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Yu D, Zhu K, Li M, Zhang F, Yang Y, Lu C, Zhong S, Qin C, Lan Y, Yu J, Petersen JD, Jiang J, Liang H, Ye L, Liang B. The origin, dissemination, and molecular networks of HIV-1 CRF65_cpx strain in Hainan Island, China. BMC Infect Dis 2024; 24:269. [PMID: 38424479 PMCID: PMC10905908 DOI: 10.1186/s12879-024-09101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND HIV-1 CRF65_cpx strain carries drug-resistant mutations, which raises concerns about its potential for causing virologic failure. The CRF65_cpx ranks as the fourth most prevalent on Hainan Island, China. However, the origin and molecular epidemiology of CRF65_cpx strains in this area remain unclear. This study aims to estimate the spatial origins and dissemination patterns of HIV-1 CRF65_cpx in this specific region. METHODS Between 2018 and 2021, a total of 58 pol sequences of the CRF65_cpx were collected from HIV-positive patients on Hainan Island. The available CRF65_cpx pol sequences from public databases were compiled. The HIV-TRACE tool was used to construct transmission networks. The evolutionary history of the introduction and dissemination of HIV-1 CRF65_cpx on Hainan Island were analyzed using phylogenetic analysis and the Bayesian coalescent-based approach. RESULTS Among the 58 participants, 89.66% were men who have sex with men (MSM). The median age was 25 years, and 43.10% of the individuals had a college degree or above. The results indicated that 39 (67.24%) sequences were interconnected within a single transmission network. A consistent expansion was evident from 2019 to 2021, with an incremental annual addition of four sequences into the networks. Phylodynamic analyses showed that the CRF65_cpx on Hainan Island originated from Beijing (Bayes factor, BF = 17.4), with transmission among MSM on Hainan Island in 2013.2 (95%HPD: 2012.4, 2019.5), subsequently leading to an outbreak. Haikou was the local center of the CRF65_cpx epidemic. This strain propagated from Haikou to other locations, including Sanya (BF > 1000), Danzhou (BF = 299.3), Chengmai (BF = 27.0) and Tunchang (BF = 16.3). The analyses of the viral migration patterns between age subgroups and risk subgroups revealed that the viral migration directions were from "25-40 years old" to "17-24 years old" (BF = 14.6) and to "over 40 years old" (BF = 17.6), and from MSM to heterosexuals (BF > 1000) on Hainan Island. CONCLUSION Our analyses elucidate the transmission dynamics of CRF65_cpx strain on Hainan Island. Haikou is identified as the potential hotspot for CRF65_cpx transmission, with middle-aged MSM identified as the key population. These findings suggest that targeted interventions in hotspots and key populations may be more effective in controlling the HIV epidemic.
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Affiliation(s)
- Dee Yu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
| | - Kaokao Zhu
- Prevention and Treatment Department, the Fifth People's Hospital of Hainan Province, 3 Xueyuan Road, Haikou, 570102, China
| | - Mu Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Yuan Yang
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Chunyun Lu
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
| | - Shanmei Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Cai Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Yanan Lan
- Guangxi medical university oncology school, 22 Shuangyong Road, Nanning, 530021, China
| | - Jipeng Yu
- The First Clinical Medical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Jindong Ding Petersen
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
- Research Unit for General Practice, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Research Unit for General Practice, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
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Ye M, Chen X, Duo L, Ma J, Cao L, Zhang C, Zheng YT. Identification of two novel HIV-1 circulating recombinant forms of CRF111_01C and CRF116_0108 in southwestern Yunnan, China. Virulence 2022; 13:19-29. [PMID: 34951549 PMCID: PMC9794008 DOI: 10.1080/21505594.2021.2010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Yunnan, the region hardest hit by HIV/AIDS in China, is also an area with the most abundant HIV-1 genetic diversity. A large number of novel HIV-1 circulating recombinant forms (CRFs) and unique recombinants were identified among injection drug users in Yunnan; however, few were found among sexual contacts. Here, we obtained 15 near full-length genome sequences (NFLGs) from HIV-1 seropositive heterosexual contacts in Yunnan who received antiretroviral therapy during the period from 2014 to 2016. Phylogenetic analysis showed that six NFLGs belonged to CRF01_AE (n = 3) and CRF106_cpx (n = 3), and the other nine sequences were novel inter-subtype recombinants. Of the recombinants, two novel CRFs (CRF111_01 C (n = 4) and CRF116_0108 (n = 4)) and one CRF106_cpx variant (n = 1) were identified. CRF111_01 C had a CRF01_AE backbone with seven subtype C fragments inserted into the gag, pol, vif, env, nef and 3'LTR regions. CRF116_0108 had a CRF08_BC backbone with a CRF01_AE fragment inserted into the pol, tat, rev, vif, vpr, vpu and env regions. Phylogeographic analyses estimated that CRF111_01 C and CRF116_0108 originated approximately 1995.7-1998.6 and 1991.7-1993.7, respectively. These identifications of two novel HIV-1 CRFs highlighted the importance of continuous surveillance in heterosexual contacts and other high-risk groups in this region and the surrounding regions.
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Affiliation(s)
- Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Lin Duo
- Yunnan Fuwai Cardiovascular Hospital, Kunming, Yunnan, China
| | - Jin Ma
- Cangyuan Va Autonomous County People’s Hospital, Lincang, Yunnan, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Chiyu Zhang
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China,CONTACT Yong-Tang Zheng
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Rashid A, Li K, Feng Y, Ahmad T, Getaneh Y, Yu Y, Hu X, Abidi SH, Shao Y. HIV-1 genetic diversity a challenge for AIDS vaccine development: a retrospective bibliometric analysis. Hum Vaccin Immunother 2022; 18:2014733. [PMID: 35016590 PMCID: PMC8973384 DOI: 10.1080/21645515.2021.2014733] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Despite recent advances in human immunodeficiency virus-1 (HIV-1) prevention, a fast, safe, and effective vaccine will probably be necessary to end the HIV/AIDS pandemic. This study was conducted to evaluate global research trends and map the key bibliometric indices in HIV-1 genetic diversity from 1998 to 2021. Methods A comprehensive online search was conducted in the Web of Science Core Collection database to retrieve published literature on HIV-1 genetic diversity. Key bibliometric indicators were calculated and evaluated using HistCiteTM, Bibliometrix: An R-tool, and VOSviewer software for windows. Results A total of 2,060 documents written by 9,201 authors and published in 250 journals were included in the final analysis. Year 2012 was the most productive year with 121 (5.87%) publications. The most prolific author was Shao Yiming (n = 74, 3.59%) from Chinese Center for Disease Control and Prevention. The United States of America was the highly contributing and influential country (n = 681, 33.05%). AIDS Research and Human Retroviruses was the most productive journal (n = 562, 27.2%). Network visualization shows that HIV-1 was the most widely used author keyword. Conclusion This study provides global research trends and detailed information on HIV-1 genetic diversity. The amount of scientific literature on HIV-1 genetic diversity research has rapidly increased in the last two decades. The maximum number of articles on HIV-1 genetic diversity was published in developed countries; therefore, a scientific research collaboration among researchers and institutes in low-income countries should be promoted and supported.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yimam Getaneh
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yueyang Yu
- School of Medicine, Nankai University, Tianjin, China.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, China.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China.,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Yao Y, Zeng Y, Huang H, Li J, Li J, Xin R. Characteristics of Four Novel Recombinant Strains from the Backbone of CRF55_01B and CRF65_cpx in Beijing by Near Full-Length Genome. AIDS Res Hum Retroviruses 2021; 37:936-945. [PMID: 34167316 DOI: 10.1089/aid.2020.0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The HIV-1 epidemic was mainly driven by men who have sex with men (MSM) recently in Beijing, China, with high genetic diversity. Novel recombinant strains were frequently reported at 3.4%-9.9%. It is imperative to interpret the recombinant modes and the putative transmission sources by near full-length genome (NFLG). Four individuals from the MSM population were identified as novel recombinant strains during surveillance of pretreatment drug resistance. NFLG sequences were harvested by near end-point dilution and nested PCR with two overlapping half fragments. Phylogenetic inference was performed with subtyping reference sequences and major parental strain sequences, to explore the patterns of genetic recombinant and potential sources of parent strains. The breakpoints were determined using SimPlot 3.5 to draw genome mosaic map, and the potential parental strains were confirmed by Mega 6.0 using segmental neighbor-joining trees. BL19487-00 and BL1948-00 sequences were obtained from epidemiologically linked individuals and shared similar breakpoints (HXB2 nt 4,497 ± 8 to 4,722) with substitution of subtype B pol gene segment in the backbone of CRF55_01B. BL3104-00 and BL4307-00 carried seven and eight breakpoints, respectively, in the backbone of CRF65_cpx with g5 CRF01_AE substitutions. The recombinant fragments were located around gag, pol, and env genes, with vpr-tat and nef-3'-LTR genes only for BL4307-00. No transmitted drug resistance was observed with the four unique recombinant forms (URFs), except for some drug resistance associated mutations. The advent of URFs around CRF55_01B and CRF65_cpx identified in recent years implied that the sexual behaviors were active and the epidemic of HIV was complicated among MSM in Beijing. Molecular epidemiological surveillance and precise control should be reinforced for this population.
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Affiliation(s)
- Yaping Yao
- Department of Science Research and Information Management, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yuhong Zeng
- School of Public Health, Capital Medical University, Beijing, China
| | - Huihuang Huang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jia Li
- Institute of STD/AIDS Prevention and Treatment, Beijing Center Disease Prevention and Control, Beijing, China
| | - Jie Li
- Institute of STD/AIDS Prevention and Treatment, Beijing Center Disease Prevention and Control, Beijing, China
| | - Ruolei Xin
- Institute of STD/AIDS Prevention and Treatment, Beijing Center Disease Prevention and Control, Beijing, China
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5
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Wang X, Zhang Y, Liu Y, Li H, Jia L, Han J, Li T, Wang X, Li J, Wen H, Li L. Phylogenetic Analysis of Sequences in the HIV Database Revealed Multiple Potential Circulating Recombinant Forms in China. AIDS Res Hum Retroviruses 2021; 37:694-705. [PMID: 33390081 DOI: 10.1089/aid.2020.0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
HIV recombination contributes greatly to its diversity and produces many circulating recombinant forms (CRFs) and unique recombinant forms (URFs). In China, 24 CRFs have been reported to date, and CRFs cause more than 80% of HIV infections. However, the prevalence of CRFs might still be underestimated, as a high level of onward transmission of URFs has been reported. In this study, we analyzed all Chinese pol region (2,253-3,252) sequences in the HIV Database to evaluate potential new CRFs in China. HIV-1 genotypes were verified by the Context-based Modeling for Expeditious Typing (COMET) tool. Maximum-likelihood (ML) trees were constructed based on sequences with unassigned genotypes. Cluster Picker 1.2.1 was used to identify transmission clusters. Meanwhile, a jumping-profile hidden Markov model (jpHMM) was used to perform recombination breakpoint analysis. Beast 1.7.5 was used to estimate the time of the most recent common ancestor of new CRFs. In the HIV databases, CRF01_AE was the most prevalent genetic form in China, accounting for 39.69% of all national infections, followed by CRF07_BC (20.47%), subtype B (17.50%), CRF08_BC (6.60%), subtype C (6.28%), CRF55_01B (2.06%), and other CRFs (1.77%). The URFs were responsible for 5.31% of all infections nationwide. Among URFs, genomes comprising BC, 01BC, 01B, and 01C were dominant. Finally, 17 potential CRFs and 1 novel CRF were identified. BEAST analysis indicates that novel CRF originated around in 2009. The data highlight that more CRFs have been spreading in China. HIV-1 pol sequences that are commonly used to explore drug resistance are helpful for the surveillance of epidemics of different HIV-1 genotypes.
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Affiliation(s)
- Xiaorui Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory of Infectious Disease Control and Prevention in Universities of Shandong, Jinan, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory of Infectious Disease Control and Prevention in Universities of Shandong, Jinan, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Wang X, Zhao J, Li X, Li H, Zhang Y, Liu Y, Chen L, Zheng C, Jia L, Han J, Li T, Wang X, Li J, Wen H, Li L. Identification of a novel HIV-1 second-generation Circulating Recombinant Form CRF109_0107 in China. J Infect 2020; 81:816-846. [PMID: 32946916 DOI: 10.1016/j.jinf.2020.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Xiaorui Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key laboratory for the prevention and control of infectious diseases (key laboratory of China's "13th Five-Year", Shandong University), 44 Wenhua, West Street, Lixia District, Jinan 250012, Shandong Province, China; Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Xi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China
| | - Hongling Wen
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key laboratory for the prevention and control of infectious diseases (key laboratory of China's "13th Five-Year", Shandong University), 44 Wenhua, West Street, Lixia District, Jinan 250012, Shandong Province, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing 100071, China.
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Abstract
HIV-1 drug resistance can compromise the effectiveness of antiretroviral therapy (ART). A survey of pretreatment HIV-1 drug resistance (PDR) was conducted in Lincang Prefecture of Yunnan Province. From 372 people living with HIV/AIDS initiating ART for the first time during 2017-2018, 322 pol sequences were obtained, of which 11 HIV-1 strain types were detected. CRF08_BC (70.2%, 226/322) was the predominant strain, followed by URF strains (10.6%, 34/322). Drug resistance mutations (DRMs) were detected among 34.2% (110/322) of the participants. E138A/G/K/R (14.3%, 46/322) and V179E/D/T (13.7%, 47/322) were the predominant DRMs. Specifically, E138 mutations commonly occurred in CRF08_BC (19.9%, 45/226). Among the DRMs detected, some independently conferred resistance, such as K65R (1.6%, 5/322), Y188C/F/L (0.9%, 3/322), K103N (0.6%, 2/322) and G190A (0.3%, 1/322), which conferred high-level resistance. The prevalence of PDR was 7.5% (95% CI: 4.6-10.3%) and the prevalence of non-nucleotide reverse transcriptase inhibitor (NNRTI) resistance was 5.0% (95% CI: 2.6-7.4%), which is below the threshold (⩾10%) of initiating a public health response. In conclusion, HIV-1 genetic diversity and an overall moderate level of PDR prevalence were found in western Yunnan. PDR surveillance should be continually performed to decide whether a public health response to NNRTI resistance should be initiated.
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Liu Y, Zhang Y, Li H, Wang X, Jia L, Han J, Li T, Li J, Li L. Natural presence of the V179D and K103R/V179D mutations associated with resistance to nonnucleoside reverse transcriptase inhibitors in HIV-1 CRF65_cpx strains. BMC Infect Dis 2020; 20:313. [PMID: 32345262 PMCID: PMC7189696 DOI: 10.1186/s12879-020-05007-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 03/31/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is increasing evidence that HIV-1 genetic diversity can have an impact on drug resistance. The aim of this study is to investigate the epidemiological situation of CRF65_cpx and the impact of natural polymorphisms of this variant on genotypic resistance. METHODS We used the BLAST search program followed by phylogenetic analysis to identify additional CRF65_cpx pol sequences from the Los Alamos HIV Sequence Database. Maximum likelihood phylogeny was estimated to clarify the epidemiological relationship of CRF65_cpx strains. Genotypic resistance was determined by submitting sequences to the Stanford HIV Drug Resistance Database. RESULTS A total of 32 CRF65_cpx pol sequences were obtained. The CRF65_cpx strains were detected in seven provinces with large geographic distance. Yunnan CRF65_cpx sequences were mainly derived from a heterosexual risk group, whereas the CRF65_cpx sequences in other provinces were almost exclusively derived from an MSM population. With one exception of V179E, the other 31 strains harbored V179D mutation. The combination of V179D and K103R, conferring intermediate resistance to EFV and NVP, was detected in seven treatment-naive MSM patients. CONCLUSIONS This study confirmed the expansion CRF65_cpx in China. Furthermore, we found the natural presence of the V179D and K103R/V179D mutations associated with resistance to NNRTIs in HIV-1 CRF65_cpx. Our findings highlight the contribution of polymorphic mutations to drug resistance and underscore the challenges in treating patients harboring CRF65_cpx strains.
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Affiliation(s)
- Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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9
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The prevalence, temporal trends, and geographical distribution of HIV-1 subtypes among men who have sex with men in China: A systematic review and meta-analysis. Epidemiol Infect 2020; 147:e83. [PMID: 30869019 PMCID: PMC6518548 DOI: 10.1017/s0950268818003400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this meta-analysis was to provide a comprehensive overview of human immunodeficiency virus (HIV)-1 subtypes and to investigate temporal and geographical trends of the HIV-1 epidemic among men who have sex with men (MSM) in China. Chinese and English articles published between January 2007 and December 2017 were systematically searched. Pooled HIV-1 prevalence was calculated, and its stability was analysed using sensitivity analysis. Subgroups were based on study time period, sampling area and prevalence. Publication bias was measured using Funnel plot and Egger's test. A total of 68 independent studies that included HIV-1 molecular investigations were eligible for meta-analysis. Circulating recombinant form (CRF) 01_AE (57.36%, 95% confidence interval (CI) 53.76–60.92) was confirmed as the most prevalent HIV-1 subtype among MSM in China. Subgroup analysis for time period found that CRF01_AE steadily increased prior to 2012 but decreased during 2012–2016. Further whereas CRF07_BC increased over time, B/B′ decreased over time. CRF55_01B has increased in recent years, with higher pooled estimated rate in Guangdong (12.22%, 95% CI 10.34–13.17) and Fujian (8.65%, 95% CI 4.98–13.17) provinces. The distribution of HIV-1 subtypes among MSM in China has changed across different regions and periods. HIV-1 strains in MSM are becoming more complex. Long-term molecular monitoring in this population remains necessary for HIV-1 epidemic control and prevention.
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10
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Zhang Y, Su B, Li H, Han J, Zhang T, Li T, Wu H, Wang X, Li J, Liu Y, Li L. Triple HIV-1 Infection Is Associated With Faster CD4 + T-Cell Decline. Front Microbiol 2020; 11:21. [PMID: 32038599 PMCID: PMC6992562 DOI: 10.3389/fmicb.2020.00021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/07/2020] [Indexed: 11/24/2022] Open
Abstract
HIV-1 dual infection occurs when an individual is simultaneously or sequentially infected with two or more genetically distinct HIV-1 strains. According to the number of infected strains, HIV-1 dual infection can be divided in double infection and triple infection and so on. Currently, the majority of dual infection cases have been reported to be double infections which can result in detrimental clinical outcomes. The high incidence of double infection among specific high-risk populations increases the likelihood of triple infection, which has been sporadically described. There is no doubt that we are concerned about the association between triple infection and disease progression. However, this relationship is still unclear on the population level. In this study, 70 individuals from the Beijing PRIMO cohort were longitudinally followed up with a median time of 15.75 months for the purpose of investigating the incidence of dual infection. Phylogenetic analyses using bulk and single-genome sequences showed that nine individuals acquired double infection, with the incidence of 9.21 per 100 person-years, and three individuals with triple infection were identified, with the incidence of 3.07 per 100 person-years. The further survival analysis demonstrated that the triple infection group exhibited faster CD4+ T-cell decline. In summary, these results demonstrate for the first time that the triple HIV-1 infection might reduce CD4+ T-cell counts, which would predict a more rapid disease progression.
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Affiliation(s)
- Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bin Su
- Center for Infectious Diseases, Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tong Zhang
- Center for Infectious Diseases, Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing Key Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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11
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Liu Y, Li H, Wang X, Han J, Jia L, Li T, Li J, Li L. Natural presence of V179E and rising prevalence of E138G in HIV-1 reverse transcriptase in CRF55_01B viruses. INFECTION GENETICS AND EVOLUTION 2019; 77:104098. [PMID: 31678241 DOI: 10.1016/j.meegid.2019.104098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/31/2022]
Abstract
There is increasing evidence that naturally occurring HIV-1 genetic diversity can have an impact on drug resistance. Recently, our previous study has demonstrated the natural presence of the V179D and K103R/V179D mutations associated with resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs) in HIV-1 CRF65_cpx strains. The aim of this study is to investigate the presence of natural drug-resistance mutations (DRMs) in other HIV-1 subtypes or CRFs circulating in China. A total of 14,403 pol sequences from China were retrieved from the Los Alamos HIV Sequence Database, 10,041 of which were treatment naïve and presented substantial genetic diversity. Besides the natural presence of V179D and K103R/V179D in CRF65_cpx, the natural presence of V179E was found in CRF55_01B. In all but one of the 228 patients infected with CRF55_01B, NNRTI resistance mutation V179E was present and the combination of V179E and E138G was detected in 14 treatment-naïve patients, with a rate of 6.2%. A significant trend for increasing prevalence of E138G mutation in CRF55_01B strains over time was observed (p < .001). Phylogenetic analysis was conducted to clarify the epidemiological relationship of CRF55_01B strains. Most of the sequences containing E138G mutation scattered in the big CRF55_01B cluster, which indicated the rising prevalence of E138G was mainly due to multiple mutation events rather than local transmission clusters of a particular variant containing E138G mutation. Our findings highlight the importance of molecular surveillance of CRF55_01B strains and the urgent need for implementation of effective preventive measures to reduce the transmission of CRF55_01B.
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Affiliation(s)
- Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
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12
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Chen M, Ma Y, Chen H, Dai J, Luo H, Yang C, Dong L, Jin X, Yang M, Yang L, Song L, Song Z, Jia M. Spatial clusters of HIV-1 genotypes in a recently infected population in Yunnan, China. BMC Infect Dis 2019; 19:669. [PMID: 31357947 PMCID: PMC6664787 DOI: 10.1186/s12879-019-4276-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/10/2019] [Indexed: 12/04/2022] Open
Abstract
Background As a gateway for HIV-1 in China, Yunnan has experienced dramatic changes in HIV-1 epidemics, during which HIV-1 genotypes have become complex. To track dynamic changes in HIV-1 genotypes, an HIV-1 molecular epidemiological study was implemented in the recently infected population in Yunnan. Methods From 6,357 HIV-1-positive samples diagnosed during the first half of 2015 in Yunnan, 586 samples were identified as recent infections with BED-capture enzyme immunoassay (CEIA) and were subjected to phylogenetic analyses. Spatial scanning analyses for the main HIV-1 genotypes were also performed. Results Among the 439 specimens successfully genotyped, more than ten genotypes were detected, including CRF08_BC (45.3%), CRF07_BC (19.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (11.4%), subtype C (2.1%), CRF85_BC (1.1%), CRF55_01B (0.9%), subtype B (0.5%), CRF64_BC (0.5%), CRF59_01B (0.2%), CRF83_cpx (0.2%) and CRF87_cpx (0.2%). Females, Chinese, heterosexual contact and intravenous drug injection were significantly associated with CRF08_BC infection; homosexual contact was significantly associated with CRF01_AE and CRF07_BC infection; males and non-Chinese had a higher risk of URF infection than females. Among all HIV-1 genotypes, the geographic coverage of CRF08_BC was the largest. For CRF08_BC, CRF07_BC, URFs and CRF01_AE, spatial clusters were detected. The two CRF08_BC clusters and one URF cluster were associated with heterosexual transmission, and two of CRF01_AE clusters were associated with homosexual transmission. Transmitted drug resistance (TDR)-associated mutations were detected in 2.4% of individuals. Conclusions The diversity of HIV-1 genotypes increased in recent infections because of a long-term HIV-1 epidemic in Yunnan. The predominant HIV-1 strains showed distinct demographic characteristics and formed spatial clusters. These findings improved our understanding of the evolution of HIV-1 in Yunnan and provided information for further HIV-1 control and prevention. Electronic supplementary material The online version of this article (10.1186/s12879-019-4276-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Xiaomei Jin
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Min Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Lijun Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Zhizhong Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, No. 158, Dongsi Street, Xishan District, Kunming, 650022, Yunnan Province, China.
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13
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Liu W, Feng Y, Wang C, Wang Y, Kong D, Qu S, Liang S, Ma L, Xiao Y. Identification of a Novel HIV Type 1 CRF01_AE/CRF07_BC Recombinant Virus in Men Who Have Sex with Men in GuangXi, China. AIDS Res Hum Retroviruses 2019; 35:402-406. [PMID: 30152708 DOI: 10.1089/aid.2018.0157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This study reports a novel HIV-1 recombinant virus (GX2016EU10) isolated from a 24-year-old man, who was infected by homosexual sex in Guangxi, China. The near full-length genome analyses showed GX2016EU10 kept the CRF07_BC parental backbone with three CRF01_AE segments inserted into gag, pol, vpu, env, and nef genes, respectively. The recombinant breakpoints were completely different from the other CRF01_AE/CRF07_BC recombinant forms reported. GX2016EU10 was CCR5-tropic through GHOST cell identification. The emergence of GX2016EU10 indicates that the HIV-1 epidemic among men who have sex with men in Guangxi is increasing in complexity, which poses a serious challenge to prevention and control.
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Affiliation(s)
- Weinan Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Chen Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Desheng Kong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuiling Qu
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shujia Liang
- Guangxi Center for Disease Prevention and Control, Nanning, People's Republic of China
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yao Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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14
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Lin YL, Song B, Shao B, Liu SY, Huo QQ, Li J, Wang JY, Wang FX. Identification of a Novel HIV-1 Unique Recombinant Form Comprising CRF01_AE, Subtype B', and CRF65_cpx Among Men Who Have Sex with Men in Jilin, China. AIDS Res Hum Retroviruses 2018; 34:714-718. [PMID: 29786452 DOI: 10.1089/aid.2018.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
The current HIV-1 epidemic in China is featured by diverse subtypes and continual emergence of new recombinant viruses. This study identified a novel unique recombinant form (URF), JL16013, among men who have sex with men (MSM) in Jilin, China. The JL16013 virus was different from all known subtypes and set up a distinct branch on the phylogenetic tree. This virus had a CRF01_AE backbone with two subtype B' fragments and one CRF65_cpx fragment inserted into gag, pol, env, and nef regions, suggesting that this novel URF might have originated from the CRF01_AE, subtype B', and CRF65_cpx viruses that were cocirculating in Jilin province. This was the first report of the CRF01_AE/B'/CRF65_cpx recombinant in China. Identification of this URF indicated the severity and complexity of the HIV-1 epidemic among MSM in Jilin province. Timely surveillance of new HIV-1 infections and new recombinants among the MSM population is urgently required.
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Affiliation(s)
- Yuan-Long Lin
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Song
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Shao
- Department of Epidemiology and Health Statistics, Public Health College of Jilin Medical University, Jilin, China
| | - Si-Yu Liu
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qing-Qing Huo
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jin Li
- Department of Infectious Diseases, Changchun Infectious Disease Hospital, Changchun, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, China
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15
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Wang JY, Chen XH, Shao B, Huo QQ, Liu SY, Li J, Wang FX. Identification of a New HIV-1 Circulating Recombinant Form CRF65_cpx Strain in Jilin, China. AIDS Res Hum Retroviruses 2018; 34:709-713. [PMID: 29724111 DOI: 10.1089/aid.2018.0086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This study reported a new HIV-1 circulating recombinant form CRF65_cpx virus isolated from a man who have sex with men (MSM) in Jilin, China. The near full-length genome of this virus was composed of 14 mosaic gene fragments derived from CRF01_AE, subtype B' (Thai B) and subtype C, highly similar to the CRF65_cpx viruses recently identified in Yunnan and Anhui of China. Phylogenetic tree analysis suggested that this CRF65_cpx strain was not generated among MSM in Jilin, but originated in southern regions of China and spread to Jilin by MSM population. The emergence of CRF65_cpx in Jilin indicated HIV-1 epidemic in this area was more and more complicated and the MSM population has become the important source for generation of new recombinant viruses. Real-time surveillance of new HIV-1 infections among MSM population is quite required.
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Affiliation(s)
- Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xiao-Hong Chen
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Shao
- Department of Epidemiology and Health Statistics, Public Health College of Jilin Medical University, Jilin, China
| | - Qing-Qing Huo
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si-Yu Liu
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jin Li
- Changchun Infectious Disease Hospital, Changchun, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
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16
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Chen M, Jia MH, Ma YL, Luo HB, Chen HC, Yang CJ, Dai J, Yang L, Dong LJ, Lu R, Song LJ, Han Y, Lu JY, Cheung AKL, Chen ZW, Lu L. The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China. Epidemiol Infect 2018; 146:775-781. [PMID: 29534773 PMCID: PMC9134363 DOI: 10.1017/s0950268818000389] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 11/05/2022] Open
Abstract
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.
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Affiliation(s)
- M. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - M. H. Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. L. Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. B. Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. C. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - C. J. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - R. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. Han
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Y. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - A. K. L. Cheung
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Z. W. Chen
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - L. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, China
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17
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Miao J, Ran J, Song Y, Liu Y, Gao L, Miao Z, Zhang C, Feng Y, Xia X. Characterization of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B'/C (CRF96_cpx), in Yunnan, China. AIDS Res Hum Retroviruses 2018; 34:393-397. [PMID: 29258320 DOI: 10.1089/aid.2017.0288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Currently, complex HIV-1 recombinations among the B', C, and CRF01_AE genotypes have frequently arisen in Yunnan, China. A novel HIV-1 complex circulating recombinant form (CRF) consisting of B', C, and CRF01_AE (CRF96_cpx) was recently characterized from three epidemiologically unlinked individuals. Two strains of them were isolated from the injecting drug users in this study, the remaining one strain (JL. RL01) was obtained from a previous report in Jilin province. Phylogenetic analysis based on near full-length genome revealed that CRF96_cpx formed a distinct monophyletic cluster supported by a high bootstrap value of 100%, distantly related to all known HIV-1 subtypes/CRFs. CRF96_cpx had a CRF01_AE backbone with three subtype B' and C segments inserted, respectively, in the gag and pol region. Furthermore, subregion tree analysis showed that CRF01_AE backbone and subtype B segment inserted originated from a Thai-CRF01_AE lineage, whereas subtype C fragment inserted was from an India C lineage. They are different from previously documented CRF01_AE/B/C forms in its distinct backbone, inserted fragment size, and breakpoints. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in Yunnan, China.
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Affiliation(s)
- Jing Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jieyu Ran
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yindi Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yang Liu
- Yunnan SCISPARK Genetic Testing Lab, Kunming SCISPARK Biotechnology Co., Ltd, Kunming, China
| | - Li Gao
- Department of Infectious Diseases, Yunnan Provincial Hospital of Infectious Diseases, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Chunyue Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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18
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Li Y, Feng Y, Li F, Xue Z, Hu J, Xing H, Ruan Y, Shao Y. Genome Sequence of a Novel HIV-1 Circulating Recombinant Form (CRF79_0107) Identified from Shanxi, China. AIDS Res Hum Retroviruses 2017; 33:1056-1060. [PMID: 28557610 DOI: 10.1089/aid.2017.0066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Yuxueyun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zidong Xue
- Shanxi Center for Disease Control and Prevention, Taiyuan, China
| | - Jing Hu
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Guangxi Medical University, Nanning, China
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19
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Xiao P, Li J, Fu G, Zhou Y, Huan X, Yang H. Geographic Distribution and Temporal Trends of HIV-1 Subtypes through Heterosexual Transmission in China: A Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:E830. [PMID: 28737729 PMCID: PMC5551268 DOI: 10.3390/ijerph14070830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/09/2017] [Accepted: 07/21/2017] [Indexed: 11/17/2022]
Abstract
Background: Heterosexual transmission (HST) has become the current predominant transmission pathways of the HIV-1 epidemic in China. The aim of this study was to explore the geographic and dynamic change of HIV-1 subtypes through HST in China from published studies. Methods: Several electronic databases were searched to identify the studies, and the overall prevalence of HIV-1 subtypes was estimated by a meta-analysis method. Subgroup analysis was conducted by study region and time period. Publication bias was evaluated using Egger's test. The χ² test was used to evaluate the proportion differences among subgroups. Sensitivity analysis was carried out to assess the stability of the overall prevalence estimates. Results: 42 studies were included in our final analysis. The overall prevalence of CRF01_AE was 46.34% (95% CI: 40.56-52.17%), CRF07_BC was 19.16% (95% CI: 15.02-23.66%), B/B' was 13.25% (95% CI: 9.68-17.25%), CRF08_BC was 10.61% (95% CI: 7.08-14.70%), and C was 4.29% (95% CI: 1.85-7.48%). In subgroup analysis, the prevalence of CRF01_AE and CRF07_BC increased, while the prevalence of B/B' decreased over time, whereby the prevalence of CRF07_BC and CRF08_BC have exceeded that of B/B' since 2010. A significant higher prevalence of CRF01_AE was found in the South provinces, CRF07_BC in East provinces, CRF08_BC and C in Southwest provinces, and B/B' in North provinces. Conclusions: The HIV-1 prevalent strains have evolved into complicated and diverse subtypes, and the proportion of HIV-1 subtypes through HST has changed constantly in different regions and periods in China. This highlights the urgent need to vigorously strengthen the prevention and control of the HIV-1 epidemic.
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Affiliation(s)
- Peipei Xiao
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Jianjun Li
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Gengfeng Fu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Ying Zhou
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Xiping Huan
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
| | - Haitao Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China.
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210009, China.
- Jiangsu Research Institute of Schistosomiasis Control, Wuxi 214064, China.
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20
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Wang Y, Kong D, Xu W, Li F, Liang S, Feng Y, Zhang F, Shao Y, Ma L. Identification of a Novel HIV Type 1 CRF01_AE/B'/C Recombinant Isolate in Sichuan, China. AIDS Res Hum Retroviruses 2017; 33:621-628. [PMID: 28287833 DOI: 10.1089/aid.2017.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Yan Wang
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
- 2 Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing, People's Republic of China
- 3 Clinical Center for HIV/AIDS, Capital Medical University Beijing, People's Republic of China
| | - Desheng Kong
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
| | - Weisi Xu
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
| | - Fan Li
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
| | - Shu Liang
- 4 Sichuan Center for Disease Control and Prevention , Chengdu, People's Republic of China
| | - Yi Feng
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
| | - Fujie Zhang
- 2 Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing, People's Republic of China
- 3 Clinical Center for HIV/AIDS, Capital Medical University Beijing, People's Republic of China
| | - Yiming Shao
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
| | - Liying Ma
- 1 State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention , Beijing, People's Republic of China
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21
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Wang X, Zhang M, Li J, Li T, Sun C, Li H, Liu Y, Liu S, Zhuang D, Bao Z, Han J, Li J, Li L. Genetic Characterization of a Unique Recombinant Strain Identified in Yunnan with Genome Comprising B and C. AIDS Res Hum Retroviruses 2017; 33:614-620. [PMID: 28398773 DOI: 10.1089/aid.2017.0013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since the first identification of HIV-1 outbreak in Dehong, Yunnan province has been the epidemic center of HIV in China. Owing to the special geographic location and the frequent population mobility, Yunnan province contained complex HIV subtype distribution. Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been found in recent years. In this study, a unique HIV-1 recombinant strain genome (YN10134) was characterized from an HIV-positive female in Yunnan, China. This virus genome had a complex intersubtype recombinant structure with eight breakpoints, composed of subtypes B and C. Although the sequence had a similar breakpoint with CRF07_BC in the start position in Env, the phylogenetic analysis showed that the segment was not originated from CRF07_BC. The identification of the URF indicated the severity of the HIV epidemic in Yunnan province and the urgent need for epidemiological surveillance of the new recombination.
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Affiliation(s)
- Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Min Zhang
- Anhui Medical University, Anhui, China
| | - Jianjian Li
- AIDS Care Center (YNACC), Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Tianyi Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changrong Sun
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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22
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Wu Y, Ren X, Yin D, Wang H, Wan Z, Li X, Hu G, Tang S. Characterization of a novel HIV-1 unique recombinant form between CRF07_BC and CRF55_01B in men who have sex with men in Guangzhou, China. PLoS One 2017; 12:e0175770. [PMID: 28403241 PMCID: PMC5389846 DOI: 10.1371/journal.pone.0175770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 12/02/2022] Open
Abstract
Here, we report the genetic diversity of HIV-1 and emergence of novel HIV-1 unique recombinant forms (URF) in both HIV-infected intravenous drug users (IDU) and men who have sex with men (MSM) in Guangzhou, China. We further characterized a novel URF strain isolated from an HIV-infected MSM, GD698. Near full-length genome (NFLG) phylogenic analysis showed that this novel URF was composed of CRF07_BC and CRF55_01B, with two recombinant breakpoints (nt 6,003 and 8,251 relative to the HXB2 genome) in the vpu/env and env genes, respectively. Twenty six percent of the genome is classified as CRF55_01B, spanning part of vpu and most of the env gene. The remaining 74% of the genome is classified as CRF07_BC. Both the backbone CRF07_BC sequence and CRF55_01B fragment were clustered with the HIV-1 isolates found in MSM. The emergence of the novel HIV-1 recombinant indicates the ongoing recombinants derived from the CRF07_BC and CRF55_01B isolates, and provides critical insights into our understanding of the dynamics and complexity of the HIV-1 epidemic in China.
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Affiliation(s)
- Yue Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Xuqi Ren
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Guangdong Provincial Dermatology Hospital, Guangzhou, China
| | - Dan Yin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhengwei Wan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiufen Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Guifang Hu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (ST); (GH)
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (ST); (GH)
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23
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Hu Y, Wan Z, Zhou YH, Smith D, Zheng YT, Zhang C. Identification of Two New HIV-1 Circulating Recombinant Forms (CRF87_cpx and CRF88_BC) from Reported Unique Recombinant Forms in Asia. AIDS Res Hum Retroviruses 2017; 33:353-358. [PMID: 27762598 DOI: 10.1089/aid.2016.0252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1. According to the criterion of new CRFs, two new HIV-1 CRFs (CRF87_cpx and CRF88_BC) were identified from these available URFs. CRF87_cpx comprised HIV-1 subtypes B, C, and CRF01_AE, and CRF88_BC comprised subtypes B and C. HIV Blast and bootscan analysis revealed that besides the three representative strains, there were two additional CRF87_cpx strains. Furthermore, we defined seven dominant URFs (dURF01-dURF07), each of which contained two strains sharing same recombination map and can be used as sequence references to facilitate the finding of new potential CRFs in future. These results will benefit the molecular epidemiological investigation of HIV-1 in Asia.
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Affiliation(s)
- Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Yan-Heng Zhou
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, China
| | - Davey Smith
- Division of Infectious Diseases, University of California San Diego, La Jolla, California
- Veterans Affairs Healthcare System San Diego, San Diego, California
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chiyu Zhang
- CAS Key Laboratory of Molecular Virology & Immunology, Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
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24
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Li Y, Miao J, Miao Z, Song Y, Wen M, Zhang Y, Guo S, Zhao Y, Feng Y, Xia X. Identification of a Novel HIV Type 1 Circulating Recombinant Form (CRF86_BC) Among Heterosexuals in Yunnan, China. AIDS Res Hum Retroviruses 2017; 33:279-283. [PMID: 27593341 DOI: 10.1089/aid.2016.0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, multiple circulating recombinant forms (CRFs) and unique recombinant forms of human immunodeficiency virus type 1 (HIV-1) have been described in Yunnan, China. Here, we identified a novel HIV-1 CRF (CRF86_BC) isolated from three heterosexuals with no obvious epidemiologic linkage in western Yunnan (Baoshan prefecture) in China. CRF86_BC had a subtype C backbone with four subtype B fragments inserted into the pol, vpr, vpu, env, and nef gene regions, respectively. Furthermore, subregion tree analysis revealed that subtype C backbone originated from an Indian C lineage and subtype B segment inserted was from a Thai B lineage. They are different from previously documented B/C forms in its distinct backbone, inserted fragment size, and break points. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in this region.
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Affiliation(s)
- Yanping Li
- Pharmaceutical College, Guangxi Medical University, Guangxi, China
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Jing Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Yindi Song
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Min Wen
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Ya Zhang
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Shimin Guo
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Yuan Zhao
- Center of Chinese Medicine, Yunnan Traditional Chinese Medicine Institute, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
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25
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Lu X, Kang X, Liu Y, Cui Z, Guo W, Zhao C, Li Y, Chen S, Li J, Zhang Y, Zhao H. HIV-1 molecular epidemiology among newly diagnosed HIV-1 individuals in Hebei, a low HIV prevalence province in China. PLoS One 2017; 12:e0171481. [PMID: 28178737 PMCID: PMC5298910 DOI: 10.1371/journal.pone.0171481] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/21/2017] [Indexed: 11/23/2022] Open
Abstract
New human immunodeficiency virus type 1 (HIV-1) diagnoses are increasing rapidly in Hebei. The aim of this study presents the most extensive HIV-1 molecular epidemiology investigation in Hebei province in China thus far. We have carried out the most extensive systematic cross-sectional study based on newly diagnosed HIV-1 positive individuals in 2013, and characterized the molecular epidemiology of HIV-1 based on full length gag-partial pol gene sequences in the whole of Hebei. Nine HIV-1 genotypes based on full length gag-partial pol gene sequence were identified among 610 newly diagnosed naïve individuals. The four main genotypes were circulating recombinant form (CRF)01_AE (53.4%), CRF07_BC (23.4%), subtype B (15.9%), and unique recombinant forms URFs (4.9%). Within 1 year, three new genotypes (subtype A1, CRF55_01B, CRF65_cpx), unknown before in Hebei, were first found among men who have sex with men (MSM). All nine genotypes were identified in the sexually contracted HIV-1 population. Among 30 URFs, six recombinant patterns were revealed, including CRF01_AE/BC (40.0%), CRF01_AE/B (23.3%), B/C (16.7%), CRF01_AE/C (13.3%), CRF01_AE/B/A2 (3.3%) and CRF01_AE/BC/A2 (3.3%), plus two potential CRFs. This study elucidated the complicated characteristics of HIV-1 molecular epidemiology in a low HIV-1 prevalence northern province of China and revealed the high level of HIV-1 genetic diversity. All nine HIV-1 genotypes circulating in Hebei have spread out of their initial risk groups into the general population through sexual contact, especially through MSM. This highlights the urgency of HIV prevention and control in China.
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Affiliation(s)
- Xinli Lu
- College of Life Science, Hebei University, Baoding, Hebei, China
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Xianjiang Kang
- College of Life Science, Hebei University, Baoding, Hebei, China
- * E-mail: (SC); (XK)
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ze Cui
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Wei Guo
- NO. 201 hospital of the People’s Liberation Army of China, Liaoyang, Liaoning, China
| | - Cuiying Zhao
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Yan Li
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Suliang Chen
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
- * E-mail: (SC); (XK)
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuqi Zhang
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
| | - Hongru Zhao
- Hebei Provincial Center for Disease Control and Prevention, Shjiazhuang, Hebei, China
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26
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Jia D, Zhao J, Li T, Sun C, Li H, Zheng C, Chen L, Liu Y, Liu S, Zhuang D, Wang X, Bao Z, Li J, Li L. Near Full-Length Genomic Sequences of Two Novel HIV-1 Recombinant Forms Identified in Shenzhen, China. AIDS Res Hum Retroviruses 2017; 33:82-86. [PMID: 27460636 DOI: 10.1089/aid.2016.0162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most HIV subtypes prevalent in China can be found in Shenzhen, including CRF07_BC, CRF01_AE, CRF08_BC, CRF55_01B, and subtype B. Multiple subtypes spreading in the same population always lead to the emergence of unique recombinant strains. Here, we report two unique recombinant forms (SZ44LS7251 and SZ95LS8027) of HIV-1 identified in a heterosexual population. Recombinant analyses were fulfilled based on the near full-length genomes. Both strains comprise subtypes B, C, and CRF01_AE. Phylogenetic analysis reveals that SZ44LS7251 is the second generation recombination originated from CRF55_01B andCRF07_BC, whereas SZ95LS8027 comprises CRF01_AE and CRF07_BC.The emergence of second generation recombination of HIV with complicated genomic structures supposed that high ratio of super infections or coinfections might happen in the Shenzhen area.
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Affiliation(s)
- Dijing Jia
- Graduate School, Anhui Medical University, Anhui, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Graduate School, Anhui Medical University, Anhui, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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27
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Li X, Li W, Zhong P, Fang K, Zhu K, Musa TH, Song Y, Du G, Gao R, Guo Y, Yan W, Xuan Y, Wei P. Nationwide Trends in Molecular Epidemiology of HIV-1 in China. AIDS Res Hum Retroviruses 2016; 32:851-9. [PMID: 27080587 DOI: 10.1089/aid.2016.0029] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Taha Hussein Musa
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guoping Du
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Rong Gao
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yan Guo
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wenjuan Yan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yang Xuan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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Li T, Sun G, Jia D, Sun C, Wang Z, Liu S, Liu Y, Li H, Wang X, Li J, Li L. Near Full-Length Genome Sequences of Two Novel HIV-1 Recombinant Forms Detected in Henan Province, China. AIDS Res Hum Retroviruses 2016; 32:722-7. [PMID: 27080756 DOI: 10.1089/aid.2016.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guoqing Sun
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Dijing Jia
- Anhui Medical University, Changsha, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Wang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Song Y, Feng Y, Miao Z, Wang B, Yang M, Zhang AM, Liu L, Xia X. Near-Full-Length Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B'/C (CRF78_cpx), in Yunnan, China. AIDS Res Hum Retroviruses 2016; 32:601-6. [PMID: 26885715 DOI: 10.1089/aid.2015.0351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report a novel HIV circulating recombinant form (CRF78_cpx) composed mainly of CRF01_AE with inserts from subtypes B and C identified from three epidemiologically unlinked individuals in Yunnan province, China. Two of the subjects are heterosexual men and one is a male intravenous drug user. Sequencing and analyzing the near-full-length genome of these three isolates (YNTC88, YNTC19, and YNTC35) revealed identical recombination breakpoints in all three viruses, but considerable genetic diversity between them, across the genomes, indicating that this is not a newly created CRF, only newly detected. CRF78_cpx differs from previously documented CRF01-AE/B'/C forms in its distinct backbone, inserted fragment size, and breakpoints, and is not related to other described recombinants in the region such as CRF07_BC or CRF65_cpx (also composed of CRF01_AE, B', and C). Our present findings further enrich the diversity of the prevalent HIV-1 CRFs in Yunnan, which is considered as an epicenter of HIV-1 infections in China.
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Affiliation(s)
- Yindi Song
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Yue Feng
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Ming Yang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Li Liu
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Yunnan Provincial Center for Molecular Diagnosis, Kunming University of Science and Technology, Kunming, China
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Junqueira DM, Almeida SEDM. HIV-1 subtype B: Traces of a pandemic. Virology 2016; 495:173-84. [PMID: 27228177 DOI: 10.1016/j.virol.2016.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/18/2022]
Abstract
Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Centro Universitário Ritter dos Reis - UniRitter, Departamento de Ciências da Saúde, Avenida Orfanotrófio, 555 - Teresópolis, Porto Alegre, RS, Brazil.
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Instituto de Ciências da Saúde, Universidade FEEVALE, Rodovia RS 239, 2755 - Vila Nova, Novo Hamburgo, RS, Brazil.
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Chen M, Ma Y, Chen H, Luo H, Dai J, Song L, Yang C, Mei J, Yang L, Dong L, Jia M, Lu L. Multiple Introduction and Naturally Occuring Drug Resistance of HCV among HIV-Infected Intravenous Drug Users in Yunnan: An Origin of China's HIV/HCV Epidemics. PLoS One 2015; 10:e0142543. [PMID: 26562015 PMCID: PMC4642981 DOI: 10.1371/journal.pone.0142543] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/25/2015] [Indexed: 02/07/2023] Open
Abstract
Background The human immunodeficiency virus 1 (HIV-1) epidemic in China historically stemmed from intravenous drug users (IDUs) in Yunnan. Due to a shared transmission route, hepatitis C virus (HCV)/HIV-1 co-infection is common. Here, we investigated HCV genetic characteristics and baseline drug resistance among HIV-infected IDUs in Yunnan. Methods Blood samples of 432 HIV-1/HCV co-infected IDUs were collected from January to June 2014 in six prefectures of Yunnan Province. Partial E1E2 and NS5B genes were sequenced. Phylogenetic, evolutionary and genotypic drug resistance analyses were performed. Results Among the 293 specimens successfully genotyped, seven subtypes were identified, including subtypes 3b (37.9%, 111/293), 3a (21.8%, 64/293), 6n (14.0%, 41/293), 1b (10.6%, 31/293), 1a (8.2%, 24/293), 6a (5.1%, 15/293) and 6u (2.4%, 7/293). The distribution of HCV subtypes was mostly related to geographic location. Subtypes 3b, 3a, and 6n were detected in all six prefectures, however, the other four subtypes were detected only in parts of the six prefectures. Phylogeographic analyses indicated that 6n, 1a and 6u originated in the western prefecture (Dehong) and spread eastward and showed genetic relatedness with those detected in Burmese. However, 6a originated in the southeast prefectures (Honghe and Wenshan) bordering Vietnam and was transmitted westward. These subtypes exhibited different evolutionary rates (between 4.35×10−4 and 2.38×10−3 substitutions site-1 year-1) and times of most recent common ancestor (tMRCA, between 1790.3 and 1994.6), suggesting that HCV was multiply introduced into Yunnan. Naturally occurring resistance-associated mutations (C316N, A421V, C445F, I482L, V494A, and V499A) to NS5B polymerase inhibitors were detected in direct-acting antivirals (DAAs)-naïve IDUs. Conclusion This work reveals the temporal-spatial distribution of HCV subtypes and baseline HCV drug resistance among HIV-infected IDUs in Yunnan. The findings enhance our understanding of the characteristics and evolution of HCV in IDUs and are valuable for developing HCV prevention and management strategies for this population.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijun Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jingyuan Mei
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- * E-mail: (MJ); (LL)
| | - Lin Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, 650500, China
- * E-mail: (MJ); (LL)
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Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (BETHESDA, MD.) 2015; 6:107-20. [PMID: 26546308 PMCID: PMC4704709 DOI: 10.1534/g3.115.024208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 01/19/2023]
Abstract
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.
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Affiliation(s)
- Nicolas Alcala
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Amalio Telenti
- Genomic Medicine, The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
| | - Séverine Vuilleumier
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland
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Liu Y, Gui T, Jia L, Li L, Bao Z, Li H, Wang X, Liu S, Zhuang D, Li T, Li J. Phylogenetic Analysis of HIV-1 CRF65_CPX Reveals Yunnan Province Is Still a Source Contributing to the Spread of HIV-1 in China. J Acquir Immune Defic Syndr 2015; 70:e120-2. [DOI: 10.1097/qai.0000000000000775] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Phanuphak N, Lo YR, Shao Y, Solomon SS, O'Connell RJ, Tovanabutra S, Chang D, Kim JH, Excler JL. HIV Epidemic in Asia: Implications for HIV Vaccine and Other Prevention Trials. AIDS Res Hum Retroviruses 2015; 31:1060-76. [PMID: 26107771 DOI: 10.1089/aid.2015.0049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
| | - Ying-Ru Lo
- HIV, Hepatitis, and STI Unit, WHO Regional Office for the Western Pacific, Manila, Philippines
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sunil Suhas Solomon
- Johns Hopkins University School of Medicine, Baltimore, Maryland
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Robert J. O'Connell
- Department of Retrovirology, U.S. Army Medical Component, Armed Forces Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - David Chang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jean Louis Excler
- U.S. Military HIV Research Program, Bethesda, Maryland
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
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Shao B, Song B, Cao L, Du J, Sun D, Lin Y, Wang B, Wang F, Wang S. Molecular epidemiology is becoming complex under the dynamic HIV prevalence: The perspective from Harbin, China. J Med Virol 2015; 88:807-14. [PMID: 26470641 DOI: 10.1002/jmv.24407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2015] [Indexed: 11/07/2022]
Abstract
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.
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Affiliation(s)
- Bing Shao
- Department of Epidemiology, Public Health College of Jilin Medical University, Jilin, China.,Department of Infectious Diseases, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Song
- Department of Infectious Diseases, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lijun Cao
- Department of Infectious Diseases, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Juan Du
- Basic chemistry laboratory, College of Pharmacy of Jilin Medical University, Jilin, China
| | - Dongying Sun
- Department of Epidemiology, Public Health College of Harbin Medical University, Harbin, China
| | - Yuanlong Lin
- Department of Infectious Diseases, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Binyou Wang
- Department of Epidemiology, Public Health College of Harbin Medical University, Harbin, China
| | - Fuxiang Wang
- Department of Infectious Diseases, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Sunran Wang
- Public Health College of Jilin Medical University, Jilin, China
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Han J, Liu S, Guo W, Bao Z, Wang X, Li L, Liu Y, Zhuang D, Li H, Jia L, Gui T, Sui H, Li T, Li J. Development of an HIV-1 Subtype Panel in China: Isolation and Characterization of 30 HIV-1 Primary Strains Circulating in China. PLoS One 2015; 10:e0127696. [PMID: 26018591 PMCID: PMC4446268 DOI: 10.1371/journal.pone.0127696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background The complex epidemic and significant diversity of HIV-1 strains in China pose serious challenges for surveillance and diagnostic assays, vaccine development and clinical management. There is a lack of HIV-1 isolates in current canonical HIV-1 subtype panels that can represent HIV-1 diversity in China; an HIV-1 subtype panel for China is urgently needed. Methods Blood samples were collected from HIV-1 infected patients participating in the drug-resistance surveillance program in China. The samples were isolated, cultured and stored as neat culture supernatant. The HIV-1 isolates were fully characterized. The panel was used to compare 2 viral load assays and 2 p24 assays as the examples of how this panel could be used. Results An HIV-1 subtype panel for China composed of 30 HIV-1 primary strains of four subtypes (B [including Thai-B], CRF01_AE, CRF07_BC and G) was established. The samples were isolated and cultured to a high-titer (106-109 copies/ml)/high-volume (40ml). The HIV-1 isolates were fully characterized by the final viral load, p24 concentration, gag-pol and envC2V3 sequencing, co-receptor prediction, determination of the four amino acids at the tip of the env V3-loop, glycosylation sites in the V3 loop and the drug-resistance mutations. The comparison of two p24 assays and two viral load assays on the isolates illustrated how this panel may be used for the evaluation of diagnostic assay performance. The Pearson value between p24 assays were 0.938. The viral load results showed excellent concordance and agreement for samples of Thai-B, but lower correlations for samples of CRF01_AE. Conclusion The current panel of 30 HIV-1 isolates served as a basis for the development of a comprehensive panel of fully characterized viral isolates, which could reflect the current dynamic and complex HIV-1 epidemic in China. This panel will be available to support HIV-1 research, assay evaluation, vaccine and drug development.
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Affiliation(s)
- Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Wei Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Hongshuai Sui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 0007, Beijing, P.R. China
- * E-mail:
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Bagaya BS, Vega JF, Tian M, Nickel GC, Li Y, Krebs KC, Arts EJ, Gao Y. Functional bottlenecks for generation of HIV-1 intersubtype Env recombinants. Retrovirology 2015; 12:44. [PMID: 25997955 PMCID: PMC4445978 DOI: 10.1186/s12977-015-0170-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 11/13/2022] Open
Abstract
Background Intersubtype recombination is a powerful driving force for HIV evolution, impacting both HIV-1 diversity within an infected individual and within the global epidemic. This study examines if viral protein function/fitness is the major constraint shaping selection of recombination hotspots in replication-competent HIV-1 progeny. A better understanding of the interplay between viral protein structure-function and recombination may provide insights into both vaccine design and drug development. Results In vitro HIV-1 dual infections were used to recombine subtypes A and D isolates and examine breakpoints in the Env glycoproteins. The entire env genes of 21 A/D recombinants with breakpoints in gp120 were non-functional when cloned into the laboratory strain, NL4-3. Likewise, cloning of A/D gp120 coding regions also produced dead viruses with non-functional Envs. 4/9 replication-competent viruses with functional Env’s were obtained when just the V1-V5 regions of these same A/D recombinants (i.e. same A/D breakpoints as above) were cloned into NL4-3. Conclusion These findings on functional A/D Env recombinants combined with structural models of Env suggest a conserved interplay between the C1 domain with C5 domain of gp120 and extracellular domain of gp41. Models also reveal a co-evolution within C1, C5, and ecto-gp41 domains which might explain the paucity of intersubtype recombination in the gp120 V1-V5 regions, despite their hypervariability. At least HIV-1 A/D intersubtype recombination in gp120 may result in a C1 from one subtype incompatible with a C5/gp41 from another subtype.
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Affiliation(s)
- Bernard S Bagaya
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - José F Vega
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Meijuan Tian
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - Gabrielle C Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Yuejin Li
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Kendall C Krebs
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - Yong Gao
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA. .,Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
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Gui T, Zhao J, Sun C, Chen L, Liu Y, Zheng C, Li H, Li T, Bao Z, Wang X, Li J, Li L. Genetic Characterization of a Unique Recombinant Originating from CRF55_01B, CRF01_AE, and CRF07_BC in Shenzhen, China. AIDS Res Hum Retroviruses 2015; 31:559-63. [PMID: 25748656 DOI: 10.1089/aid.2014.0337] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple subtypes were found to be epidemic in the Shenzhen men who have sex with men (MSM) population, which always predicts the emergence of a unique recombinant. In 2012, CRF55_01B was first reported, which later was proven to have originated in MSM in Shenzhen city. In this study, we reported a unique recombinant form (URF) of HIV-1 identified in a man who has had sex with men in Shenzhen city. The strain showed a genomic schematic map similar to CRF55_01B with subtype C segments inserted in the gag and pol genes. The full-length genome was amplified in two halves with 1-kb overlap regions. The PCR products were cloned and sequenced. A recombination detection program showed that two subtype C fragments and two subtype B fragments were inserted into the CRF01_AE backbone genome in the gag and pol regions. In the phylogenetic tree, the subtype C fragments clustered with CRF07_BC variants and the other segments grouped with CRF55_01B strains except for one segment that clustered with CRF01_AE. Similar breakpoints between our strain and CRF65_cpx were also observed. The data suggested that the URF strain might be the recombinant form of CRF55_01B, CRF01_AE, and CRF07_BC. This is the first report of a third generation of recombination of HIV-1 that originated from CRF55_01B in China. The identification of the URF indicated the severity of the HIV epidemic in Shenzhen MSM and the urgent need for epidemiological surveillance of the new recombination.
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Affiliation(s)
- Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Chen Y, Chen S, Kang J, Fang H, Dao H, Guo W, Lai C, Lai M, Fan J, Fu L, Andrieu JM, Lu W. Evolving molecular epidemiological profile of human immunodeficiency virus 1 in the southwest border of China. PLoS One 2014; 9:e107578. [PMID: 25207977 PMCID: PMC4160289 DOI: 10.1371/journal.pone.0107578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/19/2014] [Indexed: 11/23/2022] Open
Abstract
Background We have previously reported in Xishuangbanna (Banna) Dai Autonomous Prefecture, a well-developed tourist destination in the southwest border of China, that HIV-1 transmitted dominantly through heterosexual contact with less divergent genotypes and few drug resistant mutations [1]. Due to the rapid increase of newly diagnosed HIV-1 cases per year in Banna in recent years, it’s important to evaluate the evolution of HIV-1 molecular epidemiology for the better understanding of ongoing HIV-1 outbreak in this region. Methodology/Principal Findings By sequencing of HIV-1 pol genes and phylogenetic analysis, we conducted a molecular epidemiologic study in 352 HIV-1-seropositive highly active antiretroviral treatment (HAART)-naïve individuals newly diagnosed at the Banna Center for Disease Control and Prevention between 2009 and 2011. Of 283 samples (84.1% taken from heterosexually acquired adults, 10.6% from needle-sharing drug users, 2.8% from men who have sex with men, 0.4% from children born from HIV-1-infected mothers, and 2.1% remained unknown) with successful sequencing for pol gene, we identified 108 (38.2%) HIV-1 subtype CRF08_BC, 101 (35.7%) CRF01_AE, 49 (17.3%) CRF07_BC, 5 (1.8%) C/CRF57_BC, 3 (1.1%) B’, 1 (0.4%) B/CRF51_01B, and 16 (5.7%) unique recombinants forms. Among these infected individuals, 104 (36.7%) cases showed drug resistant or resistance-relevant mutations, and 4 of them conferring high-level resistance to 3TC/FTC, EFV/NVP or NFV. Phylogenetic analysis revealed 21 clusters (2–7 sequences) with only 21.2% (60/283) sequences involved. Conclusion/Significance In contrast to our previous findings, CRF08_BC, replaced CRF01_AE, became the dominant genotype of HIV-1 in Banna prefecture. The viral strains with drug resistance mutations were detected frequently in newly diagnosed HIV-1-infected individuals in this region.
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Affiliation(s)
- Yingyu Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Jun Kang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hua Fang
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Hong Dao
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mingyue Lai
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Jianhua Fan
- Xishuangbanna Center for Disease Control and Prevention, Jinghong, Yunnan, People’s Republic of China
| | - Linchun Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jean-Marie Andrieu
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
| | - Wei Lu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Institut de Recherche sur les Vaccins et l’Immunologie des Cancers et du Sida, Université Paris Descartes/Institut de Recherche pour le Développement, Paris, France
- * E-mail:
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