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

Genetic characterization of a novel HIV-1 CRF01_AE/CRF07_BC recombinant form among men who have sex with men in Guangdong, China

Genome recombination is a major strategy employed by HIV to generate new variants for the benefit of escaping immune surveillance. Near full-length genome phylogenic analysis was utilized to characterize HIV diversity in a male patient in Guangdong, China. The result showed a unique recombinant form (URF) composed of two circulating recombinant forms, CRF01_AE (92%) and CRF07_BC (8%), using six recombinant breakpoints, nt 2794, 3092, 4482, 5988, 7021, and 7722. The emergence of this URF indicates that HIV-1 co-infection or super-infections are common. The increasing genetic complexity of the HIV-1 epidemic in China warrants continued investigation.

Identification of a Novel HIV-1 B/C/CRF01_AE Recombinant Isolate in Guangxi, China

Continual generation of HIV-1 recombinant forms might contribute to its genetic diversity. In this study, a novel B/C/CRF01_AE recombinant virus (GX2016EU13) was identified, which was isolated from a HIV-positive man who was infected through heterosexual sex in Guangxi, China. GX2016EU13 was identified as CCR5-tropic. As shown in the near full-length genome (NFLG) analyses, five recombinant breakpoints were found only in the pol gene of GX2016EU13, which divided the NFLG into three subtype B segments, two subtype C segments, and one CRF01_AE segment. The whole gag sequence of GX2016EU13 belongs to subtype B, and the whole env sequence of GX2016EU13 belongs to CRF01_AE. The recombinant form was distinct from the other circulating recombinant forms and unique recombinant forms reported. The emergence of GX2016EU13 may suppose the complexity of the HIV-1 epidemic in high-risk sexual populations in Guangxi, China.

Epidemiological surveillance of HIV-1 transmitted drug resistance among newly diagnosed individuals in Shijiazhuang, northern China, 2014-2015

BACKGROUND

The widespread use of antiretroviral therapy (ART) has led to considerable concerns about the prevalence of transmitted drug resistance (TDR). Sexual contact, particularly men who have sex with men (MSM) was the most prevalent form of HIV transmission in Shijiazhuang. Hence, we conducted an epidemiological surveillance study on TDR among newly diagnosed individuals who infected-HIV through sexual contact in from 2014-2015.

METHODS

Genotypic resistance mutations were defined using the WHO-2009 surveillance list. Potential impact on antiretroviral drug was predicted according to the Stanford HIV db program version 7.0. The role of transmission clusters in drug resistant strains was evaluated by phylogenetic and network analyses.

RESULTS

In this study, 589 individuals were recruited and 542 samples were amplified and sequenced successfully. The over prevalence of TDR was 6.1%: 1.8% to nucleoside reverse transcriptase inhibitors (NRTIs), 2.0% to non- NRTIs (NNRTIs) and 2.4% to protease inhibitors (PIs), respectively. We did not find significant differences in the TDR prevalence by demographic and clinical characteristics (p > 0.05). Using network and phylogenetic analysis, almost 60.0% sequences were clustered together. Of these clusters, 2 included at least two individuals carrying the same resistance mutation, accounting for 21.2% (7/33) individuals with TDR. No significant difference was observed in the clustering rate between the individuals with and without TDR.

CONCLUSIONS

We obtained a moderate level TDR rate in studied region. These findings enhance our understanding of HIV-1 drug resistance prevalence in Shijiazhuang, and may be helpful for the comprehensive prevention and control of HIV-1.

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

Recent studies have revealed that three major viral strains (CRF07_BC, CRF01_AE, and subtype B) have been cocirculating among men who have sex with men in Beijing. Cocirculation of multiple subtypes in the same population contributes significantly to the emergence of recombinant viruses. This study reports a near full-length genome of a novel, second-generation HIV-1 recombinant (BJ2015EU16) between CRF07_BC and CRF01_AE. The analysis of BJ2015EU16 shows that the genome comprises three interlaced segments, including two CRF07_BC and one CRF01_AE segments, with CRF07_BC as the backbone. There were two recombinant breakpoints in the vpu and env genes of BJ2015EU16. This is different from a previously identified CRF01_AE/07_BC recombinant strain from Beijing. The new emergence of the unique recombinant form increases the complexity of the HIV epidemic in the Beijing homosexual group, and the ongoing generation of recombinant viruses may provide an important basis for future analysis of the recombination mechanism of HIV-1.

The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China

Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (15.8%), CRF07_BC (14.4%), subtype C (2.7%), CRF55_01B (0.7%), subtype B (0.3%) and CRF64_BC (0.3%). CRF08_BC and CRF01_AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08_BC, URFs, CRF01_AE and CRF07_BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01_AE, CRF07_BC and CRF08_BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially during 1991-1999 and 1994-1999, respectively. The EPS for CRF08_BC underwent two exponential growth phases in 1994-1998 and 2001-2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.

Surging HIV-1 CRF07_BC epidemic among recently infected men who have sex with men in Fujian, China

A rapidly increasing number of HIV-1 infections have been identified among men who have sex with men (MSM) in Fujian province of China since 2010. We aimed to investigate the causative factors underlying this surging epidemic. Using immunoassays for HIV-1 diagnosis and phylogenetic analysis for viral genotyping, we found that the number of MSM infections doubled from 171 in 2011 to 340 in 2013 with a significantly increased prevalent rate from 4.1% to 5.2%. Majority of these increased infections took place in Fuzhou, Xiamen, and Quanzhou, three large cities in Fujian, mainly among youth, unemployed, business, and well-educated MSMs. Phylogenetic analysis revealed three major HIV-1 genotypes including CRF01_AE, CRF07_BC, and B/B' yet the surging MSM infections were primarily associated with the rapid sexual spread of CRF07_BC in addition to CRF01_AE. In particular, there was a significant proportional expansion of CRF07_BC infections among recently infected MSMs from 19% in 2012 to 41.9% in 2013. This increase was accompanied by emergence of complex patterns of viral recombination including multiple hybrid variants derived from CRF01_AE and CRF07_BC. Full-genome analysis indicated that CRF07_BC in Fujian was likely originated from similar strains previously found among IDUs in Yunnan province but with unique recombination break points. Our findings indicated that HIV-1 CRF07_BC has adapted for rapid sexual transmission, resulting in the surging HIV-1 epidemic and the emergence of new recombinant strains among MSMs in Fujian. Our findings have implications to vaccine and passive immunization trials in Fujian with emphasis on the induction of cross-subtype protective immunity.

Identification of a Novel HIV-1 Unique Recombinant Form Between B, CRF01_AE and CRF07_BC in Men Who Have Sex with Men in Guangxi, China

B, CRF01_AE and CRF07_BC are three major HIV-1 subtypes circulating in China. Here we detected a novel CCR5-tropic HIV-1 recombinant virus (GX2016EU23), which was isolated from an HIV-1-infected man who had sex with men (MSM) in Guangxi, China. Phylogenetic analysis of the near full-length genome showed that GX2016EU23 consisted of at least seven segments, that is two B, two CRF01_AE, and three CRF07_BC segments. Recombinant breakpoints of GX2016EU23 were observed in the gag, pol, rev, and env regions. This is the first detection of a novel HIV-1 recombinant (B/CRF01_AE/CRF07_BC) in MSM in Guangxi. The emergence of this novel recombinant suggests the increasing genetic diversity of the HIV-1 epidemic among the MSM group in China.

Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE and CRF07_BC among recently infected antiretroviral therapy-naïve men who have sex with men in Jiangsu province, China, 2012 to 2015: A molecular epidemiology-based study

The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015. We collected information on demographics and sexual behaviors and a blood sample for HIV genome RNA extraction, RT-PCR amplification, and DNA sequencing. Multiple alignments were made using Gene Cutter, with the selected reference sequences of various subtypes/recombinants from the Los Alamos HIV-1 database. Phylogenetic and Bayesian evolutionary analysis was performed by MEGA version 6.0, Fasttree v2.1.7. and BEAST v1.6.2. Categorical variables were analyzed using χ test (or Fisher exact test where necessary). χ test with trend was used to assess the evolution of HIV-1 subtype distribution over time. All data were analyzed using SPSS20.0 software package (IBM Company, New York, NY).HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (60.06%), CRF07_BC (22.29%), subtype B (5.88%), CRF67_01B (5.26%), CRF68_01B (2.79%), CRF55_01B (1.55%), CRF59_01B (0.93%), and CRF08_BC (0.62%). Two unique recombination forms (URFs) (0.62%) were also detected. Four epidemic clusters and 1 major cluster in CRF01_AE and CRF07_BC were identified. The introduction of CRF01_AE strain (2001) was earlier than CRF07_BC strain (2004) into MSM resided in Jiangsu based on the time of the most recent common ancestor.Our study demonstrated HIV-1 subtype diversity among ART-naïve MSM recently infected with HIV-1 in Jiangsu. We first depicted the spatiotemporal dynamics, traced the dates of origin for the HIV-1 CRF01_AE/07_BC strains and made inference for the effective population size among newly infected ART-naïve MSM in Jiangsu from 2012 to 2015. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster would be of great value to the monitoring of the epidemic and control of transmission, improvement of antiretroviral therapy strategies, and design of vaccines.

A Novel Recombinant Form of HIV-1 CRF01_AE/CRF07_BC Identified by Near Full-Length Genome in Shaanxi, China

Recently multiple kinds of unique recombinant forms of HIV-1 CRF01_AE/CRF07_BC were identified in China. In this study, we report another near full-length genome of a novel recombinant form (SN121) between CRF01_AE and CRF07_BC from an HIV-1-infected male through heterosexual behavior in Shaanxi province, China. The analysis of SN121 showed that the genome composed of seven interlaced segments, including three CRF07_BC and four CRF01_AE segments with CRF01_AE as the backbone. Six breakpoints were observed in the pol and env gene regions, which are different from the previously identified CRF01_AE/07_BC recombinant forms in China. This novel emerging recombinant form suggested the complicated genetic diversity and the active local transmission of HIV-1 in Shaanxi province. Further monitoring should be performed to elucidate the possible molecular evolution of this novel recombinant form.

Near Full-Length Genome Sequence of a Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/CRF07_BC) Detected Among Blood Donors in North China

In this study, a novel CRF01_AE/07_BC HIV-1 recombinant form, with five breakpoints in the pol, vpr, env, and nef gene regions, was identified from a voluntary blood donor in North China. Our study showed that this HIV-1 recombinant form might be a second-generation recombinant form from two predominant strains in the men who have sex with men (MSM) population, with the CRF07_BC fragments belonging to a CRF07_BC lineage specific to Chinese MSM and the CRF01_AE fragments belonging to the CRF01_AE lineage 5 common among MSM in northern China. Our findings supported the high-risk blood donation behaviors of MSM, implied the increasing complexity of the HIV-1 epidemic among the Chinese MSM population, and called more attention to the effectiveness of the screening test for the growing number of new HIV-1 recombinant forms.

Characterization of a New HIV-1 CRF01_AE/CRF07_BC Recombinant Virus in Guangxi, China

Currently, more and more kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in China. A novel second-generation CCR5-tropic HIV-1 recombinant virus (GX2016EU09) was identified here, which was isolated from a HIV-1-infected man who had sex with men (MSM) in Guangxi, China. Phylogenetic analysis of near full-length genome (NFLG) showed that the novel HIV-1 recombinant GX2016EU09 clustered with CRF01_AE reference sequences, but set up a distinct branch. Recombinant analysis showed that the NFLG of GX2016EU09 composed of CRF01_AE (as the backbone) and CRF07_BC, with nine recombination break points observed in the gag, pol, vif, vpr, tat, rev, vpu, env, and nef regions. To our knowledge, this HIV-1 URF differs from previously documented CRF01_AE/CRF07_BC forms. The emergence of a novel CRF01_AE/CRF07_BC recombinant strain indicates the increasing complexity of the HIV-1 epidemic among the MSM group in Guangxi, China.

Characterization of a Novel HIV-1 Second-Generation Recombinant Form in Men Who Have Sex with Men in Beijing, China

Cocirculation of multiple subtypes in the same population contributes significantly to the emergence of recombinant viruses. BJ2015EU19, a novel CCR5-tropic human immunodeficiency virus (HIV)-1, second-generation recombinant virus, was isolated from a man who has sex with men in Beijing, China. Phylogenetic analysis of the near full-length genome showed that BJ2015EU19 consisted of seven fragments from CRF01_AE and CRF07_BC. There were six recombinant breakpoints in the pol, vpu, env, and nef genes of BJ2015EU19, which were different from the other circulating recombinant forms and unique recombinant forms (URFs). The new emergence of the URF increases the complexity of the HIV epidemic in the Chinese homosexual group, and the ongoing generation of recombinant viruses may provide an important basis for future analysis of the recombination mechanism of HIV-1.

Genome Sequence of a Novel HIV-1 Circulating Recombinant Form (CRF79_0107) Identified from Shanxi, China

We report a novel HIV-1 circulating recombinant form (CRF79_0107) from three epidemiologically unlinked patients through sexual contact in Shanxi province of China. This is the first second-generation circulating recombinant form identified in China. The breakpoint analysis of recombinants showed that CRF79_0107 was composed of CRF01_AE and CRF07_BC, with three CRF07_BC segments inserted into the CRF01_AE backbone. The emergence of CRF79_0107 increases the complexity of the HIV epidemic in China.

Low Rates of Transmitted Drug Resistances Among Treatment-Naive HIV-1-infected Students in Beijing, China

Beijing has seen a rising epidemic of HIV among students. However, little information was known about the molecular epidemiologic data among HIV-infected students. In this study, the diversity and the prevalence of transmitted drug resistance (TDR) in pol sequences derived from 237 HIV-infected students were analyzed. TDR mutations were found in five men who have sex with men (MSM) population among students. The overall prevalence of TDR in students was 2.1%, comprising 1.3% of protease inhibitors and 0.8% of non-nucleoside reverse transcriptase inhibitors. Our finding indicates a low-level prevalence of TDR mutations among students in Beijing.

Genetic transmission networks reveal the transmission patterns of HIV-1 CRF01_AE in China

OBJECTIVES

The epidemic of HIV-1 CRF01_AE has become a major public health issue in China. This study aimed to characterise the transmission patterns of genetic networks for CRF01_AE nationwide and elucidate possible opportunities for prevention.

METHODS

We isolated and conducted genetic transmission network analysis of all available CRF01_AE pol sequences (n=4704) from China in the Los Alamos HIV sequence database.

RESULTS

A total of 1391 (29.6%) sequences were identified as belonging to 400 separate networks. Of men who have sex with men (MSM) in the networks, 93.8% were linked to other MSM and only 2.4% were linked to heterosexual women. However, 11.8% heterosexual women in the networks were linked to MSM. Lineages composed mainly of MSM had higher transmission than those that were mostly heterosexuals. Of the 1391 individuals in networks, 513 (36.9%) were linked to cases diagnosed in different provinces. The proportion of individuals involved in inter-province links was interrelated with the number of migrant people (Spearman's r=0.738, p=0.001).

CONCLUSIONS

The outcome of this study could help improve our ability to understand HIV transmission among various regions and risk groups in China, and highlighted the importance of targeting MSM and migrants by prevention and intervention efforts.

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.

Amino acids at positions 3, 168, and 169 are associated with the ability of Nef proteins from HIV-1 CRF01_AE to downmodulate CD4

Several HIV-1 subtypes are co-circulating among various high-risk groups in China, and an increasing prevalence of CRF01_AE was observed among MSM (men who have sex with men) within recent years. Patients infected with CRF01_AE may experience a more rapid disease progression than patients infected with non-CRF01_AE; however, the underlying mechanisms remains elusive. HIV-1 Nef is a multifunctional protein and plays critical roles in viral pathogenesis. Nef downregulates CD4 and human leukocyte antigen (HLA) to promote viral transmission and escape from the host immune response. In this study, we investigated the CD4 downmodulation activity of Nef proteins isolated from HIV-1 CRF01_AE and analyzed a potential relationship of Nef's capacity to downregulate CD4 with disease progression. We found that the majority of these Nefs from HIV-1 CRF01_AE efficiently downregulated CD4; Nefs with weaker CD4 downmodulation activity tended to be associated with higher CD4 levels and lower viral loads. Further elucidation revealed that amino acid residues at positions 3, 168, and 169 of CRF01_AE Nefs were associated with the capacity to downregulate CD4. Our data suggest that the capacity of Nef-mediated CD4 downregulation is not the only determinant for controlling disease progression, and other host and viral factors should be considered to explain the rapid disease progression of patients infected with HIV-1 CRF01_AE.

Four Closely Related HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Identified in East China

Five near full-length genomes of novel second-generation HIV-1 recombinant virus (JS150021, JS150029, JS150129, JS150132, and AH150183) were identified from five HIV-positive people in Jiangsu and Anhui province, east China. Phylogenic analyses showed that these five sequences are all composed of two well-established circulating recombinant forms (CRFs) CRF07_BC and CRF01_AE, grouped into four new discovered recombinant forms, which show several very similar but not identical recombinant breakpoints. The four recombinant forms are also identified to be a sort of family or related viruses, seems to be the results of different recombination events. The emergence of a serious new closely related CRF07_BC/CRF01_AE recombinant strain indicates the increasing complexity of sexual transmission of the HIV-1 epidemic in China.

Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences

Human immunodeficiency virus (HIV) has a number of circulating recombinant forms that are the product of recombination between different HIV subtypes. The first circulating recombinant form of HIV-1 to be identified was CRF01_AE, which originated in Central Africa and is now most prevalent in Southeast and East Asia. In this study, we investigated the timescale, evolutionary history, and population genetics of the HIV-1 CRF01_AE strains primarily responsible for the epidemic in Asia. A further aim of our study was to define and standardize the nomenclature and provide well-characterized reference sequences for the phylogenetic transmission clusters of CRF01_AE. We analysed a data set of 334 near-complete genome sequences from various risk groups, sampled between 1990 and 2011 from nine countries. Phylogenetic analyses of these sequences were performed using maximum likelihood and Bayesian methods. Our study confirms that the diversity of HIV-1 CRF01_AE originated in Central Africa in the mid-1970s, was introduced into Thailand between 1979 and 1982, and began expanding there shortly afterwards (1982-1984). Subsequently, multiple clusters significantly contributed to China's HIV epidemic. A Bayesian skyline plot revealed the rapid expansion of CRF01_AE in China around 1999-2000. We identified at least eight different clusters of HIV-1 CRF01_AE formed by rapid expansion into different risk groups and geographic regions in China since the late 1980s.

Identification of a Novel HIV Type 1 CRF01_AE/B'/C Recombinant Isolate in Sichuan, China

We report in this study a novel HIV-1 unique recombinant virus (XC2014EU01) isolated from an HIV-positive man who infected through heterosexual sex in Sichuan, China. The near full-length genome analyses showed that XC2014EU01 harbored one subtype B segment in pol region and two subtype C segments in gag-pol region in a CRF01_AE backbone. The unique mosaic structure was distinctly different from the other CRF01_AE/B'/C recombinant forms reported. Phylogenetic tree analyses revealed that the subtype B region originated from a Thailand subtype B' lineage, the subtype C regions were from an India C lineage, and the backbone was from CRF01_AE. XC2014EU01 was still identified as CCR5-tropic, and plasma of XC2014EU01 infected person had the media neutralizing activity. The emergence of XC2014EU01 may increase the complexity of the HIV-1 epidemic among high-risk populations and the difficulty of vaccine research and development.

Defining HIV-1 transmission clusters based on sequence data

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.

HIV-1 CRF01_AE strain is associated with faster HIV/AIDS progression in Jiangsu Province, China

The goal of this study was to assess risk factors associated with HIV/AIDS progression. Between May 2007 and December 2014, 114 subjects were enrolled in Wuxi City and examined every 6 months. The pol gene sequence was amplified to ascertain the HIV-1 subtype. A Cox proportional hazards regression model was used to estimate the factors associated with HIV/AIDS progression. The median follow-up time for all 114 subjects was 26.70 months (IQR: 18.50-41.47), while the median progression time of the 38 progressed subjects was 24.80 months (IQR: 14.13-34.38). Overall, the CRF01_AE subtype was correlated with a significant risk of accelerated progression compared to non-CRF01_AE subtypes (HR = 3.14, 95%CI: 1.39-7.08, P = 0.006). In addition, a lower CD4 count (350-499) at baseline was associated with a risk of accelerated HIV/AIDS progression compared to higher CD4 count (≥500) (HR = 4.38, 95%CI: 1.95-9.82, P < 0.001). Furthermore, interaction analyses showed that HIV-1 subtypes interacted multiplicatively with transmission routes or CD4 count at baseline to contribute to HIV/AIDS progression (P = 0.023 and P < 0.001, respectively). In conclusion, the CRF01_AE subtype and a lower CD4 count at baseline tend to be associated with the faster progression of HIV/AIDS. Understanding the factors affecting HIV/AIDS progression is crucial for developing personalized management and clinical counselling strategies.

HIV prevalence and phylogenetic characteristics among entry travelers in Xishuangbanna prefecture, Yunnan province, between 2003 and 2012

Xishuangbanna is a popular tourist destination in southern Yunnan Province, bordering with Vietnam and Laos, and Myanmar. There are more than 2 million cross-border travelers annually entering China at two land ports, Daluo and Mohan. To clarify the characteristics of HIV-1 prevalence among entry travelers, a retrospective epidemic investigation was conducted. Between 2003 and 2012, 196 among 91 432 entry travelers were detected to be HIV-1-positive, accounting for infection rate of 0.21%. Eighty-one gag-pol gene sequences were obtained for phylogenetic analyses and subsequent recombination analysis. It was shown that the most prevalent HIV-1 subtype in this population was circulating recombinant form (CRF) 01_AE (42, 51.86%), followed by CRF08_BC (17, 20.99%), CRF07_BC (4, 4.94%), B' (2, 2.47%), C (2, 2.47%), other recombinants (9, 11.11%), and undefined subtype (5, 6.17%). HIV-1 genotype distribution among travelers entering at two land ports is different, CRF01_AE and CRF08_BC accounted for a larger percentage among individuals from Daluo, whereas the proportions of subtype C and undefined URFs were larger among individuals from Mohan. The undefined subtype indicates the occurrence of novel HIV-1 subtype or CRF. This finding is useful for developing of AIDS prevention strategies.

Primate immunodeficiency virus classification and nomenclature: Review

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.

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.

Evolutionary Dynamics and Complicated Genetic Transmission Network Patterns of HIV-1 CRF01_AE among MSM in Shanghai, China

To explore the evolutionary dynamics and molecular transmission patterns of HIV-1 CRF01_AE in depth among men who have sex with men (MSM) in Shanghai, we constructed phylogenetic tree and genetic transmission networks based on 1, 152 pol sequences from MSM, 282 from other risk groups and 795 references. Phylogenetic analyses identified two distinct major CRF01_AE lineages and a Shanghai-based sub-lineage. The estimated tMRCAs for lineage 1 and 2 were 1996.0 (1992.9-1999.2) and 1997.8 (1994.3-2001.4), respectively. Of the 1, 152 MSM, 681 (59.1%) were identified as belonging to 241 separate networks. Of these 681 individuals in networks, 74.2% were linked to cases diagnosed in different years, 4.3% were linked to heterosexual women, and 0.7% were linked to persons who inject drugs. A total of 71 networks including 180 individuals diagnosed in Shanghai with the same domicile were found. Recent infection (P = 0.022) and sampling year after 2011 (P < 0.001) were significantly associated with potential transmission links among the networks. Besides, a significant transmission of viruses with drug resistant mutations at V179D/E were found in the networks. Given these findings, we propose that genetic transmission analysis is a useful tool in HIV intervention strategies to curb the spread of virus and promoting public health.

Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses

The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.

Shift in HIV/AIDS Epidemic in Southeastern China: A Longitudinal Study from 1987 to 2015

Objective: The aim of this study was to investigate the shift in the epidemiological features of HIV/AIDS during the last three decades in Fujian Province, southeastern China, so as to provide evidence for the development of novel HIV/AIDS control strategies. Methods: Data pertaining to the conventional surveillance, sentinel surveillance and epidemiological survey in Fujian Province during the period from 1987 to 2015 were collected. The epidemiological trends were described, and the subtypes of HIV strain were genotyped. In addition, the response to antiretroviral therapy was evaluated, and HIV genotypic resistance was assayed. Results: There was an increasing trend observed in the reported cases of HIV/AIDS in Fujian Province. From 1987 to the end of 2015, a total of 8651 HIV/AIDS cases were reported across the province, with totally 1557 deaths found. Among the total cases, the ratio of male/female cases was 3.7:1, which appeared to be an increasing trend; 77.1% cases were detected in young and middle-aged populations aged 19 to 50 years, however, the new HIV infections recently tended to occur in young people aged 15 to 18 years and in populations aged 50 years and older. Among all infected individuals, 49.3% were married, however, the percentage of unmarried cases increased from 6.67% before 1994 to 40.1% in 2015; 64.8% had junior high school education or lower, however, the proportion of HIV/AIDS cases with junior college education or above gradually increased from 6.5% in 2009 to 21.4% in 2015. The reported HIV/AIDS cases were predominantly found in coastal regions; however, a rapidly increasing trend was seen in the number of HIV/AIDS cases in inland regions, and the geographical variation of the cases gradually reduced. There were multiple routes of HIV transmission found in Fujian Province, and 94.2% infections were sexually transmitted, with a large increase in the percentage of male homosexual transmission. A variety of HIV-1 subtypes were genotyped in the province during the study period, and CRF01-AE and CRF07-BC intersubtype recombinant forms were predominant; however, a declining trend in the proportion of HIV-1 CRF01-AE recombinant virus and a significant rise in the proportion of HIV-1 CRF07-BC recombinant virus were observed. Over 90% HIV inhibition was found in all cases receiving antiretroviral therapy during the period from 2011 to 2015, indicating a low prevalence of HIV drug resistance. Conclusions: An increasing trend is still observed in the HIV/AIDS epidemics in Fujian Province, southeastern China. However, the epidemiological pattern of HIV/AIDS has recently changed in the province, and effective control interventions targeting the shift in the epidemiological features of HIV/AIDS should therefore be implemented to control the spread of the epidemic.

A Novel HIV-1 Second-Generation Recombinant Form (CRF01_AE/07_BC) Among Heterosexuals in Nei Monggoi Autonomous Region in China

Increasing second-generation recombinant forms (CRF01_AE/07_BC) have been detected in China recently. Here, we isolated a novel CRF01_AE/07_BC second-generation recombinant form in HIV-1-positive Nei Monggoi's heterosexuals with one CRF07_BC inserted into the CRF01_AE backbone. Polygenetic analyses showed that the CRF01_AE region was grouped with the previously reported cluster 5 lineage, which spreads among the sexual population in north of China, inferring that this recombinant event occurred through heterosexual contact in the north of China possibly. The growing emergence of recombinant forms means coexistence of multiple strains and complexity of the HIV-1 epidemic, which reminds us of the urgent necessity to focus the HIV surveillance among the high-risk populations nationwide in China, particularly to enhance preventive measures in HIV-1 low-prevalence areas.

Near Full-Length Genome Sequences of Two Novel HIV-1 Recombinant Forms Detected in Henan Province, China

In recent years, the population infected through sexual contact has seen the fastest growing prevalence of HIV transmission in Henan province, China. Here, we report two novel human immunodeficiency virus type 1 (HIV-1) recombinant form detected from a comprehensive HIV-1 molecular epidemiologic study among heterosexuals. Recombinant analyses of the near full-length genome of the two novel HIV-1 recombinant isolates: 01B.CN.2012.11092 was CRF01_AE that was partly replaced by a subtype B' fragment of 414 bp (from 4482-4896 according to the HXB2 calibrator). 01BC.CN.2011.11312 was composed of three segments (CRF01_AE/CRF_07BC/B') with breakpoints 4274 and 4833 according to the HXB2 calibrator. They are different from previously identified recombinant strains reported in China.

Identification of a Novel CRF01_AE/CRF07_BC Recombinant Form in Men Who Have Sex with Men in Sichuan, China

A novel second-generation CCR5-tropic HIV-1 recombinant virus (XC2014EU09) was identified here, which was isolated from a HIV-positive man who had sex with men (MSM) in Sichuan, China. Phylogenic analyses showed that XC2014EU09 was composed of two well-established circulating recombinant forms (CRF01_AE and CRF07_BC). Different from the other four reported CRF01_AE/CRF07_BC recombinant forms, three recombinant breakpoints of XC2014EU09 with four fragments were observed in the vpr, env, and nef genes, respectively, as follows: ICRF01_AE (636-5,843 nt), IICRF07_BC (5,844-8,393 nt), IIICRF01_AE (8,394-9,119 nt), and IVCRF07_BC (9,120-9,600 nt). The emergence of CRF01_AE/CRF07_BC recombinant strain indicates the increasing complexity of the HIV-1 epidemic among the MSM group in China.

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.

Characterization of the Near Full-Length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant in an Injection Drug User from Southern Taiwan

HIV-1 CRF07_BC became prevalent in Taiwan after the epidemic among injection drug users (IDUs). We describe a unique recombinant form (URF) consisting of CRF01_AE and CRF07_BC (named URF_0107-H8) genes detected from an IDU. The 8.8 kb near full-length genome of URF_0107-H8 had a CRF01_AE backbone with two CRF07_BC fragments in the reverse transcriptase and integrase region [RT-Int; HXB2 nucleotide (nt) positions 2942-4709] and within the envelop (nt 8467-8722) gene. Phylogenetic analyses revealed that its 1.8 kb RT-Int sequence clustered with those of CRF07_BC strains from Taiwan, while sequences of CRF01_AE portions were more similar to those of Central African origin than contemporaneous CRF01_AE isolates in Taiwan or prevalent in East or Southeast Asia. Recombination breakpoints and phylogenetic relationships of URF_0107-H8 were different from those of CRF01_AE/CRF07_BC URFs previously reported from China. This highlighted the importance of continual monitoring of genetic evolution of HIV strains and the emergence of new recombinants.

Molecular Genotyping of HIV-1 Strains from Newly Infected Men Who Have Sex with Men in Harbin, China

In this study, blood samples from newly HIV-1 infected men who have sex with men (MSM) were collected, and HIV-1 genotypes were identified based on gag p17-p24 and nef gene regions. We found that participants aged from 20 to 40 years old were the major infection group in Harbin. CRF01_AE was the predominant genotype, contributing to 84.7% of HIV-1 infections, followed by subtype B (4.7%), CRF07_BC (3.5%), and subtype B' (Thai B, 1.2%). Moreover, five unique recombinant forms (5.9%) were also identified, including genotypes 01B, 01C, and 01/02. The recombinant CRF01_AE/CRF02_AG was first reported in China. These results suggested that current HIV-1 genotype epidemic among MSM in Harbin is more complicated and that intersubtype recombinants have emerged. Therefore, timely regional epidemiological surveillance of HIV-1 genotype and development of prevention measures for new HIV-1 infections among MSM are quite important.

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.

Prevalence of different HIV-1 subtypes in sexual transmission in China: a systematic review and meta-analysis

Sexual transmission has become the primary route of HIV transmission in China. Therefore, a comprehensive overview of HIV-1 subtype distribution is necessary for the prevention and control of the HIV epidemic. The present study aimed to provide a comprehensive prevalence estimate of different HIV-1 subtypes in sexual transmission in China. We conducted a systematic literature review for studies of HIV-1 subtypes in English and Chinese through several databases. Eligible articles were screened and selected by two authors independently. Random-effects model were applied to calculate the pooled prevalence of different HIV-1 subtypes, and subgroup analyses examined prevalence estimates across time, locations, and populations. A total of 130 eligible studies were identified, including 18 752 successfully genotyped samples. The pooled prevalence of CRF01_AE, subtype B, CRF07_BC, CRF08_BC, and subtype C were 44·54% (95% CI 40·81-48·30), 18·31% (95% CI 14·71-22·17), 16·45% (95% CI 13·82-19·25), 2·55% (95% CI 1·56-3·73), 0·37% (95% CI 0·11-0·72), respectively. The prevalence of subtype B in sexual transmission decreased, while the prevalence of CRF01_AE and CRF07_BC in sexual transmission, and CRF08_BC in heterosexual transmission increased. There is significant variation in HIV-1 subtype distribution between regions. The distribution of HIV-1 subtypes and circulating recombinant forms have changed significantly. The high genetic variability of HIV-1 poses a significant challenge for disease control and surveillance in China.

Short Communication: The Distribution of Potential N-Linked Glycosylation Sites in Gp120 Differs Among Major HIV-1 Subtypes Circulating in China

CRF01_AE shows an obvious sexual transmission advantage over other major HIV-1 subtypes circulating in China. Previous studies showed that the presence or absence of potential N-linked glycosylation sites (PNGSs) in variable loops might affect HIV-1 transmission; it is therefore of interest to compare the distribution of potential PNGSs on envelopes of different subtypes circulating in China. Compared to CRF07_BC, CRF08_BC, B, and B' subtypes isolated in China, CRF01_AE subtypes isolated from both China and outside China had significantly fewer PNGSs in total and in V2/V4, while they had significantly more PNGSs in V5. HIV-1 subtype CRF01_AE has a unique PNGS distribution pattern in Gp120, which may contribute to its advantage in sexual transmission in China.

Differences in clinical and psychiatric outcomes between prevalent HIV-1 molecular subtypes in a multiethnic Southeast Asian sample

OBJECTIVE

In Southeast Asia, subtypes B and CRF01_AE are the prevalent human immunodeficiency virus-1 (HIV-1) subtypes. This study examines the intersubtype differences in clinical indicators and psychiatric symptoms in a multiethnic sample.

METHODS

The study site was a national HIV treatment center. Data were extracted from the Molecular Epidemiology Research study and the HIV-Psychiatry Integrated Mental Health Project, and analyzed according to groups defined by viral subtype.

RESULTS

Of 177 subjects, 54.8% were infected with subtype CRF01_AE; 42.9% screened positive on the Hospital Anxiety and Depression Scale (HADS). The CRF01_AE group was significantly older (mean 38.29 years vs. 34.62 years, P=.031) and had advanced immunosuppression (CD4 <200) just prior to HADS screening (33.0% vs. 13.5%, P=.003). By multivariate logistic regression, homosexual transmission [odds ratio (OR) 0.388, 95% confidence interval (CI) 0.158-0.951, P=.038], subtype CRF01_AE (OR 2.898, 95% CI 1.199-7.001, P=.018) and positive HADS screening (OR 2.859, 95% CI 1.261-8.484, P=.012) were associated with advanced immunosuppression; and only advanced immunosuppression was associated with screening positive on the HADS (OR 3.270, 95% CI 1.299-8.227, P=.012).

CONCLUSION

Subtype CRF01_AE is associated with advanced immunosuppression but not with symptoms of anxiety and depression. The results suggest that psychiatric symptoms are associated with advanced HIV disease regardless of subtype.

Study of antibody repertoires to the CD4 binding site of gp120 of a Chinese HIV-1-infected elite neutralizer, using 454 sequencing and single-cell sorting

Broadly neutralizing antibodies (NAbs) against the CD4 binding site of HIV gp120 (CD4bs) have provided important information for vaccine design. In this study, we combined deep sequencing and single memory B cell sorting to isolate CD4bs-directed NAbs from a Chinese HIV-1-infected elite neutralizer. We first performed 454 pyrosequencing to capture the IGHV1, IGKV, and IGLV germline gene families. IGHV1-2*02, the heavy chain germline V gene (VH) of the CD4bs-directed bNAb VRC01, was found to have a relatively low somatic mutation rate. When an identity/divergence plot was used to interrogate the 454 sequencing data, no VRC01-like sequences were found within the dataset. We next used a pair of CD4bs-specific probes (RSC3/ΔRSC3) to sort the B cells from this Chinese donor and identified a CD4bs-directed Ab that showed limited neutralization capability. Interestingly, the VH gene of this weak NAb belongs to the IGHV5-51 lineage, with a somatic mutation rate of 7.99 %. Our study thus demonstrates that CD4bs-directed NAbs can be produced by rearrangement from other VH genes, such as IGHV5-51 in this donor, rather than IGHV1-2*02. The 454 sequencing data and NAb obtained from this study will provide useful insights into the CD4bs-directed B-cell response during HIV-1 infection as well as the diversity of neutralizing antibodies.

Estimating HIV-1 Transmission Routes for Patients With Unknown Risk Histories by Viral Sequence Phylogenetic Analyses

OBJECTIVE

To estimate routes of transmission among HIV-infected persons with unknown-risk histories in China.

DESIGN/METHOD

All newly reported cases of HIV infection between year 1985 and 2009 were obtained from the National Databank of Chinese Center for Disease Control and Prevention (China CDC). A large number of unknown-risk HIV-positive samples were found. To estimate the transmission routes, HIV gag sequences were amplified by reverse transcription polymerase chain reaction and phylogenetically analyzed. The cases with unknown-risk history were compared with those with known-risk histories from the same local region and time period. A statistical model was developed to predict the transmission routes and was validated on known-risk samples, before testing 324 unknown-risk samples collected from 1996 to 2006.

RESULTS

Newly reported cases of HIV infection in China increased steadily between 1985 and 2009, from just a handful of cases to 30,340 in 2009. Injecting drug use (IDU) was the dominant route of transmission among reported cases in the early years and decreased from 83.4% in 1985-2001 to 28.2% in 2009. Conversely, sexual transmission increased from 6.9% in 1985-2001 to 60.9% in 2009. Among the 324 unknown-risk HIV sequences collected from 1996 to 2006, our model identified 100 samples most likely transmitted by blood, 114 by IDU, and 110 by sexual transmission. Our validation samples showed that our model has 90.8%, 94.8%, and 69.6% sensitivity and 87.3%, 87.5%, and 85.5% specificity, for blood, IDU, and sexual transmission, respectively.

CONCLUSIONS

We developed a model to estimate transmission route of unknown-risk HIV-positive samples and found that these unknown-risk patients could be transmitted by blood, IDU, or sex.

Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana

Southern Africa continues to be the epicenter of the HIV/AIDS epidemic. This HIV-1 subtype C epidemic has a predominantly heterosexual mode of virus transmission and high (>15%) HIV prevalence among adults. The epidemiological dynamics of the HIV-1C epidemic in southern Africa are still poorly understood. Here, we aim at a better understanding of HIV transmission dynamics by analyzing HIV-1 subtype C sequences from Mochudi, a peri-urban village in Botswana. HIV-1C env gene sequences (gp120 V1C5) were obtained through enhanced household-based HIV testing and counseling in Mochudi. More than 1200 sequences were generated and phylogenetically distinct sub-epidemics within Mochudi identified. The Bayesian birth-death skyline plot was used to estimate the effective reproductive number, R, and the timing of virus transmission, to classify sub-epidemics as "acute" (those with recent viral transmissions) or "historic" (those without recent viral transmissions). We identified two of the 15 sub-epidemics as "acute." The median estimates of R among the clusters ranged from 0.72 to 1.77. The majority of HIV lineages, 11 out of 15 clusters with 5+ members, appear to have been introduced to Mochudi between 1996 and 2002. The median peak duration of viral transmissions was 7.1 years (range 2.9-9.7 years). The median life span of identified HIV sub-epidemics, i.e., the time between the inferred epidemic origin and its most recent sample, was 13.1 years (range 10.2-22.1 years). Most viral transmissions within the sub-epidemics occurred between 1997 and 2007. The time period during which infected people are infectious appears to have decreased since the introduction of the national ART program in Botswana. Real-time HIV genotyping and breaking down local HIV epidemics into phylogenetically distinct sub-epidemics may help to reveal the structure and dynamics of HIV transmission networks in communities, and aid in the design of targeted interventions for members of the acute sub-epidemics that likely fuel local HIV/AIDS epidemics.

Heterogeneous Evolution of HIV-1 CRF01_AE in Men Who Have Sex with Men (MSM) and Other Populations in China

Introduction

The HIV epidemic in men who have sex with men (MSM) continues to grow in most countries. However, the phylodynamic and virological differences among HIV-1 strains circulating in MSM and other populations are not well characterized.

Methods

Nearly full-length genomes (NFLGs) of the HIV-1 CRF01_AE were obtained from the Los Alamos HIV database. Phylogenetic analyses were conducted using the NFLG, gag, pol and env genes, using the maximum likelihood method. Selection pressure analyses at the codon level were performed for each gene in the phylogenetic clusters using PAML.

Results

Sequences isolated from MSM in China clustered in Clusters 1 (92.5%) and 2 (85.71%). The major risk factor for Cluster 3 was heterosexual transmission (62.16%). The ratio of non-synonymous to synonymous substitutions in the env gene (0.7–0.75) was higher than the gag (0.26–0.34) or pol (0.21–0.26) genes. In env gene, Cluster 1 (4.56×10^-3subs/site/year) and 2 (6.01×10^-3subs/site/year) had higher evolutionary rates than Cluster 3 (1.14×10^-3subs/site/year). Positive selection affected 4.2–6.58% of the amino acid sites in the env gene. Two sites (HXB2:136 and 316) evolved similarly in Clusters 1 and 2, but not Cluster 3.

Conclusion

The HIV-1 CRF01_AE in MSM is evolving differently than in other populations.

Trends of HIV subtypes and phylogenetic dynamics among young men who have sex with men in China, 2009-2014

To investigate the origins of HIV transmission and phylogenetic dynamics among men who have sex with men (MSM), a total of 1205 newly diagnosed HIV-infected 16-25 year-olds were recruited in 13 provinces across China between 2009 and 2014. Based on phylogenetic analyses of partial pol sequences, HIV-1 subtypes including CRF01_AE (45.3%), CRF07_BC (37.8%), subtype B (6.1%), and B' (3.7%), as well as some other recombinants (7.1%) were identified. In addition to two distinct CRF01_AE clusters [cluster 4 (33.7%, 406/1205) and cluster 5 (7.1%, 85/1205)], we identified a new CRF07_BC cluster (cluster 1) (36.0%, 434/1205), which entered Chinese MSMs in 2004, and had been rapidly spreading since about 2004, which indicating the third wave of the HIV epidemic among the population. Moreover, two new clusters of CRF_01B recombinants were found in this study. The complexities of HIV subtypes and recombinants strongly supports the necessity for a comprehensive study about risk behaviors and their relationship with increasing HIV epidemic subtypes among the MSM group. Implementation and evaluation of comprehensive harm reduction strategies in Chinese MSM are urgently needed.

A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF)

BACKGROUND

In this study, the prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored.

METHODS

Available HIV-1 complete genomes of CRF01_AE were retrieved from the HIV database. The two alignments were evaluated with RDP3. Recombinants were defined as cases in which the recombination signal was supported by at least 3 methods with P-values of ≤0.05 after Bonferroni correction for multiple comparisons implemented in RDP3. Phylogenetic analysis was performed to further investigate the role of intrasubtype recombinants in epidemics.

RESULTS

Here, 124 out of the 339 sequences from around the world (36.6 %) showed significant evidence of recombination. Here, 84 of these recombinants were from China, accounting for 54.9 % of local total sequences (84 out of 153). The results indicated non-negligible levels of intrasubtype recombination. Subsequent phylogenetic analysis indicated that a considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms. Three large, well-supported intrasubtype recombinants clusters were identified here. Through a survey of risk factors and sampling cities and provinces, cluster I and cluster II were found to be prevalent primarily among men who have sex with men in major northern cities. Cluster III was prevalent among heterosexuals and intravenous drug users in southern and southwestern provinces.

CONCLUSIONS

The current work highlighted the remarkable prevalence of intrasubtype recombination within the CRF01_AE epidemic and emphasized the value of intrasubtype recombinants, which came to circulate in the same manner as intersubtype recombinants.

The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.

HIV Epidemic in Asia: Implications for HIV Vaccine and Other Prevention Trials

An overall decrease of HIV prevalence is now observed in several key Asian countries due to effective prevention programs. The decrease in HIV prevalence and incidence may further improve with the scale-up of combination prevention interventions. The implementation of future prevention trials then faces important challenges. The opportunity to identify heterosexual populations at high risk such as female sex workers may rapidly wane. With unabating HIV epidemics among men who have sex with men (MSM) and transgender (TG) populations, an effective vaccine would likely be the only option to turn the epidemic. It is more likely that efficacy trials will occur among MSM and TG because their higher HIV incidence permits smaller and less costly trials. The constantly evolving patterns of HIV-1 diversity in the region suggest close monitoring of the molecular HIV epidemic in potential target populations for HIV vaccine efficacy trials. CRF01_AE remains predominant in southeast Asian countries and MSM populations in China. This relatively steady pattern is conducive to regional efficacy trials, and as efficacy warrants, to regional licensure. While vaccines inducing nonneutralizing antibodies have promise against HIV acquisition, vaccines designed to induce broadly neutralizing antibodies and cell-mediated immune responses of greater breadth and depth in the mucosal compartments should be considered for testing in MSM and TG. The rationale and design of efficacy trials of combination prevention modalities such as HIV vaccine and preexposure prophylaxis (PrEP) remain hypothetical, require high adherence to PrEP, are more costly, and present new regulatory challenges. The prioritization of prevention interventions should be driven by the HIV epidemic and decided by the country-specific health and regulatory authorities. Modeling the impact and cost-benefit may help this decision process.

Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China

Unlike most areas of China, HIV transmission via men who have sex with men (MSM) is increasing rapidly, and has become the main route of HIV transmission in Harbin city. The purpose of the current study was to elaborate the molecular epidemiologic characteristics of the new HIV epidemic. Eighty-one HIV-1 gag gene sequences (HXB2:806-1861) from local HIV infections were isolated; CRF01_AE predominated among HIV infections (71.6%), followed by subtype B (16.5%), CRF07_BC (6.2%), and unique recombinant strains (URFs; 6.2%). URFs were most often identified in the MSM population, which consisted of a recombination of CRF01_AE with subtype B or CRF07_BC. Six clusters were formed in this analysis; clusters I and II mainly circulated in southwest China. Clusters III and IV mainly circulated in southwest, southeast, and central China. Clusters V and VI mainly circulated in north and northeast China. Clusters III and IV may facilitate the transmission of the CRF01_AE strain from the southwest to the north and northeast regions of China. HIV subtypes are becoming diverse with the persistent epidemic in this geographic region. In brief, our results indicate that the molecular epidemiology of HIV is trending to be more complex. Thus, timely molecular epidemiologic supervision of HIV is necessary, especially for the MSM population.

The biological characteristics of predominant strains of HIV-1 genotype: modeling of HIV-1 infection among men who have sex with men

To investigate the molecular subtypes of prevalent HIV-1 strains and characterize the genetics of dominant strains among men who have sex with men. Molecular epidemiology surveys in this study concentrated on the prevalent HIV-1 strains in Liaoning province by year. 229 adult patients infected with HIV-1 and part of a high-risk group of men who have sex with men were recruited. Reverse transcription and nested PCR amplification were performed. Sequencing reactions were conducted and edited, followed by codon-based alignment. NJ phylogenetic tree analyses detected two distinct CRF01_AE phylogenetic clusters, designated clusters 1 and 2. Clusters 1 and 2 accounted for 12.8% and 84.2% of sequences in the pol gene and 17.6% and 73.1% of sequences in the env gene, respectively. Another six samples were distributed on other phylogenetic clusters. Cluster 1 increased significantly from 5.6% to 20.0%, but cluster 2 decreased from 87.5% to 80.0%. Genetic distance analysis indicated that CRF01_AE cluster 1 in Liaoning was homologous to epidemic CRF01_AE strains, but CRF01_AE cluster 2 was different from other scattered strains. Additionally, significant differences were found in tetra-peptide motifs at the tip of V3 loop between cluster 1 and 2; however, differences in coreceptor usage were not detected. This study shows that subtype CRF01_AE strain may be the most prevalent epidemic strain in the men who have sex with men. Genetic characteristics of the subtype CRF01_AE cluster strain in Liaoning showed homology to the prevalent strains of men who have sex with men in other parts of China.