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CRF07_BC is one of the most prevalent HIV-1 strains in China, and Xinjiang Uygur Autonomous Region has ever been considered to be a second epidemic center after Yunnan Province in previous studies. Here we use HIV-1 pol gene sequences identified from Hetian Prefecture located in Xinjiang Autonomous Region to reconstruct the epidemic history of HIV CRF07_BC strain circulating in this region. We found that CRF07_BC is the predominant HIV-1 form in Hetian Prefecture, and the estimated tMRCA analysis shows that there is no enough evidence supporting Xinjiang Autonomous Region as a second epidemic center of spreading HIV-1. It may imply that every city may be only a point among the HIV spreading network because of the frequent migration of population in the whole country nowadays.

CRF01_AE, which has led a new epidemic in many provinces in China and has displayed complex characteristics, has now evolved into multiple clusters in China. Some clusters often circulate in specific regions or among specific risk populations in China. To better determine the characteristics of CRF01_AE circulating in Anhui Province, we analyzed CRF01_AE based on gag and pol sequences. Our results showed that CRF01_AE circulating in Anhui Province was clearly divided into three clusters. Cluster 1 covered 90% of the sequences in all CRF01_AE. Among Cluster 1, the sequences from men who have sex with men (MSM) and heterosexuals were interwoven. It is suggested that MSM may play a bridge role in transmitting HIV-1 among the different risk groups.

CRF01_AE and subtype B are the two major HIV-1 clades circulating in China. Heterosexual transmission is the predominant route for the spread of HIV and heterosexuals often include men who have sex with men and intravenous drug users. Furthermore, many kinds of circulating recombinant forms (CRF) and unique recombinant forms (URF) between CRF01_AE and subtype B were recently identified in Southeast Asia. Therefore it is inevitable that the new recombinant of CRF01_AE/B will emerge among them. Here we identified a novel recombinant of CRF01_AE/B, isolated from heterosexuals, which has a distinctly different genome structure from other CRF01Bs and URFs reported before. The analysis of the near full-length sequence of JS2011001 shows that it is composed of at least five interlaced CRF01_AE and B segments. Recently, many kinds of URFs and CRFs began to prevail within a short period in China, which implies that a mix of HIV-1 infections is common in China and more attention should focus on it.

CRF01_AE and subtype B are the two of major HIV-1 clades circulating in China. HIV spread more rapidly among men who have sex with men (MSM) than among populations with other risk behaviors. In Jiangsu province in China, the HIV-1 incidence among MSM was more than 3.8%. Our previous study showed that almost equal proportions of CRF01_AE, B, and CRF07_BC were circulating among MSM. Moreover, many kinds of CRF01Bs have been identified among MSM in Southeast Asia in recent years. It is therefore inevitable that recombination between CRF01_AE and subtype B will emerge among MSM in Jiangsu province in China. Here we identify a novel recombinant of CRF01_AE/B that has a distinctly different genome structure from other CRF01Bs and unique recombinant forms (URFs) previously identified. An analysis of the near full-length sequence of JS2010001 showed that it is composed of at least three interlaced CRF01_AE and B segments. Recently, many kinds of URFs and C circulating recombinant forms (CRFs) have emerged among MSM in China within a short period of time, which suggests that dual infection of HIV-1 among MSM in China is very common and that more effective intervening measures to prevent the spread of HIV among MSM should be taken.

The occurrence of a novel CRF01_AE-associated recombinant in Jiangsu implies the importance of characterizing full-length CRF01_AE genomic sequence from injecting drug users (IDUs). Here, we reported a near full-length CRF01_AE sequence 07JSWX045 obtained from a Jiangsu IDU, using a modified method. The sequence analyses of 07JSWX045 revealed several interesting findings. First, 07JSWX045 was phylogenetically close to CRF01_AE strains circulating among Jiangsu men who have sex with men (MSM), implying a recent common ancestor. Second, 07JSWX045 was not genetically associated with the CRF01_AE part of the new CRF01_AE/07_BC recombinant found in Jiangsu. Third, both 07JSWX045 and the CRF01_AE parent of CRF01/07 recombinant phylogenetically clustered with two different CRF01_AE subgroups circulating in Fujian, respectively. It suggests that at least two genetically independent CRF01_AE descendants are circulating in Jiangsu possibly via two independent introductions from Fujian. Fourth, two AZT resistance mutations in the RT gene were detected within patient JSWX045, who did not receive any antiviral therapy before sampling, providing valuable bioinformatics sites for investigating the epidemic origin and molecular properties of Jiangsu CRF01_AE strains. Furthermore, patient JSWX045 had two high-risk behaviors including injection drug use and heterosexual contact. He might have been initially infected with CRF01_AE via heterosexual contact, and then introduced this subtype to other people via injection drug use. Therefore, increasing concern is urgently needed for those persons who often have more than two high-risk behaviors.

Our recent study showed that almost equal proportions of B, CRFs_BC, and CRF01_AE were circulating among MSM in Jiangsu, suggesting that there is a very high likelihood of generating new intersubtypes/CRFs recombinants. Here, we report an epidemiologically linked cohort including 22 HIV-1-positive IDUs in Jiangsu. Fifteen blood samples were collected to investigate HIV-1 subtype characterization. The analyses of gag-RT regions showed that 14 of these samples belonged to CRF07_BC. Importantly, we detected, for the first time, a novel second-generation HIV-1 recombinant (07JSNJ001) between CRF01_AE and CRF07_BC. The analyses of the near full-length genomic sequence of 07JSNJ001 (GenBank accession number FJ238521) showed that 07JSNJ001 is composed of at least 10 interlaced CRF07_BC and CRF01_AE segments, quite distinct from any previously identified CRF and URF around the world. The detection of the CRF01_AE/CRF07_BC recombinant may be a harbinger of more new intersubtypes/CRFs recombinants occurring in Jiangsu Province.