Emergence of a new HIV type 1 CRF01_AE variant in Guangxi, Southern China

Characterization and Recombinant Genotypes of HIV-1 in Gansu Province, China

It is important to monitor the diversity and evolution of HIV-1 genotypes, especially in some remote and undeveloped regions in China where the diversity and distribution of HIV-1 genotypes are not fully clear. To investigate the genotypes and distribution of HIV-1 in far Northwestern Gansu Province of China, we selected 220 HIV-1-positive plasma samples from the Center for Disease Control and Prevention (CDC) in Gansu from January 2016 to December 2018. The viral load of inclusion samples were over 1,000 copies per milliliter. The gag, pol, and env gene of HIV-1 were amplified by nested reverse transcription-polymerase chain reaction kit, sequenced, and then identified genotypes using HIV-BLAST tool and the neighbor-joining method. One hundred fifty of 220 inclusion samples were successfully determined HIV-1 genotypes. Our results show that circulating recombinant forms (CRF) 07_BC and CRF01_AE are predominant and accounted for 46.7% and 28.0%, respectively. Other HIV-1 subtypes and genotypes included B/B' (6.0%), CRF08_BC (4.0%), and C (1.3%). In addition, we reported CRF65_cpx and CRF55_01B subtypes in Gansu for the first time. Phylogenetic tree analysis showed that the sequences of different samples are scattered in different genotype groups, and no obvious aggregation occurs. Our results indicate the genetic variety and complexity of HIV-1 and provide critical information for HIV/AIDS control and prevention in Gansu Province.

The genotype distribution, infection stage and drug resistance mutation profile of human immunodeficiency virus-1 among the infected blood donors from five Chinese blood centers, 2014-2017

Human immunodeficiency virus-1 (HIV-1) exhibits high diversity and complexity in China, challenging the disease surveillance and antiretroviral therapy. Between July 1, 2014 and January 30, 2017, we investigated the profiles of HIV-1 infection stages, genotype distribution and drug resistance mutations (DRMs) using plasma samples from HIV Western blot (WB) confirmed blood donors from five Chinese blood centers (Chongqing, Guangxi, Luoyang, Mianyang, and Urumqi). HIV pol regions consisted of whole protease and partial reverse transcriptase were genotyped and analyzed for DRMs. Lag-Avidity testing was performed to identify the infection stages. Of the 356 HIV-1 WB positive samples tested by Lag-avidity assay, 19.1% (68/356) were recent infections. Genotyping on 356 amplified sequences presented the subtype distributions as following: CRF07_BC (65.7%), CRF08_BC (7.3%), CRF01_AE (19.1%), B (4.2%), CRF55_01B (3.1%), CRF59_01B (0.3%) and CRF68_01B (0.3%). No significant difference in genotype distribution was observed between recent and long-term infections. 48 DRMs were identified from 43 samples, indicating a drug resistance prevalence of 12.1% (43/356), which include seven protease inhibitors (PIs) accessory DRMs (Q58E, L23I and I84M), two PIs major DRMs (M46I, M46L), seven nucleoside RT inhibitors DRMs (D67N, K70Q, K219R and M184L), and 32 non-nucleoside RT inhibitors DRMs (K103N, V179E, K238N, V179D, E138G, G190E, A98G, Y188D and E138A). In addition, we had also identified CRFs from the 01B subtype including CRF55_01B (3.1%), CRF59_01B (0.3%) and CRF68_01B (0.3%). As an important part of the continuous monitoring of HIV-1 circulating strains among blood donors, our findings were expected to contribute to the comprehensive AIDS control and development of proper diagnostics for HIV-1 in China.

Prevalence of Different Genotypes of HIV-1 in Injection Drug Users in China: A Systematic Review and Meta-Analysis

BACKGROUND

Since 1981, an increasing trend in HIV has been observed for transmission via injection drug users (IDUs), sexual transmission and mother-to-child transmission. The IDUs are blamed for early increases in HIV-positive cases in China.

OBJECTIVE

HIV genotypes of IDUs were comprehensively analysed to trace the source and relationships of the AIDS epidemic in China.

METHODS

Relevant databases written in English and Chinese were searched. Overall, 7,149 publications were identified in six databases. After screening 7,104 articles according to the inclusion and exclusion criteria, 45 studies consisting of 2,765 cases were finally identified. A meta-analysis was conducted using R MATLAB software, RevMan and SPSS. Subgroup analyses focused on time frame, region, and location of different genotypes of IDUs in China.

RESULTS

There were five dominant HIV-1 genotypes among the 2,765 IDU cases. The proportions of CRF07_BC, CRF01_AE, CRF08_BC, subtype B/B', and subtype C were 45.18% (95% CI: 33.55-57.08%), 16.00% (95% CI: 9.39-23.82%), 13.43% (95% CI: 7.32-20.84%), 3.58% (95% CI: 1.52-6.24%), and 0.90% (95% CI: 0.04-2.43%), respectively. HIV genotypes transmitted among IDUs in China are primarily CRF07-BC, followed by CRF01-AE and CRF08-BC. Across the different time frames and regions, CRF07_BC was the most prevalent HIV-1 genotype among IDUs, while CRF08_BC was the most prevalent genotype in the southwest region.

CONCLUSION

Our study reveals that CRF07-BC was the dominant prevalent strain among IDUs from 1991 to 2015 in China, while CRF08-BC was the dominant prevalent strain among IDUs in southwestern China. This systematic review and meta-analysis shows evidence of the comprehensive prevalence of different genotypes, data and characteristics of HIV among IDUs in China.

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.

Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China

As the most dominant HIV-1 strain in China, CRF01_AE needs to have its evolutionary and demographic history documented. In this study, we provide phylogenetic analysis of all CRF01_AE pol sequences identified in mainland China. CRF01_AE sequences were collected from the Los Alamos HIV Sequence Database and the local Chinese provincial centers of disease control and prevention. Phylogenetic trees were constructed to identify major epidemic clusters. Bayesian coalescent-based method was used to reconstruct the time scale and demographic history. There were 2965 CRF01_AE sequences from 24 Chinese provinces that were collected, and 5 major epidemic clusters containing 85% of the total CRF01_AE sequences were identified. Every cluster contains sequences from more than 10 provinces with 1 or 2 dominant transmission routes. One cluster arose in the 1990s and 4 clusters arose in the 2000s. Cluster I is in the decline stage, while the other clusters are in the stable stage. Obvious lineage can be observed among sequences from the same transmission route but not the same area. Two large clusters in high-level prevalence were found in MSM (Men who have sex with men), which highlighted that more emphasis should be placed on MSM for HIV control in mainland China.

Molecular linkage tracing of HIV-1 transmission events in seroconcordant couples in Guangxi Province, Southeastern China

Background

Guangxi Province in Southeastern China has one of the highest HIV-1 infection and transmission rates in stable couples. However, the mode of transmission at the molecular level has seldom been reported amongst this group. It is important to investigate this issue to support the treatment-as-prevention approach and for efficient interventions.

Methods

HIV-1 subgenomic regions (1.2 kb of pol and a 660-bp env C2V5 fragment) were sequenced in 42 couples. A couple linkage assessment was performed by phylogenetic analysis of sequences and Bayesian analysis of genetic distances. A subset of pairs was selected for single-genome amplification.

Results

Thirty-five pairs (83.3 %, 35/42) were identified as linked, 3 pairs (7.1 %, 3/42) were identified as indeterminate, and 4 pairs (9.5 %) were identified as unlinked. The predominant intra-couple-transmitted HIV-1 subtype was CRF01_AE (80 %, 28/35). The median genetic distance of linked couples was 0.5 %.

Conclusion

The majority of HIV-1 transmission events in this study occurred within the partnership, and the predominant HIV-1 subtype was CRF01_AE. Further research on the mode of HIV transmission in other locations is needed.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-3578-2) contains supplementary material, which is available to authorized users.

Nationwide Trends in Molecular Epidemiology of HIV-1 in China

To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.

Near Full-Length Genomic Characterization of a Novel HIV Type 1 CRF01_AE/CRF07_BC Recombinant Form Transmitted Between a Heterosexual Couple in Guangxi, China

In this research, we reported a new second generation recombinant form (GXDY460B) between circulating recombinant form (CRF)01_AE and CRF07_BC in a seroconversion couple who obtained the virus from her husband by heterosexual behavior. The analysis result of the near full-length genomic characterization showed that the genome comprises at least 12 interlaced segments, including six CRF07_BC and six CRF01_AE segments, with CRF07_BC as the main framework. Cocirculation of multiple virus subtypes and multiple infection routes have existed for a long time in Guangxi, but the recombinant strain was rarely reported among heterosexual transmission population because of its lower crowd confounding degree than men who have sex with men and injecting drug user population. It is the first time that the unique recombinant form (URF) between CRF01_AE and CRF07_BC was identified among heterosexual transmission in Guangxi. The emergence of the novel recombinant helps to understand the pattern of the URF virus.

The Epidemic Dynamics of Four Major Lineages of HIV-1 CRF01_AE Strains After Their Introduction into China

The epidemic of HIV-1 CRF01_AE in China was driven by multiple lineages of HIV-1 viruses introduced in the 1990s and increasing; it is important to investigate their epidemic status in China. In this study, we download all available CRF01_AE sequences (n = 2,931) from China and their associated epidemiological information in the Los Alamos HIV database for our analysis to explore their epidemic status in China. The results showed there were 11 distinct clusters of CRF01_AE strains in China, and 4 major clusters that accounted for 80.0% (1,793/2,241) of Chinese CRF01_AE strains in total had led a real epidemic. Clusters 1 and 2 were epidemic among heterosexuals and injecting drug users in southern and southwestern China, while Clusters 3 and 4 were predominant among homosexuals in eastern and central China and northeastern China, respectively. HIV-1 CRF01_AE strains detected in heterosexuals had the most complex characteristic, underscoring its important role in the occurrence of multiple CRF01_AE lineages. Furthermore, epidemic history reconstruction analysis using the birth-death susceptible-infected-removed package revealed that the four clusters had gone through varying epidemic stages. Clusters 2 and 3 were near the peak of the local epidemic, while Clusters 1 and 4 were just in the very early stage of their epidemic. The epidemic status of CRF01_AE clusters in the future is mainly determined by the effect of prevention and control. Our study provides new insights into the understanding of the epidemic dynamics of CRF01_AE in China.

Genetic Characteristics of CRF01_AE Among Newly Diagnosed HIV-1-Infected 16- to 25-Year Olds in 3 Geographic Regions of Guangxi, China

The aim of this study was to analyze the distribution of clusters and drug resistance of CRF01_AE among newly diagnosed, treatment-naïve HIV-infected teenagers and young adults in 3 major HIV-affected geographic regions of Guangxi Province, including the cities of Hezhou, Liuzhou, and Nanning. Samples were sequentially collected from newly diagnosed HIV-infected 16- to 25-year olds in these 3 regions from 2009 to 2013. The viral genome was extracted, and the partial pol gene was amplified and sequenced. Phylogenetic analyses were used to determine HIV-1 subtypes and CRF01_AE clusters. Transmitted drug resistance (TDR) mutations were identified using the 2009 WHO list of TDR mutations. A total of 216 sequences were obtained from CRF01_AE strains, which accounted for 83.1% of the 260 genotyped samples, of which 36 were from Hezhou, 147 from Liuzhou, and 33 in Nanning. Most (83.3%, 180/216) were from heterosexuals, followed by injection drug users (5.6%), homosexuals (4.2%), and unknown risk group (6.9%). Based on phylogenetic analyses by the maximum likelihood method, 5 distinct clusters (cluster 1-5) were identified with 213 (98.6%) sequences, whereas 3 (1.4%) sequences were ungrouped. In Hezhou, 88.9% (32/36) of CRF01_AE infections were caused by cluster 2, and 11.1% (4/36) were caused by cluster 1. In Liuzhou, 83.0% (122/147) of the CRF01_AE strains were found in cluster 1, 11.6% (17/147) from cluster 2, 1.4% (2/147) from cluster 3, 2.7% (4/147) from cluster 4, and 0.7% (1/147) from cluster 5. The distribution of CRF01_AE clusters was more even in Nanning than it was in the other 2 regions, with 18.2% (6/33) from cluster 1, 36.3% (12/33) from cluster 2, 9.1% (3/33) from cluster 3, 18.2% (6/33) from cluster 4, and 12.1% (4/33) from cluster 5. The most frequent TDR mutations were M46I (2) in the protease region and Y181C (2) from the reverse transcriptase fragment. Clusters 1 and 2 of CRF01_AE strains were prevalent in Liuzhou and Hezhou, respectively. However, multiple CRF01_AE clusters existed in Nanning. This can be partially explained by the high mobility of laborers in Nanning, the capital city of Guangxi. The prevalence of TDR was low.

Cross-neutralizing antibody profile of Chinese HIV-1-infected individuals and the viral envelope features from elite neutralizers

OBJECTIVE

Knowledge about the profile of neutralization responses and the viral envelope features of HIV-1-infected individuals in China may provide new insights for vaccine design against local viruses.

METHODS

Eight hundred sixty plasma samples from antiretroviral treatment-naive HIV-1-infected individuals in Xinjiang province (611) and Guangxi province (249), who had acquired infection over 3 years through intravenous drug use or sexual contact, were examined for their ability to neutralize diverse envelope-pseudoviruses of 5 subtypes. The sequence features of the envelopes from elite neutralizers were analyzed.

RESULTS

From Xinjiang and Guangxi, 29.1% and 5.2% of plasmas displayed intrasubtype cross neutralization against subtype B and subtype C, respectively. From Xinjiang, 10.6% of the plasmas displayed broad neutralization against the 3 subtypes, B, C, and CRF01_AE; whereas only 2.4% from Guangxi displayed broad neutralization. Envelopes from 6 elite neutralizers were obtained by single-genome amplification. The variations of their envelopes including the lengths, glycans, and net charges in V1, V2, and V4 regions were compared with those from CRF07_BC env sequences from the HIV Sequence Database. The Envs from 3 elite neutralizers displayed the sensitivities to the monoclonal broadly neutralizing antibodies such as PG9, PG16, and 4E10. Some unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers were found.

CONCLUSIONS

The neutralization profile of HIV-1-infected individuals in the 2 regions of China, where the HIV-1 subtypes are the representative in China, and the unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers provide useful information for viral infection prevention and an insight for vaccine design against locally epidemic viruses.

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.

Near full-length genome characterization of a new CRF01_AE/CRF08_BC recombinant transmitted between a heterosexual couple in Guangxi, China

Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE is transmitted mainly by sexual activity in Guangxi, southwestern China. Other subtypes, including CRF07_BC, CRF08_BC, and subtype B, are also prevalent in this region. Cocirculation of multiple subtypes, as well as a high rate of drug use, creates favorable conditions for the emergence of recombinant viruses in Guangxi. In the present study, we identified a new HIV-1 unique recombinant form (CRF01_AE /08BC) transmitted from the infected index patient to his seronegative sexual partner. This is the first near full-length genome characterization of a CRF01_AE /08BC recombinant virus in Guangxi, and provides an important basis for future analysis on potential new recombinant transmission events.

Multiple independent introductions of HIV-1 CRF01_AE identified in China: what are the implications for prevention?

Background

HIV-1 CRF01_AE accounts for an important fraction of HIV infections in Asia including China, but little is known about the phylogenetic and evolutionary history of this CRF (circulating recombinant form). In the current study, we collected a large number of 1,957 CRF01_AE gag p17 sequences with known sampling year (1990-2010) from 5 global regions representing 15 countries to better understand the phylogenetic relationships and epidemic history of CRF01_AE strains in China.

Methodology/Principal Findings

CRF01_AE gag p17 sequences were retrieved from public databases to explore phylogenetic relationships and phylogeographic dynamics of CRF01_AE in Asia by using maximum-likelihood phylogenetics and Bayesian coalescent-based analyses. We found close phylogenetic relationships between sequences from Thailand, Vietnam and China. Moreover, at least 5 independent introductions and 5 independent autochthonous clades of CRF01_AE, which descended from Thailand or Vietnam were identified in China from 1991 through 2003.

Conclusion/Significance

The current study not only defines the migration of CRF01_AE clades to/in Asia, but also demonstrates the criticalness of identifying the circulating strains in the population for the development of vaccine and microbicides.

Identification of 3 distinct HIV-1 founding strains responsible for expanding epidemic among men who have sex with men in 9 Chinese cities

Supplemental Digital Content is Available in the Text.

Objectives:

To investigate the epidemiological relationships between HIV-1 strains that are spread among the men who have sex with men (MSM) populations of 9 cities across China and to analyze the origins and divergence times of the major epidemic strains found in the MSM population.

Methods:

A total of 583 HIV-1-positive subjects were recruited from high-risk MSM populations in 9 cities across China between 2009 and 2011. Nucleotide sequences of 1.0-kb pro-RT regions were amplified and sequenced. Phylogenetic and Bayesian molecular clock analyses were performed.

Results:

The overall distribution of HIV-1 genotypes was as follows: CRF01_AE, 62.1%; CRF07_BC, 18.2%; subtype B (United States–European), 15.9%; subtype B', 0.7%; other recombinants, 3.1%. In addition to the 2 distinct CRF01_AE clusters [cluster 1 (n = 157, 26.9%) and cluster 2 (n = 196, 33.6%)] previously reported by our group, we identified a novel CRF07_BC cluster (cluster 3) (n = 94, 16.1%) unique to China's MSM population whose strains were homologous and could be detected in all 9 cities. These 3 lineages of HIV-1 strains (clusters 1–3) accounted for 76.7% (447 of 583) of infections among MSM in China as a whole. Clusters 1, 2, and 3 were estimated to have been introduced into the MSM population in 1999, 2001, and 2001, respectively, indicating that the newly identified CRF07_BC cluster 3 is not a young lineage. However, it spread quickly in recent years.

Conclusions:

We identified 3 distinct HIV-1 lineages (clusters 1–3) responsible for the recent upsurge of the AIDS epidemic among MSM in China. These 3 HIV-1 variants are spread widely among MSM throughout China, demonstrating remarkable founding effects.

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

Objectives:

We sought to comprehensively analyze the origin, transmission patterns and sub-epidemic clusters of the HIV-1 CRF01_AE strains in China.

Methods:

Available HIV-1 CRF01_AE samples indentified in national molecular epidemiologic surveys were used to generate near full-length genome (NFLG) sequences. The new and globally available CRF01_AE NFLG sequences were subjected to phylogenetic and Bayesian molecular clock analyses, and combined with epidemiologic data to elucidate the history of CRF01_AE transmission in China.

Results:

We generated 75 new CRF01_AE NFLG sequences from various risk populations covering all major CRF01_AE epidemic regions in China. Seven distinct phylogenetic clusters of CRF01_AE were identified. Clusters 1, 2 and 3 were prevalent among heterosexuals and IDUs in southern and southwestern provinces. Clusters 4 and 5 were found primarily among MSM in major northern cities. Clusters 6 and 7 were only detected among heterosexuals in two southeast and southwest provinces. Molecular clock analysis indicated that all CRF01_AE clusters were introduced from Southeast Asia in the 1990s, coinciding with the peak of Thailand's HIV epidemic and the initiation of China's free overseas travel policy for their citizens, which started with Thailand as the first destination country.

Conclusion:

China's HIV-1 epidemic of sexual transmissions, was initiated by multilineages of CRF01_AE strains, in contrast to the mono-lineage epidemic of B′ strain in former plasma donors and IDUs. Our study underscores the difficulty in controlling HIV-1 sexual transmission compared with parenteral transmission.

HIV-1 diversity, drug-resistant mutations, and viral evolution among high-risk individuals in phase II HIV vaccine trial sites in southern China

HIV-1 prevalence in Guangxi, China, has been growing since 1996, when the first case was reported. Over half of HIV-1 positive patients in Guangxi Province were injecting drug users (IDUs), possibly because of the province’s location near drug-trafficking routes. Since a phase II HIV vaccine trial is ongoing there, a current characterization of the subtypes of HIV-1 among IDUs in Guangxi would provide critical information for future HIV vaccine trials, as well as further control and prevention of HIV-1 transmission. Thus, we conducted a molecular epidemiological investigation of HIV-1 samples from 2008–2010 among IDUs in multiple cities in Guangxi Province. Our results, based on the gag/pol fragment, indicated a very high proportion (78.47%) of HIV-1 CRF08_BC recombinants, some CRF01_AE (15.38%) recombinants, and a low proportion of CRF07_BC (6.15%) recombinants among the IDUs. The high proportion of CRF08 HIV-1 strains among recent IDUs matches the vaccine candidate constructs. However, future vaccine development should also incorporate CRF01-targeted vaccine candidates. Distinct Env sequence evolution patterns were observed for CRF08_BC and CRF01_AE, indicating that different local selection pressures have been exerted on these two HIV-1 subtypes. Unique drug-resistant mutations were also detected, and our data indicate that HIV treatment programs should consider pre-existing drug-resistant mutations.

Emerging variability in HIV-1 genetics among recently infected individuals in Yunnan, China

Background

Yunnan has the longest endured Human Immunodeficiency Virus-1 (HIV-1) epidemic in China, and the genetic diversity of HIV-1 constitutes an essential characteristic of molecular epidemiology in this region. To obtain a more comprehensive picture of the dynamic changes in Yunnan’s HIV-1 epidemic, a cross-sectional molecular epidemiological investigation was carried out among recently infected individuals.

Methodology/Principal Findings

We sequenced partial gag (HXB2∶781–1861) and env (HXB2∶7002–7541) genes from 308 plasma samples of recently infected patients. With phylogenetic analysis, 130 specimens generated interpretable genotyping data. We found that the circulating genotypes included: CRF08_BC (40.8%), unique recombinant forms (URFs, 27.7%), CRF01_AE (18.5%), CRF07_BC (9.2%), subtype B (2.3%) and C (1.5%). CRF08_BC was the most common genotype, and was predominant in both intravenous drug users (IDUs) and heterosexually transmitted populations. CRF08_BC and CRF07_BC still predominated in eastern Yunnan, but CRF08_BC showed increasing prevalence in western Yunnan. Strikingly, the URFs raised dramatically in most regions of Yunnan. Seven different types of URFs were detected from 12 prefectures, suggesting that complicated and frequent recombination is a salient feature of Yunnan’s HIV-1 epidemic. Among URFs, two BC clusters with distinctive recombination patterns might be potential new CRF_BCs. CRF01_AE was no longer confined to the prefectures bordering Myanmar, and had spread to the eastern part of Yunnan, especially the capital city of Kunming, with a large number of infections in the transient population. The ratios of the main genotypes showed no statistical differences between infected IDUs and heterosexually transmitted infections.

Conclusions/Significance

The changing patterns of the dominant HIV-1 genotypes in Yunnan indicate the complex evolving dynamic nature of the epidemic. Understanding new trends in molecular epidemiology of HIV-1 infection is critical for adjusting current prevention strategies and vaccine development in Yunnan.

Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE in China

To explore the epidemic history of HIV-1 CRF01_AE in China, 408 fragments of gag gene sequences of CRF01_AE sampled in 2002-2010 were determined from different geographical regions and risk populations in China. Phylogenetic analysis indicates that the CRF01_AE sequences can be grouped into four clusters, suggesting that at least four genetically independent CRF01_AE descendants are circulating in China, of which two were closely related to the isolates from Thailand and Vietnam. Cluster 1 has the most extensive distribution in China. In North China, cluster 1 and cluster 4 were mainly transmitted through homosexuality.The real substance of the recent HIV-1 epidemic in men who have sex with men(MSM) of North China is a rapid spread of CRF01_AE, or rather two distinctive natives CRF01_AE.The time of the most recent common ancestor (tMRCA) of four CRF01_AE clusters ranged from the years 1990.9 to 2003.8 in different regions of China. This is the first phylogenetic and temporal dynamics study of HIV-1 CRF01_AE in China.