Characterization of a novel HIV-1 second-generation circulating recombinant form (CRF102_0107) among men who have sex with men in Anhui, China
Authors: Xi Li, Jianjun Wu, Yu Zhang, Yuelan Shen, Hanping Li, Hui Xing, Yongjian Liu, Xiaohui Yang, Xinping Ding, Bing Hu, Jingwan Han, Jingyun Li, Bin Su, Xiaolin Wang, Lin Li
Journal: Journal of Infection (2019)

The high level of genetic variation along with highly recombinogenic reverse transcriptase enzyme of HIV-1 contribute to the emergence of increasing number of circulating recombinant forms (CRFs). Up to date,101 CRFs have been assigned and published with public sequence data, which is available on the Los Alamos HIV Sequence Database (www.hiv.lanl.gov). Most CRFs were found in heterosexual or drug users in the past. Recent correspondence in this Journal has reported on a novel HIV-1 circulation recombinant form (CRF100_01C) comprising CRF01_AE and C among heterosexual in Yunnan, China.1Feng Y. Zhang C. Zhang M. et al.First report of a novel HIV-1 recombinant form (CRF100_01C) comprising CRF01_AE and C among heterosexuals in Yunnan, China.J Infect. 2018; 77: 561-571Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar CRF01_AE participated in the recombination soon after it became one of the major HIV epidemic strains in China.2Guo H. Hu H. Zhou Y. et al.A novel HIV-1 crf01_ae/b recombinant among men who have sex with men in Jiangsu Province, China.AIDS Res Hum Retrovir. 2014; 30: 706-710Crossref PubMed Scopus (17) Google Scholar CRF07_BC was introduced into men who have sex with men (MSM) population in China at the beginning of the 21st century.3Zhang Y. Pei Z. Li H. et al.Characterization of a novel HIV-1 circulating recombinant form (CRF80_0107) among men who have sex with men in China.AIDS Res Hum Retrovir. 2019; 35: 419-423Crossref PubMed Scopus (21) Google Scholar Less than 20 years after CRF07_BC entered China, the second generation CRF (CRF102_0107) was found in MSM in China. During that time several CRFs and URFs comprising CRF01_AE and CRF07_BC lineages were coming out among MSM in Beijing, Jilin, Sichuan, Guangxi, Zhejiang, and Inner Mongolia, China.3Zhang Y. Pei Z. Li H. et al.Characterization of a novel HIV-1 circulating recombinant form (CRF80_0107) among men who have sex with men in China.AIDS Res Hum Retrovir. 2019; 35: 419-423Crossref PubMed Scopus (21) Google Scholar, 4Li Y. Feng Y. Li F. et al.Genome sequence of a novel HIV-1 circulating recombinant form (CRF79_0107) identified from Shanxi, China.AIDS Res Hum Retrovir. 2017; 33: 1056-1060Crossref PubMed Scopus (32) Google Scholar, 5Wang C. Wang Y. Kong D. et al.Characterization of a novel HIV-1 S-Generation recombinant form in men who have sex with men in Beijing, China.AIDS Res Hum Retrovir. 2017; 33: 1175-1179Crossref PubMed Scopus (7) Google Scholar, 6Wang Y. Wei H. Xu W. et al.Identification of a novel CRF01_ae/CRF07_bc recombinant form in men who have sex with men in Sichuan, china.AIDS Res Hum Retrovir. Jul 2016; 32: 718-721Crossref PubMed Scopus (12) Google Scholar, 7Jiao Y. Wang Y. Kong D. et al.Characterization of a new HIV-1 CRF01_AE/CRF07_BC recombinant virus form among men who have sex with men in Beijing, China.AIDS Res Hum Retroviruses. 2018; 34: 550-554Crossref PubMed Scopus (12) Google Scholar The high frequency of second generation recombination may be due to the higher risk behaviors in MSM, such as unprotected anal intercourse, multiple sexual partners, low rates of condom use and some other factors. In this study, we defined a novel second-generation CRF (CRF102_0107) containing 10 segments from subtypes B, C and CRF01_AE. To analyze its evolutionary history, three epidemiologically unlinked HIV-1 positive plasma samples named FY058,FY336 and FY405 were collected from the MSM population in Fuyang, Anhui province. All three participants signed informed consent forms before investigation and peripheral blood collection. The clinical and demographic information are summarized in Table 1.Table 1Demographic characteristics of study subjects infected with CRF102_0107.Strain nameSampling yearSampling regionGenderAgeEthnic groupMarriageRisk factorAccession no.FY0582017Fuyang, AnhuiMale40HandivorcedMSMMN178644FY3362018Fuyang, AnhuiMale28HanmarriedMSMMN178645FY4052018Fuyang, AnhuiMale36HandivorcedMSMMN178646CRF, circulating recombinant form; MSM, men who have sex with men. Open table in a new tab CRF, circulating recombinant form; MSM, men who have sex with men. The near full-length genome (NFLG) of HIV strains were amplified and sequenced. Finally, the NFLG of FY058 and the NFLG of FY336 were successfully amplified. The NFLG of FY058 and FY336 were 8957 bp (HXB2, 623-9,564) and 8,999 bp (HXB2, 608-9,589) in size, respectively. This two NFLG sequences were submitted to the Basic Local Alignment Search Tool (Blast) for searching for more similar sequences, but no high similarity sequences(>95%) were found. Due to the unsuccessful NFLG amplification of FY405, only a partial sequence of its pol region (HXB2, 2253-3,314) was obtained. Considering that more partial genome sequences were submitted to the Los Alamos database than NFLG sequences, The pol region sequences of FY405 was used for more blast analysis, and the result showed that no sequences with high similarity (>95%) were found. Two NFLG sequences (FY058 and FY336) together with the pol sequences of FY405 were further aligned with 34 reference sequences which were provided by Foley, Brian Thomas (HIV Databases, [email protected]) including two or more HIV-1 reference strains of each subtype (A1, A2, B, C, D, F1, F2, G, H, J, and K), CRF01_AE, CRF07_BC and outgroup O. This alignment was then manually edited using BioEdit v7.2.5 software. A phylogenetic tree was constructed by the neighbor-joining method based on Kimura 2-parameter model with 1000 bootstrap replicates in MEGA6 software and embellished in FigTree v1.4.4 software. For the purpose of recombination analysis, the jumping profile hidden Markov model (jpHMM) (http://jphmm.gobics.de/submission_hiv) was applied. Subsequently, a subregion neighbor-joining tree was constructed to determine the origin cluster of 4 main segments (I Ⅱ Ⅲ Ⅳ) from CRF01_AE and CRF07_BC according to the jpHMM result. Finally, to better understand the time of the most recent common ancestor (tMRCA) of CRF102_0107, the bayesian molecular clock analyses was performed in BEAST v1.7.5. The phylogenetic tree showed that the three sequences from epidemiologically unlinked patients formed a distinct monophyletic cluster distinctly related to all known HIV-1 subtypes/CRFs with a high bootstrap value of 100% (Fig. 1A). As shown in the recombination analysis result (Fig. 1B), the two NFLG sequences were composed of CRF01_AE and subtypes B and C. And the pol partial sequence of FY405 shared same breakpoints with FY058 and FY336. Subtype B and C segments of CRF102_0107 were further submitted for BLAST, the results showed highest similarity to (>95%) CRF07_BC strains. The comparison of genomic maps between CRF07_BC and CRF102_0107 also showed that the BC segments of CRF102_0107 were highly coincidences with CRF07_BC (Fig. 1C). Subregion phylogenetic analyses of 4 genomic segments I (790-2,613 nt),Ⅱ(2,613-3,843 nt),Ⅲ(4,164-6,211 nt),Ⅳ(6,489-8,260 nt) were further conducted to explore their likely parental lineages. The high bootstrap values in phylogenetic tree supported close relationship with CRF01_AE or CRF07_BC subtype references respectively. Subregion phylogenetic analyses indicated that the segment I and segment Ⅳ of CRF102_0107 belonged to the CRF01_AE cluster 5, which is mainly circulating among the MSM population in China (Fig. 2A).8Wang X. He X. Zhong P. et al.Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China.Sci Rep. 2017; 7: 6330Crossref PubMed Scopus (30) Google Scholar The segment Ⅱ and segment Ⅲ of CRF102_0107 were clustered with the CRF07_BC cluster, which was also identified among MSM (Fig. 2A).3Zhang Y. Pei Z. Li H. et al.Characterization of a novel HIV-1 circulating recombinant form (CRF80_0107) among men who have sex with men in China.AIDS Res Hum Retrovir. 2019; 35: 419-423Crossref PubMed Scopus (21) Google Scholar The segments (I Ⅱ Ⅲ Ⅳ) of CRF102_0107 are closely related to the clusters associated with MSM according to the subregional analysis, suggesting that CRF102_0107 may be predominantly prevalent in the MSM. The Bayesian analysis shows that the (tMRCA) of the segment I and the segment Ⅲ from CRF102_0107 were predicted in 2010.9 [95% highest probability density (HPD): 2008.2, 2013.6] and 2011.4 [95% HPD: (2008.6,2013.8)], respectively (Fig. 2B). The (tMRCA) of the segment II and the segment IV from CRF102_0107 were predicted in 2008.2 [95% HPD: (2001.5,2012.8)] and 2007.1 [95%highest probability density (HPD): 2003.4, 2010.6], respectively(Fig. 2B). The segments Ⅰ and Ⅲ originated around 2010.9–2011.4. The segments Ⅱ and Ⅳ originated around 2007.1-2008.2. Hence, it is speculated that the CRF102_0107 had been occurred a recombination in two time periods, respectively. HIV-1 had been increasing rapidly among MSM in China, with the transmission rate of male homosexuality rising from 2.5% in 2006 to 28.0% in 2016 among new cases diagnosed annually. In addition to the rapid spread among MSM, HIV had recently increased in diversity. Several co-circulating subtypes were found in the MSM population, including CRF01_AE and CRF07_BC.3Zhang Y. Pei Z. Li H. et al.Characterization of a novel HIV-1 circulating recombinant form (CRF80_0107) among men who have sex with men in China.AIDS Res Hum Retrovir. 2019; 35: 419-423Crossref PubMed Scopus (21) Google Scholar,4Li Y. Feng Y. Li F. et al.Genome sequence of a novel HIV-1 circulating recombinant form (CRF79_0107) identified from Shanxi, China.AIDS Res Hum Retrovir. 2017; 33: 1056-1060Crossref PubMed Scopus (32) Google Scholar,9Zhang X. Li S. Li X. et al.Characterization of HIV-1 subtypes and viral antiretroviral drug resistance in men who have sex with men in Beijing, China.AIDS. 2007; 21: S59-S65Crossref PubMed Scopus (68) Google Scholar,10Han X. An M. Zhang M. et al.Identification of 3 distinct HIV-1 founding strains responsible for expanding epidemic among men who have sex with men in 9 Chinese cities.J Acquir Immune Defic Syndr. 2013; 64: 16-24Crossref PubMed Scopus (63) Google Scholar The prevalence of two or more subtypes in the same population always indicates the emergence of new recombinant strains. The high probability of high-risk sexual behaviors in MSM infected population and other factors, such as unstable sexual partners, higher prevalence rate and genetic diversity in MSM population, which were more possible to occur the recombination and second-generation recombination of HIV-1.3Zhang Y. Pei Z. Li H. et al.Characterization of a novel HIV-1 circulating recombinant form (CRF80_0107) among men who have sex with men in China.AIDS Res Hum Retrovir. 2019; 35: 419-423Crossref PubMed Scopus (21) Google Scholar In the past studies, multiple CRFs had been reported in MSM population in China. With the rapid spread of CRF07_BC in MSM in China, CRF01_AE and CRF07_BC have become two dominant subtypes among MSM. It is predictable that more and more new second-generation CRFs composed of CRF01_AE and CRF07_BC will be defined in the future. In summary, a novel HIV-1 circulating recombinant form CRF102_0107 whose genome consists of CRF01_AE and CRF07_BC with 9 breakpoints and 10 segments was defined, which has more complex recombinant form than others. The emergence of CRF102_0107 indicates that CRF01_AE and CRF07_BC have been transmitted to individuals with similar social behaviors. The complex social behaviors of MSM infected population will further complicate the molecular epidemic of HIV-1 in China. In recent years, some CRFs and URFs between CRF01_AE and CRF07_BC had appeared successively in MSM in China. We can predict that there will be more second-generation CRFs containing CRF01_AE and CRF07_BC in the future. This study was supported by the NSFC (81773493), the State Key Laboratory of Pathogen and Biosecurity (AMMS), Anhui provincial Program of Prevent medicine & Public Health (Grant#2017jk002), National Grand Program on Key Infectious Disease Control (Grant#2017ZX10201101).