strain Originating from CRF07_BC and CRF01_AE by Heterosexual Transmission in the Lingshan Prefecture of Guangxi Province, China

Recently, an increasing number of circulating recombinant forms (CRFs) and unique recombinant forms of HIV-1 have been identified in China, contributing substantially to the genetic variability of this virus. This study reports a novel second-generation recombinant form of HIV-1 (GX2015QZLS204), composed of segments from the CRF07_BC and CRF01_AE strains, which was isolated from an HIV-positive male individual infected through heterosexual contact, while residing in the Guangxi province of southwest China. Analysis of the near full-length genome sequence showed that one segment of the CRF01_AE virus subtype was inserted into the CRF07_BC subtype backbone. Recombination analysis demonstrated that the genome of GX2015QZLS204 was separated into seven segments with six breakpoints. Subregion trees constructed by the neighbor-joining method confirmed that the CRF01_AE segment was from the previously identified CRF01_AE cluster 2, and the CRF07_BC segment correlated with the CRF07_BC strain originating from the Jiangxi and Xinjiang provinces of China. The emergence of GX2015QZLS204 highlights the frequent generation of novel recombinant forms and the increasing complications of the HIV-1 epidemic among heterosexual transmission (HET) groups in China. This highlights the importance of monitoring HIV-1 molecular epidemiological characteristics and the urgent need for reduction of the HIV-1 epidemic among HET groups in China.

Identification of a Novel HIV-1 Second-Generation (CRF01_AE/B) Among Men Who Have Sex with Men in Tianjin, China

In this study, we report a novel HIV-1 second-generation recombinant form composed of CRF01_AE and subtype B detected from a married HIV-positive male subject infected through homosexual behavior in Tianjin in northern China. The near full-length genome analyses showed that two regions of subtype B inserted into the CRF01_AE backbone with four recombinant breakpoints observed in the pol gene region. Subregion tree analyses demonstrated that the CRF01_AE regions of the recombinant were greatly clustered with the CRF01_AE subcluster 4 lineage, which was found primarily among men who have sex with men (MSM) in northern China. To the best of our knowledge, this is the first detection of a novel HIV-1 second-generation recombinant form (CRF01AE/B) in Tianjin, which indicates active transmission networks of HIV-1 infection among MSM in this region. The emergence of the novel second-generation recombinant form highlights the increasing complexity of HIV-1 epidemic among MSM population and the importance to monitor potential novel circulating recombinant forms.

Cross-Continental Dispersal of Major HIV-1 CRF01_AE Clusters in China

Since the 1990s, several distinct clusters of human immunodeficiency virus-type 1 (HIV-1) CRF01_AE related to a large epidemic in China have been identified, but it is yet poorly understood whether its transmission has dispersed globally. We aimed to characterize and quantify the genetic relationship of HIV-1 CRF01_AEs circulating in China and other countries. Using representative sequences of Chinese clusters as queries, all relevant CRF01_AE pol sequences in two large databases (the Los Alamos HIV sequence database and the UK HIV Drug Resistance Database) were selected with the online basic local alignment search (BLAST) tool. Phylogenetic and phylogeographic analyses were then carried out to characterize possible linkage of CRF01_AE strains between China and the rest of the world. We identified that 269 strains isolated in other parts of the world were associated with five major Chinese CRF01_AE clusters. 80.7% were located within CN.01AE.HST/IDU-2, most of which were born in Southeast Asia. 17.8% were clustered with CN.01AE.MSM-4 and -5. Two distinct sub-clusters associated with Chinese men who have sex with men (MSM) emerged in HK-United Kingdom and Japan after 2000. Our analysis suggests that HIV-1 CRF01_AE strains related to viral transmission in China were initially brought to the United Kingdom or other countries during the 1990s by Asian immigrants or returning international tourists from Southeast Asia, and then after having circulated among MSM in China for several years, these Chinese strains dispersed outside again, possibly through MSM network. This study provided evidence of regional and global dispersal of Chinese CRF01_AE strains. It would also help understand the global landscape of HIV epidemic associated with CRF01_AE transmission and highlight the need for further international collaborative study in this field.

Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/B) from Men Who Have Sex with Men in Guangxi Zhuang Autonomous Region, China

We report here a novel HIV-1 recombinant form (18GXD4705) composed of CRF01_AE and subtype B, acquired from an unmarried HIV-positive young man subject infected through homosexual contact in Guangxi Province of eastern China. The phylogenetic analysis of the near full-length genome of 18GXD4705 indicated that one subtype B segment was inserted into the CRF01_AE backbone, with one recombinant breakpoint demonstrated in the pol region. The CRF01_AE region (I and III) of recombinant correlated with a previously reported subcluster 4 lineage. The B subregions (II) are greatly clustered together, with B strain references. The continued generation of this novel recombinant increases the genetic complexity and diversity of the HIV epidemic in Guangxi. In addition, further molecular epidemiological investigations should be conducted to continuously monitor the dynamic transmission of HIV-1 in the region.

Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017

OBJECTIVE

To investigate the evolutionary dynamics and characteristic of the molecular transmission networks of HIV-1 CRF01_AE in Nanjing.

METHODS

Viral samples were collected from 580 newly diagnosed HIV-1-infected patients. HIV-1 pol sequences were obtained and used for for molecular evolutionary analyses. The ML trees were constructed by MEGA 6.0 using under GTR+ G + I model with 1000 bootstrap replicates. The emergence and estimation of tMRCA and the evolutionary rate of the different CRF01_AE clusters were inferred using Bayesian phylogenetic analysis approaches implemented in the BEAST package. Pairwise genetic distances were calculated under the Tamura-Nei 93 model, a genetic distance threshold of ≤1.2% was used to identify potential transmission clusters. Network diagrams were plotted using Cytoscape 3.3.0.

RESULTS

Of these HIV-1-infected patients, 551 (91.5%) were males. The largest number of infections were attributed to homosexual (462, 79.7%). A total of 518 full-length pol genes were successfully amplified, based on the phylogenetic analysis CRF01_AE was the most predominantly circulating strain (45.0%, 233/518). As shown in the ML tree, three distinct clusters were observed. The 'Nanjing lineage' 1, 2, 3 has an estimated tMRCA around1996.61, 1993.61, 1984.61 respectively. Of 233 Nanjing sequences, 123 (55.2%) distributed in 30 molecular clusters, average Links/node was 7.8 with range (1-33), most of Nanjing strains shared links with local strains.

CONCLUSION

HIV-1 CRF01_AE was the most predominantly circulating strain, the epidemic of CRF01_AE in Nanjing was driven by multiple clusters of HIV-1 strains, and most CRF01_AE stains in our study were estimated to have originated in China in the 1990s.

Another Near Full-Length Sequence of an HIV-1 CRF01_AE/CRF07_BC Recombinant Virus from a Man Who Has Sex with Men in Tianjin, China

Surprisingly, more new unique recombinant forms (URFs) of CRF01_AE/CRF07_BC recombinant viruses were found in Tianjin, China, recently. Here we identified another novel HIV-1 recombinant virus (TJ20170315) isolated from an HIV-1 positive man who has sex with men in Tianjin, China. Phylogenetic analysis of the near full-length genome of TJ20170315 showed that it formed a monophyletic branch within the cluster of CRF01_AE reference sequences. Recombinant analysis showed that the virus kept the CRF01_AE parental backbone, and one CRF07_BC segment was inserted into gag, pol genes of the CRF01_AE backbone. Nowadays, multiple kinds of circulating recombinant forms (CRFs) and URFs were identified among men who has sex with men in China. The emergency of URFs highlights the complexity of HIV-1 infection in Tianjin, China, and implies that the next new CRF and HIV-1 epidemic are coming on the road.

Genomic Characterization of a Novel HIV-1 CRF01_AE/07_BC Recombinant Virus from a Married Man Who Has Sex with Men in Tianjin, China

We report in this study a novel HIV-1 second-generation recombinant form (TJIH0172) composed of CRF01_AE and CRF07_BC isolated from a married HIV-positive male subject infected through homosexual behavior in Tianjin, China. The phylogenetic analysis of the near full-length genome of TJIH0172 reveals that one region of CRF07_BC inserted into the CRF01_AE backbone with two recombinant breakpoints observed in the vpu and env gene regions, respectively. The CRF01_AE regions (the regions I and III) of the recombinant are greatly clustered with the CRF01_AE subcluster 4 lineage, which is mainly circulating among men who have sex with men (MSM) in northern China. The CRF07_BC region (II) is clustered with two sequences (JX960600 and KF250366), which were discovered in the MSM population in Liaoning Province and Beijing city in northern China, respectively. The emergence of the novel recombinant strain from a married man who has sex with men in Tianjin, China, highlights the increasing complexity of the HIV-1 epidemic between MSM and their female partners and further molecular epidemiological investigation should be taken to track married MSM and their female partners to prevent HIV transmit from HIV high-risk populations to general populations.

Critical amino acid residues and potential N-linked glycosylation sites contribute to circulating recombinant form 01_AE pathogenesis in Northeast China

Supplemental Digital Content is available in the text

Objective:

The current study aimed to understand epidemiological feature and critical factors associated with pathogenesis of circulating recombinant form (CRF) 01_AE strains in Northeast China.

Design:

Compared analysis was made between CRF01_AE and non-CRF01_AE samples to understand the pathogenicity features of CRF01_AE. Further analyses between CRF01_AE samples with high or low CD4⁺ cell counts and between samples with different coreceptor usages were done to explore the possible factors correlating to the pathogenesis of CRF01_AE viruses.

Methods:

The genotypes of newly identified strains were determined by phylogenetic analyses using Mega 6.06. Coreceptor usage was predicted by Geno2Pheno algorithm. Potential N-linked glycosylation site (PNGS) number was calculated using the online N-glycosite software. The properties of amino acid sequences were analyzed by the online ProtParam tool.

Results:

CRF01_AE become the main HIV-1 genotype since 2010. Compared with non-CRF01_AE group, the CRF01_AE group showed a higher proportion of samples with CD4⁺ cell count less than 200 cells/μl. Shorter amino acid length, fewer PNGSs and the presence of a basic motif R/KNXT or NR/KT in V4 correlated to a lower CD4⁺ cell count, and existence or coexistence of Thr12, Arg13, Val21 and Lys33, presence of more than 4 of net charges and lack of the PNGS within V3 favored to the X4/R5X4 coreceptor usage of CRF01_AE viruses.

Conclusion:

CRF01_AE has dominated HIV-1 genotype in Northeast China. Infection with CRF01_AE exhibited a fast disease progression, which may be associated with specific amino acid residues and PNGSs in V3 and V4 regions as well as amino acid length of V4 region.

Multiple HIV-1 Subtypes Were Found Circulating in Suqian District of Jiangsu Province, China

Jiangsu province has severe HIV-1 epidemic in China. Suqian which is located in north of the province has limited HIV epidemic information. Therefore, this study aimed to characterize the epidemic details in the area. A total of 196 plasma samples were collected from treated HIV-1-positive cases and viral RNA was extracted. Then HIV partial pol genes (nucleotide 2147-3462 by using HXB2 as calibrator) were amplified and sequenced. Finally, 84 partial pol genes were successfully obtained. The subtyping results indicate that multiple HIV-1 subtypes are circulating in Suqian district. Thereinto, CRF01_AE has been the dominant stains here and belonged to multiple lineages of CRF01_AE identified in China previously. Moreover, there is a high level of HIV drug resistance. All these results suggest HIV-1 epidemic in Suqian is rather complex and more measures must be performed for prevention and intervention in the area.

Characterization of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Virus Form in Guizhou, China

We identified a novel CRF01_AE and 07_BC HIV-1 recombinant form in Guizhou province in southwest China. The phylogenetic analysis of the near full-length sequence reveals that it was divided into five segments by four breakpoints, and the CRF01_AE regions of the recombinant were clustered with subcluster 4 lineage of CRF01_AE, which mainly circulated among men who have sex with men (MSM) in China. The CRF07_BC regions of the recombinant were clustered with CRF07_BC lineage, which circulated among Chinese MSM. This is the first detection of a novel HIV-1 second-generation recombinant form (CRF07_BC/CRF01_AE) in Guizhou, which shows the increasing significance of heterosexual transmission contributing to the complexity of the HIV-1 epidemic in southwest China, and more effort measures should be taken to monitor the genetic evolution of HIV-1 strains and prevent HIV-1 transmissions.

Genomic Characterization of a New HIV-1 CRF01_AE/CRF07_BC Recombinant Virus Form in Guizhou in Southwest China

A novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) was isolated from an HIV-positive subject among men who have sex with men (MSM) in Guizhou province in Southwest China. Recombinant analyses of the near full-length genome suggested that the strain was composed of CRF01_AE and CRF07_BC with one region of CRF07-BC inserted into a CRF01-AE backbone. Further analysis indicated that the CRF01_AE regions of the recombinant were highly clustered together with a subcluster 4 lineage of CRF01_AE, which is exclusively circulating among MSM in China. The CRF07_BC region of the recombinant was clustered with the CRF07_BC cluster, which was identified among MSM. The emergence of the novel HIV-1 recombinant may be a harbinger of more novel intersubtypes recombinants occurring in Guizhou province in Southwest China, and was of great important in understanding the dynamics and complexity of the HIV-1 epidemic in this region.

Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012

Population-level phylogenetic patterns reflect both transmission dynamics and genetic changes, which accumulate because of selection or drift. In this study, we determined whether a longitudinally sampled dataset derived from human immunodeficiency virus (HIV)-1-infected individuals over a 14-year period (1999–2012) could shed light on the transmission processes involved in the initiation of the HIV-1 epidemic in Korea. In total, 927 sequences were acquired from 1999 to 2012; each sequence was acquired from an individual patient who had not received treatment. Sequences were used for drug resistance and phylogenetic analyses. Phylogenetic and other analyses were conducted using MEGA version 6.06 based on the GTR G+I parameter model and SAS. Of the 927 samples, 863 (93.1%) were classified as subtype B and 64 were classified as other subtypes. Phylogenetic analysis demonstrated that 104 of 927 patient samples (11.2%) were grouped into 37 clusters. Being part of a transmission cluster was significantly associated with subtype-B viruses, infection via sexual contact, and the infection of young males. Of all clusters, three (~8.1%) that comprised 10 individual samples (22.2% of 45 individuals) included at least one member with total transmitted drug resistance (TDR). In summary, HIV transmission cluster analyses can integrate laboratory data with behavioral data to enable the identification of key transmission patterns to develop tailored interventions aimed at interrupting transmission chains.

Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/07_BC) from a Married Man Who Has Sex with Men in Zhejiang, China

We report here a novel HIV-1 recombinant form detected from a married HIV-positive man infected through homosexual behavior in Zhejiang, China. The breakpoint analysis of near full-length genome demonstrated a complex genome organization comprising two circulating recombinant forms (CRFs), CRF01_AE and CRF07_BC, both well-known CRFs in China. The parental CRF01_AE region (II) of recombinant clustered together with a previously reported cluster 4 lineage. The CRF07_BC regions (I and III) clustered within CRF07_BC references. The ongoing generation of intersubtype recombinant viruses increases the complexity of the HIV-1 epidemic and illustrates the necessity of persistent surveillance of the transmission of HIV-1.

Characterization of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Virus Among Men Who Have Sex with Men in Tianjin, China

We report here a novel human immunodeficiency virus type 1 (HIV-1) second-generation recombinant form comprising CRF01_AE and CRF07_BC isolated from an HIV-positive male subject infected among men who have sex with men (MSM) in Tianjin in north China. The phylogenetic analysis of the near full-length genome of TJIH0345 reveals that three regions of CRF01_AE were inserted into the CRF07_BC backbone with five recombinant breakpoints observed in the pol, vif, vpu, and env gene regions whose genome structure is distinctly different from other circulating recombinant forms and unique recombinant forms previously reported. The continued emergence of the novel recombinant strain in Tianjin, China, highlights the increasing complexity of the HIV-1 epidemic among the MSM population, and further molecular epidemiological investigation should be done to track the genetic evolution of HIV-1 strains to prevent HIV transmission.

HIV-1 genotype diversity and distribution characteristics among heterosexually transmitted population in Jiangsu province, China

Background

Heterosexual transmission has contributed greatly to the current HIV-1 epidemic in China. However, the HIV-1 genetic characteristics in the heterosexually transmitted population in Jiangsu province remained unclear.

Methods

A molecular epidemiological investigation on heterosexual transmission of HIV-1 was conducted across Jiangsu province. 301 HIV-1 patients infected through heterosexual transmission were involved in this study. The epidemiological information was investigated by trained staff via face-to-face interviews. Blood samples were taken from each patient, HIV-1 RNA was extracted from the plasma, and used for amplifying the gag and env genes followed by further products sequencing. The genotypes of HIV-1 were determined using phylogenetic tree analyses in the neighbor-joining method.

Results

A total of 262 samples were successfully taken for genotyping. The main subtypes which accounted for 90.5% of all HIV-1 strains are CRF01_AE (45.4%), CRF07_BC (21.4%), subtype B (12.6%), CRF08_BC (11.1%). Minor subtypes were also detected, such as CRF68_01B, subtype C, CRF55_01B, CRF02_AG and subtype A. Time trend analysis suggested the prevalence of subtype B and CRF08_BC decreased gradually, but the prevalence of CRF01_AE increased over time. A relatively higher prevalence of CRF07_BC in Central Jiangsu and subtype B were detected in South Jiangsu, while a relatively lower prevalence of subtype B and CRF08_BC were detected in Central Jiangsu.

Conclusion

Complex and unbalanced HIV distribution characteristics suggest that heterosexual transmission of HIV needs to be taken seriously. It is necessary to implement more effective and comprehensive intervention strategies for further control of HIV-1 dissemination.

Characterization of a New HIV-1 CRF01_AE/B Recombinant Virus Form Among Men Who Have Sex with Men in Shanghai, China

To date, there are 16 types of CRF01_AE/B circulating recombinant forms identified, and most of them are distributed in Asian countries such as China, Malaysia, and Singapore. Previous HIV molecular epidemiological surveys showed that CRF01_AE (27.6%) and B (9.6%) subtypes are predominant strains in mainland of China. At the same time, the HIV-1 virus spreads faster in the men who have sex with men (MSM) population than in other risk groups. In Shanghai district, ∼66.0% of newly reported cases were infected through homosexual transmission. In this study, we report a novel recombinant strain of CRF01_AE/B. The near full-length genome phylogenetic tree showed that the strain clustered with the CRF01_AE reference sequence and placed in the peripheral position within the branch of the CRF01_AE strain. Subregional evolutionary results indicated that the CRF01_AE subtype was derived from cluster 4 of CRF01_AE, which is mainly distributed in northern China. The subtype B was correlated with the U.S./Europe B, which are widely prevalent in the Chinese MSM population. In recent years, a large number of recombinant forms between CRF01_AE and B strains are continuously emerging in China. Therefore, understanding the current epidemic recombinant forms will have significant implications for prevention and treatment of HIV/AIDS.

Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF80_0107) Among Men Who Have Sex with Men in China

Since the emergence of CRF55_01B among men who have sex with men (MSM) group in China, more and more circulating recombinant forms (CRFs) and unique recombinant forms have been identified in the population in China. Here we characterize a novel CRF (CRF80_0107) consisted of CRF01_AE and CRF07_BC segments from three epidemiologically unlinked MSM. Two near full-length genome (NFLG) sequences were amplified and sequenced in two halves with RNA extracted from the plasma of two MSM in Beijing. Another gag-pol sequence was obtained from Los Alamos HIV Sequence Database with accession number KX198573, which was isolated from a man who has sex with men in Hebei province. Phylogenetic analysis based on NFLG sequences revealed that CRF80_0107 formed a monophyletic cluster with high bootstrap value of 100%. Recombination analysis demonstrated that the genome of CRF80_0107 was separated into eight segments by seven breakpoints. The subregion trees constructed by neighbor-joining method confirmed that those segments were originated from CRF01_AE and CRF07_BC strains circulating among MSM group in China. The emergence of CRF80_0107 indicates the frequent generation of novel recombinant forms and the increasing complication of HIV-1 epidemic among MSM group in China. This highlighted the importance of monitoring HIV-1 molecular epidemiological characteristics and the urgency for reducing HIV-1 epidemic among MSM in China.

Identification of a Novel HIV Type 1 CRF01_AE/CRF07_BC Recombinant Virus in Men Who Have Sex with Men in GuangXi, China

This study reports a novel HIV-1 recombinant virus (GX2016EU10) isolated from a 24-year-old man, who was infected by homosexual sex in Guangxi, China. The near full-length genome analyses showed GX2016EU10 kept the CRF07_BC parental backbone with three CRF01_AE segments inserted into gag, pol, vpu, env, and nef genes, respectively. The recombinant breakpoints were completely different from the other CRF01_AE/CRF07_BC recombinant forms reported. GX2016EU10 was CCR5-tropic through GHOST cell identification. The emergence of GX2016EU10 indicates that the HIV-1 epidemic among men who have sex with men in Guangxi is increasing in complexity, which poses a serious challenge to prevention and control.

Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines

The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Near-full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992-1998), about 10-15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.

Rapid and complicated HIV genotype expansion among high-risk groups in Guangdong Province, China

Background

Guangdong Province is one of the most developed and populous provinces in southern China, with frequent foreign exchanges and large transient population. The annual number of cases of HIV/AIDS reported in Guangdong has been higher than most of provinces in China for several successive years. HIV infection by heterosexual transmission occurs across the province, with transmission among men who have sex with men occurring mainly in larger urban centers. There is a lack of widespread and representative data on the distribution of HIV subtypes in Guangdong. This study aimed to thoroughly investigate and estimate the prevalence and distribution of HIV-1 subtypes using a city-based sampling strategy to better understand the characteristics of HIV transmission in Guangdong.

Methods

Archived plasma samples (n = 1205) from individuals diagnosed as HIV-1 infection in 2013 were selected randomly from all 21 cities in Guangdong Province. Genotypes were determined using env and/or gag sequences using phylogenetic analysis. The distributions of HIV genotypes in different risk groups and different cities were analyzed.

Results

A total of 15 genotypes, including six discordant genotypes, were identified. The four main HIV-1 subtypes in Guangdong were CRF01_AE (43.2%), CRF07_BC (26.3%), CRF55_01B (8.5%), and CRF08_BC (8.4%). CRF01_AE was the predominant subtype in all risk populations. The high mobility of people shaped the complexity of the HIV genotypes, while the switch of risk factors affected the distribution and future trend of HIV-1 genotypes in Guangdong. Another epicenter located in the western region in addition to the known epicenter cities in the Pearl River Delta region of Guangdong may exist.

Conclusions

Our study provides a comprehensive molecular epidemiologic dataset to understand the diversity and distribution of HIV genotypes in Guangdong, as well as to clarify the unique region- and risk group-specific transmission dynamics. The results provide critical and insightful information for more effective intervention strategies to limit HIV transmission in the future.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3788-7) contains supplementary material, which is available to authorized users.

Near Full-Length Genomic Characterization of HIV-1 CRF01_AE/B Recombinant Strains Identified in Hebei, China

This study reports a novel HIV-1 recombinant form of CRF01_AE/B that was isolated from a 22-year-old male individual (HE150308) residing in Hebei province, China. The near full-length genome (NFLG) phylogenetic tree showed that the strain was clustered with CRF01_AE reference sequences and placed at the peripheral position within the branch of CRF01_AE strains. The bootscaning and similarity plot analysis revealed that the NFLG of this novel recombinant was composed of eight interlaced segments, including four CRF01_AE and four subtype B segments separated by seven breakpoints observed in the gag, pol, and nef regions of HIV-1 genome. Phylogenetic analysis demonstrated that the CRF01_AE subregions were from the previously identified CRF01_AE cluster 5, and the B subregions were correlated with the B strains originated from Europe and America. They were all the lineages widely prevalent in men who have sex with men (MSM) population in China. In recent years, a large number of recombinants between CRF01_AE and B strains are constantly emerging in the MSM population in China. This continual and recurrent recombination between CRF01_AE and B in high-risk group people deserves more attention and further monitoring.

Identification of Two Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/07_BC) in Shaanxi, China

Sexual contact is the main route of transmission of HIV type 1 (HIV-1) pandemic in China. New unique recombinant forms (URFs) were increasingly characterized in sexual populations in recent years. We reported two URFs identified from two male HIV-1-positive patients who were infected through sexual exposure in Shaanxi, China. Phylogenetic analyses and bootscan analyses revealed that the near full-length genomes of the two URFs were having four recombinant breakpoints, with two CRF07_BC fragments inserted into CRF01_AE backbones. The CRF01_AE fragments of the two URFs clustered with previously reported a cluster 5 lineage of CRF01_AE. The four recombinant breakpoints of the two URFs were quite similar. The emergence of the new CRF01_AE/07_BC URFs indicated the complexity genetic variability and the active epidemic of HIV-1. Much more attention should be paid to monitor the emergency of recombinant strains.

Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade

HIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic. The same subtype or CRF is usually considered to have similar phenotype. Being one of the world's major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the National HIV Molecular Epidemiology Survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 counts (391 vs. 470, P < 0.0001) and higher prevalence of X4-using viruses (17.1% vs. 4.4%, P < 0.0001) compared with those infected by cluster 5. In an MSM cohort, X4-using viruses were only isolated from seroconvertors in cluster 4, which was associated with low a CD4 count within the first year of infection (141 vs. 440, P = 0.003). Using a coreceptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 use. We demonstrate that the HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in the same subtype. Since its initial spread to humans from chimpanzees, estimated to be the first half of the 20th century, HIV-1 continues to undergo rapid evolution in larger and more diverse populations. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance of monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning of the appearance of more pathogenic strains.

Near Full-Length Genomic Characterization of a Novel HIV Type 1 Recombinant Form (CRF01_AE/B) Identified from Anhui, China

HIV-1 recombinant forms contribute substantially to its genetic evolution. This study reports a novel HIV-1 second-generation recombinant form (AH150299) composed of CRF01_AE and subtype B, isolated from an HIV-positive female subject infected through heterosexual contact in Anhui province of eastern China. The analyses of the near full-length genome sequence showed that one subtype B segment was inserted into the CRF01_AE backbone, with two recombinant breakpoints observed in the vif/vpr and env/nef gene regions. Phylogenetic analysis demonstrated that the CRF01_AE region of the recombinant belongs to CRF01_AE cluster 4, and the B subregions were correlated with the B strains circulating among men who have sex with men in China. In recent years, the emergence of novel recombinant strains reflected the complexity of the HIV-1 epidemic in Anhui, suggesting the significance of continuous monitoring of the dynamic transmissions of HIV-1 in eastern China.

HIV-1 Transmissions Among Recently Infected Individuals in Southwest China are Predominantly Derived from Circulating Local Strains

Although the Guangxi region accounts for 10% of all HIV-1 cases new reported in 2011 in China, the sources of the transmitted HIV-1 strains are virtually unknown. To determine the extent to which recent HIV infections were derived from already circulating local strains as opposed to recently introduced strains, we performed a cross-sectional molecular epidemiological investigation of recent infections across Guangxi during 2012-2013. HIV-1 nucleotide sequences were amplified and sequenced. Phylogenetic analyses of pol gene regions were used to determine HIV-1 transmission source strains. Based on 229 sequences generated, the subtype/CRF distribution was as follows: CRF01_AE (61.1%), CRF07_BC (18.8%), CRF08_BC (16.6%), CRF55_01B (3.1%), and subtype B' (0.4%). In total, 213 of 229 (93.0%) sequenced transmission strains were derived from already-circulating local strains. Multivariate logistic regression analysis showed that only an age of 18-25 years was significantly associated with transmission from outside Guangxi (compared to >25 years, AOR: 5.15, 95% CI: 1.18-22.48, p < 0.01). This is the first study to use a Bayesian discrete phylogeographic approach to analyze transmission source strains in China. Our results provide useful data for designing evidence-based prevention strategies and methods for combating the rapid spread of sexually transmitted HIV in Guangxi.

Identification of a Novel HIV-1 Unique Recombinant Form Comprising CRF01_AE, Subtype B', and CRF65_cpx Among Men Who Have Sex with Men in Jilin, China

The current HIV-1 epidemic in China is featured by diverse subtypes and continual emergence of new recombinant viruses. This study identified a novel unique recombinant form (URF), JL16013, among men who have sex with men (MSM) in Jilin, China. The JL16013 virus was different from all known subtypes and set up a distinct branch on the phylogenetic tree. This virus had a CRF01_AE backbone with two subtype B' fragments and one CRF65_cpx fragment inserted into gag, pol, env, and nef regions, suggesting that this novel URF might have originated from the CRF01_AE, subtype B', and CRF65_cpx viruses that were cocirculating in Jilin province. This was the first report of the CRF01_AE/B'/CRF65_cpx recombinant in China. Identification of this URF indicated the severity and complexity of the HIV-1 epidemic among MSM in Jilin province. Timely surveillance of new HIV-1 infections and new recombinants among the MSM population is urgently required.

Identification of a New HIV-1 Circulating Recombinant Form CRF65_cpx Strain in Jilin, China

This study reported a new HIV-1 circulating recombinant form CRF65_cpx virus isolated from a man who have sex with men (MSM) in Jilin, China. The near full-length genome of this virus was composed of 14 mosaic gene fragments derived from CRF01_AE, subtype B' (Thai B) and subtype C, highly similar to the CRF65_cpx viruses recently identified in Yunnan and Anhui of China. Phylogenetic tree analysis suggested that this CRF65_cpx strain was not generated among MSM in Jilin, but originated in southern regions of China and spread to Jilin by MSM population. The emergence of CRF65_cpx in Jilin indicated HIV-1 epidemic in this area was more and more complicated and the MSM population has become the important source for generation of new recombinant viruses. Real-time surveillance of new HIV-1 infections among MSM population is quite required.