Characterization of a new HIV-1 second-generation circulating recombinant form (CRF170_0107) among men who have sex with men in Yunnan, China
Authors: Yi Li, Wei Chang, Jun Liang, Yang Liu, Li Li, Li Liu, Jing-Ying Wang, Rui-Lin Feng, Bin Liao, Yue Feng
Journal: Journal of Infection (2023)

Dear Editor, Recent correspondence in this journal has highlighted that second-generation HIV-1 recombination events between CRF01_AE and CRF07_BC are substantial and ongoing among men who have sex with men (MSM) in China.1Xiao M. Feng Y. Gao L. Yang C. Liu J. He M. et al.Characterization of a newly emerging HIV-1 second-generation recombinant form (CRF125_0107) among heterosexuals in Yunnan, China.J Infect. 2022; 84: e112-e115Abstract Full Text Full Text PDF PubMed Scopus (7) Google Scholar, 2Xing Y. Wang L. Li Y. Wang Y. Han L. Huang G. et al.Identification of a new HIV-1 intersubtype circulating recombinant form (CRF123_0107) in Hebei province, China.J Infect. 2022; 84: e36-e39Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar Genetic recombination of HIV-1, particularly in MSM, has resulted in the emergence of various unique recombinant forms (URFs) and circulating recombinant forms (CRFs).3Nchinda N. Elangovan R. Yun J. Dickson-Tetteh L. Kirtley S. Hemelaar J. et al.Global associations of key populations with HIV-1 recombinants: a systematic review, global survey, and individual participant data meta-analysis.Front Public Health. 2023; 111153638Crossref PubMed Scopus (2) Google Scholar This process allows the virus to increase its biological fitness, evade the host immune response, and produce drug-resistant variants, complicating diagnosis, treatment, and vaccine development. Recent research has shown that second-generation recombinants derived from CRF01_AE and CRF07_BC are the most prevalent among HIV-1-infected MSM in China. Among MSM, 13 of the 16 identified CRFs produced by second-generation recombination of CRF01_AE and CRF07_BC have been named and discovered to date, including CRF79_0107, CRF80_0107, CRF102_0107, CRF104_0107, CRF109_0107, CRF113_0107, CRF117_0107, CRF119_0107, CRF120_0107, CRF121_0107, CRF123_0107, CRF136_0107, and CRF140_0107.4Zhang Y.Q. Li Q.H. Li E.L. Wang Y.R. Tang Z.Y. Gao X. et al.Identification of a novel HIV-1 second-generation circulating recombinant form (CRF136_0107) among MSM in China.AIDS. 2023; 37: F19-F23Crossref PubMed Scopus (3) Google Scholar, 5〈https://www.hiv.lanl.gov/components/sequence/HIV/crfdb/crfs.comp〉.Google Scholar In this study, we identified a newly emerging second-generation HIV-1 circulating recombinant form CRF170_0107, consisting of CRF01_AE and CRF07_BC, in Yunnan and analyzed its evolutionary history. In the previous investigation of 164 newly diagnosed HIV-1-positive MSM blood samples collected between January 2016 and July 2016 by the Kunming Center for Disease Control and Prevention in Yunnan, China, we found that three PR/RT (1.2 kb) sequences (YNM46, YNM132, and YNM144) from epidemiologically unrelated individuals were detected to form a distinct cluster, suggesting that they represent a potential novel CRF. In the current study, near full-length genome amplification (NFLG) and sequencing were performed as previously described to further characterize the detailed mosaic structures for this cluster.6Grossmann S. Nowak P. Neogi U. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.J Int AIDS Soc. 2015; 1820035Crossref PubMed Scopus (31) Google Scholar The study was approved by the Ethics Committee of the Kunming Center for Disease Control and Prevention. All participants provided written informed consent for sample collection and subsequent analyses. The HIV-1 near full-length genome amplification (NFLG) sequences from the three isolates were successfully amplified and sequenced. The three sequences obtained (YNM46, YNM132, and YNM144) were deposited in GenBank under accession numbers OR210427 to OR210929. The NFLG sequences of the four isolates were 8774, 8781, and 8791 nt for strains YNM46, YNM132, and YNM144, respectively, spanning from the gag gene to part of a 3-long terminal repeat (LTR) corresponding to position 780-9412 of strain HXB2. Phylogenetic analysis revealed that these eight sequences formed a distinct monophyletic branch with a bootstrap value of 100%, distantly related to all known HIV-1 CRFs (Fig. 1A). Furthermore, the recombination structures were determined based on RIP, jpHMM and bootscanning analyses. The results showed that the three strains share the same but novel recombination forms composed of CRF01_AE and CRF07_BC, with two CRF01_AE fragments inserted into the env and nef regions of the CRF07_BC backbone (Fig. 1B). A total of four unique recombinant breakpoints were found at nucleotide positions 6135 and 8216 in the env region and 8788 and 9096 in the nef region, corresponding to the HXB2 coordinate according to the informative sites analysis (Fig. 1C). Subregion tree analyses further confirmed the breakpoints of the three NFLG sequences as follows: I (780-6135 nt) CRF07_BC, II (6136-8216 nt) CRF01_AE, III (8217-8788 nt) CRF07_BC, IV (8789-9096 nt) CRF01_AE, and V (9097-9412) CRF07_BC using HXB2 as a reference (Fig. 1D). Taken together, the phylogeny and recombinant structures of these strains were different from all previously reported CRFs, and the strains were isolated from four HIV-1-infected patients with no apparent epidemiologic link in Yunnan, fulfilling the criteria for the designation of a new CRF. Therefore, these new recombinants are initially designated as CRF170_0107. ALL four NFLG have identical five mosaic fragments consisting of two CRF01_AE fragments and three CRF07_BC segments inserted (Fig. 1C). To better understand the time of origin of CRF170_0107, we performed Bayesian molecular clock analyses using representative long fragments from CRF07_BC (I:780-6135, 5356 bp) and CRF01_AE (II:6136-8216, 2081 bp) to estimate the time to most recent common ancestor (tMRCA). As shown in Fig. 2, the estimated tMRCAs for the CRF07_BC and CRF01_AE regions were 2010.4 [95% HPD: 2009.1, 2011.9] and 2010.0 95% HPD: (2007.9, 2012.4), respectively. Thus, the tMRCA estimates of CRF07_BC and CRF01_AE were consistent, indicating that CRF170_0107 emerged around 2010. Furthermore, the MCC tree shows that the CRF07_BC backbone fragment of this strain belonged to the CRF07_BC MSM cluster, and the inserted CRF01_AE fragments originated from CRF01_AE cluster 4. Yunnan Province, in southwest China, is where the first cases of localized AIDS were discovered in China.7Xiao Y. Kristensen S. Sun J. Lu L. Vermund S.H. Expansion of HIV/AIDS in China: lessons from Yunnan Province.Soc Sci Med. 2007; 64: 665-675Crossref PubMed Scopus (98) Google Scholar It is also the province with the largest number of HIV patients in China. According to statistics, there will be more than 120,000 people living with HIV in Yunnan by the end of 2022. So far, Yunnan has been a global demonstration area for HIV prevention and treatment, achieving the "Three 90%" prevention and treatment targets by 2020.8〈https://www.ecns.cn/news/society/2020-12-01/detail-ihaehypt7617810.shtml〉.Google Scholar However, MSM remains a challenge and a key point for HIV prevention and control. Approximately 6.3% of newly diagnosed HIV-1 cases in Yunnan Province in 2020 were MSM, and more than half of the MSM in Yunnan Province are located in Kunming City, the capital of Yunnan and a famous tourist city in China.9AIDS epidemic in Yunnan has been steadily declining, with a sexual transmission rate of 97.5%, of which 6.3% is male-to-male transmission. 〈https://www.kunming.cn/news/c/2020-12-01/13101212.shtml〉.Google Scholar An epidemiological study of HIV among MSM in Kunming is essential for accurate prevention and control of AIDS in Yunnan Province. Yunnan is widely known as the center of the HIV-1 epidemic in China. This is mainly due to its unique geographical location. In addition, Yunnan has been the origin of many new HIV-1 CRFs. To date, 21 new CRFs have been discovered and named in Yunnan, accounting for nearly one-third of all HIV-1 CRFs in China. In this study, we found that CRF170_0107 had a CRF07_BC backbone with two CRF01_AE segments inserted in the env and nef regions, respectively. To our knowledge, this is the second discovery of a novel HIV-1 CRF consisting of CRF01_AE and CRF07_BC in Yunnan. We previously reported the case of CRF125, which was the first case of second-generation recombinant CRF01_AE and CRF07_BC among heterosexuals in Yunnan. CRF125_0107 has a CRF01_AE backbone derived from cluster 4 with two CRF07_BC segments inserted from the MSM cluster. In contrast to CRF125_0107, CRF170_0107 found in MSM in this study had a CRF07_BC backbone with two CRF01_AE fragments inserted, also from cluster 4. Taken together, the second-generation HIV-1 CRFs consisting of CRF01_AE and CRF07_BC in Yunnan may have the following two recombination patterns simultaneously. The first pattern is likely to occur in the heterosexual transmission population where CRF01_AE is the backbone. Meanwhile, the second pattern is observed in the MSM population where CRF07_BC serves as the backbone. These findings highlight the need for further research on the molecular epidemiology of HIV-1 in Yunnan to better understand the virus. In conclusion, we describe a newly emerging HIV-1 consisting of CRF01_AE and CRF07_BC named CRF170_0107 among MSM in Yunnan, China, which has a CRF07_BC backbone derived from the MSM cluster with two CRF01_AE segments from cluster 4 inserted in the env and nef regions, respectively. And CRF170_0107 was estimated to have originated around the year 2010. The present findings reiterate the urgent need to implement effective measures to reduce HIV-1 transmission in Yunnan, China. The work is supported by the Yunnan Provincial Major Science and Technology Special Plan (202102AA310005), and Yunnan Major Scientific and Technological Project (202202AG050013).