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Wan Z, Zhang C. How to report and make sense of a new HIV-1 circulating recombinant form? Front Microbiol 2024; 15:1343143. [PMID: 38450164 PMCID: PMC10915052 DOI: 10.3389/fmicb.2024.1343143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024] Open
Abstract
Co-circulation of multiple HIV-1 subtypes in the same high-risk groups leads to the on-going generation of various inter-subtype recombinants, including unique (URFs) and circulating (CRFs) recombinant forms, which brings a new challenge for the prevention and eradication of HIV/AIDS. Identification and prompt reporting of new CRFs will provide not only new insights into the understanding of genetic diversity and evolution of HIV-1, but also an early warning of potential prevalence of these variants. Currently, 140 HIV-1 CRFs have been described; however, their prevalence and clinical importance are less concerned. Apart from the mosaic genomic maps, less other valuable information, including the clinical and demographic data, genomic sequence characteristics, origin and evolutionary dynamics, as well as representative genomic fragments for determining the variants, are available for most of these CRFs. Accompanied with the growing increase of HIV-1 full-length genomic sequences, more and more CRFs will be identified in the near future due to the high recombination potential of HIV-1. Here, we discuss the prevalence and clinical importance of various HIV-1 CRFs and propose how to report and make sense of a new HIV-1 CRF.
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Affiliation(s)
- Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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2
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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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3
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Kusagawa S, Hamaguchi I, Tatsumi M. Development of quantified HIV-1 antigen panel for evaluating HIV Ag/Ab combination tests using the RT-qPCR method. Pract Lab Med 2022; 32:e00301. [PMID: 36204595 PMCID: PMC9530611 DOI: 10.1016/j.plabm.2022.e00301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/31/2022] Open
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A New HIV-1 K 28E 32-Reverse Transcriptase Variant Associated with the Rapid Expansion of CRF07_BC among Men Who Have Sex with Men. Microbiol Spectr 2022; 10:e0254522. [PMID: 36214682 PMCID: PMC9604004 DOI: 10.1128/spectrum.02545-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
HIV-1 CRF07_BC originated among injection drug users (IDUs) in China. After diffusing into men who have sex with men (MSM), CRF07_BC has shown a rapid expansion in this group; however, the mechanism remains unclear. Here, we identified a new K28E32 variant of CRF07_BC that was characterized by five specific mutations (E28K, K32E, E248V, K249Q, and T338S) in reverse transcriptase. This variant was mainly prevalent among MSM, and was overrepresented in transmission clusters, suggesting that it could have driven the rapid expansion of CRF07_BC in MSM, though founder effects cannot be ruled out. It was descended from an evolutionary intermediate accumulating four specific mutations and formed an independent phylogenetic node with an estimated origin time in 2003. The K28E32 variant was demonstrated to have significantly higher in vitro HIV-1 replication ability than the wild type. Mutations E28K and K32E play a critical role in the improvement of in vitro HIV-1 replication ability, reflected by improved reverse transcription activity. The results could allow public health officials to use this marker (especially E28K and K32E mutations in the reverse transcriptase (RT) coding region) to target prevention measures prioritizing MSM population and persons infected with this variant for test and treat initiatives. IMPORTANCE HIV-1 has very high mutation rate that is correlated with the survival and adaption of the virus. The variants with higher transmissibility may be more selective advantage than the strains with higher virulence. Several HIV-1 variants were previously demonstrated to be correlated with higher viral load and lower CD4 T cell count. Here, we first identified a new variant (the K28E32 variant) of HIV-1 CRF07_BC, described its origin and evolutionary dynamics, and demonstrated its higher in vitro HIV-1 replication ability than the wild type. We demonstrated that five RT mutations (especially E28K and K32E) significantly improve in vitro HIV-1 replication ability. The appearance of the new K28E32 variant was associated with the rapidly increasing prevalence of CRF07_BC among MSM.
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Geographic Transmission and Epidemic History of HIV-1 CRF01_AE, CRF07_BC, and HCV Subtype-6w among Taiwanese Persons Who Inject Drugs. Viruses 2022; 14:v14102142. [PMID: 36298695 PMCID: PMC9610456 DOI: 10.3390/v14102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
Persons who inject drugs (PWID) and their risk-related behaviors (e.g., unprotected sex and sharing needles/syringes/other injection equipment) have caused severe public health problems, especially in the rapid spread of HIV-1 and HCV. Here, we reconstructed the epidemic history of HIV-1 circulating recombinant form (CRF) 01_AE, CRF07_BC, and HCV subtype-6w among Taiwanese PWID. The timescales were estimated using phylogenetic and Bayesian coalescent analyses. The results revealed that CRF01_AE started to circulate in the Taiwanese PWID population in central Taiwan at 1992.5 (95% credible region: 1988.8–1995.9) and spread to other regions of Taiwan, while CRF07_BC was first identified in southern Taiwan at 2000.0 (95% CR: 1997.8–2002.2) and then spread northward to central-northern Taiwan. All HCV-6 strains were from Asia (that is, China, Myanmar, Taiwan, and Vietnam) and originated in 1928.1 (95% CR: 1890.2–1966.0). Furthermore, subtype-6w isolates from different regions of Taiwan appeared to share a common source that existed in the mid-1990s (95% CR: 1985.0–2001.8) or thereabouts. The routes of drug trafficking and the resulting high prevalence of HIV-1/HCV co-infections among PWID might have contributed to the virus transmission and promoted its spread worldwide. Long-term monitoring and policy implementation in at-risk populations would be useful for disease control.
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Zhang X, Li H, Liu Z, Zhao Y, Zeng Y, Dong Y, Li L, Zhang C. An HFman probe-based reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for HIV-1 detection. Mol Cell Probes 2022; 64:101834. [PMID: 35732248 DOI: 10.1016/j.mcp.2022.101834] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is suitable for the development of a rapid and cost-effective nucleic acid technique for point of care (POC) applications. However, LAMP methods often generate non-specific amplification, therefore inevitably resulting in false positive results especially when sequence-independent dyes are used to indirectly reflect the results. In this study, we established and optimized a reverse transcription LAMP (RT-LAMP) assay with a high-fidelity DNA polymerase-mediated fluorescent probe (HFman probe) for human immunodeficiency virus-1 (HIV-1) detection. The assay showed high sensitivity and specificity. Using 101 plasma samples with different HIV-1 viral load, we demonstrated that our assay can detect the major HIV-1 subtypes circulating in China, including CRF01_AE, CRF07_BC, CRF08_BC, CRF55_01B, and unique recombinant forms (URFs). We also compared our assay with an approved commercial real-time quantitative polymerase chain reaction (RT-qPCR) kit and found the sensitivity, specificity and consistency was 88.8%, 100% and 89.1%, respectively. The HFman probe-based RT-LAMP assay is a high specific detection method that is rapid, variant-tolerant and simple to operate, and thus is of great significance for timely disclosure of HIV status and rapid POC diagnosis.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ziwei Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yongjuan Zhao
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yi Zeng
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yajuan Dong
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center for Pathogen Research, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Chiyu Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Li M, Yuan Y, Li P, Deng Z, Wen Z, Wang H, Feng F, Zou H, Chen L, Tang S, Sun C. Comparison of the Immunogenicity of HIV-1 CRF07_BC Gag Antigen With or Without a Seven Amino Acid Deletion in p6 Region. Front Immunol 2022; 13:850719. [PMID: 35450078 PMCID: PMC9017423 DOI: 10.3389/fimmu.2022.850719] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/03/2022] [Indexed: 11/23/2022] Open
Abstract
HIV-1 CRF07_BC-p6Δ7, a strain with a seven amino acid deletion in the p6 region of the Gag protein, is becoming the dominant strain of HIV transmission among men who have sex with men (MSM) in China. Previous studies demonstrated that HIV-1 patients infected by CRF07_BC-p6Δ7 strain had lower viral load and slower disease progression than those patients infected with CRF07_BC wild-type strain. However, the underlying mechanism for this observation is not fully clarified yet. In this study, we constructed the recombinant DNA plasmid and adenovirus type 2 (Ad2) vector-based constructs to express the HIV-1 CRF07_BC Gag antigen with or without p6Δ7 mutation and then investigated their immunogenicity in mice. Our results showed that HIV-1 CRF07_BC Gag antigen with p6Δ7 mutation induced a comparable level of Gag-specific antibodies but stronger CD4+ and CD8+ T-cell immune responses than that of CRF07_BC Gag (07_BC-wt). Furthermore, we identified a series of T-cell epitopes, which induced strong T-cell immune response and cross-immunity with CRF01_AE Gag. These findings implied that the p6Gag protein with a seven amino acid deletion might enhance the Gag immunogenicity in particular cellular immunity, which provides valuable information to clarify the pathogenic mechanism of HIV-1 CRF07_BC-p6Δ7 and to develop precise vaccine strategies against HIV-1 infection.
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Affiliation(s)
- Minchao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yue Yuan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, Guangzhou, China
| | - Zhaomin Deng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ziyu Wen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fengling Feng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Huachun Zou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, Guangzhou, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China.,Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, China
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Chen YT, Li ZX, Xie YN, Zhao L, Hu AY, An L, Dong XY, Liu DX, Ma Q, Chen X. Genetic Characterization of a Novel HIV-1 Second-Generation Recombinant Form Originating from CRF86_BC and a Unique Recombinant Form in Yunnan, China. AIDS Res Hum Retroviruses 2021; 37:985-989. [PMID: 34465137 DOI: 10.1089/aid.2021.0121] [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: 11/12/2022] Open
Abstract
Yunnan is the first place where human immunodeficiency virus type 1 (HIV-1) became prevalent in China, and it is also the place with the most complicated HIV-1 genetic diversity in China. On October 23, 2019, a patient newly diagnosed with acquired immunodeficiency syndrome from a hospital in Baoshan, Yunnan, was recruited for genetic analysis. Near full-length genome of HIV-1 was amplified from the plasma sample. Phylogenetic analysis revealed that this sequence (BS6F24) has a close relationship with CRF86_BC and a unique recombinant form (URF) (KY406739), which was formed by recombination of subtypes B and C. Bootscan analysis confirmed that the first part (HXB2:1022-5832) and last part (HXB2:5833-9120) genomes of BS6F24 had the same recombinant structures as KY406739 and CRF86_BC, respectively. A second-generation recombinant form that originated from CRF86_BC and a URF were reported for the first time. This indicates the need for continuous monitoring of the genetic diversity of HIV-1 in Yunnan, China.
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Affiliation(s)
- Ya-Ting Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Zheng-Xu Li
- Baoshan Centre for Disease Control and Prevention, Baoshan, China
| | - Ying-Na Xie
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Lei Zhao
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - An-Yan Hu
- Baoshan Centre for Disease Control and Prevention, Baoshan, China
| | - Li An
- Baoshan Centre for Disease Control and Prevention, Baoshan, China
| | - Xian-Ya Dong
- Baoshan Centre for Disease Control and Prevention, Baoshan, China
| | - Dong-Xu Liu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Qiang Ma
- Baoshan Centre for Disease Control and Prevention, Baoshan, China
| | - Xin Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
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Wang Y, Chen X, Ye M, Pang W, Zhang C, Xiong SD, Zheng YT. Consistency of spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected drug users in China. BMC Infect Dis 2021; 21:1001. [PMID: 34563139 PMCID: PMC8465760 DOI: 10.1186/s12879-021-06711-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As the transmission routes of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) are similar, previous studies based on separate research on HIV-1 and HCV assumed a similar transmission pattern. However, few studies have focused on the possible correlation of the spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected patients. METHODS A total of 310 HIV-1/HCV coinfected drug users were recruited in Yingjiang and Kaiyuan prefectures, Yunnan Province, China. HIV-1 env, p17, pol and HCV C/E2, NS5B fragments were amplified and sequenced from serum samples. The genetic characteristics and spatial dynamics of HIV-1 and HCV were explored by phylogenetic, bootscanning, and phylogeographic analyses. RESULTS Among HIV-1/HCV coinfected drug users, eight HCV subtypes (1a, 1b, 3a, 3b, 6a, 6n, 6v, and 6u) and two HIV-1 subtypes (subtype B and subtype C), three HIV-1 circulating recombinant forms (CRF01_AE, CRF07_BC and CRF08_BC), and four unique recombinant forms (URF_BC, URF_01B, URF_01C and URF_01BC) were identified. HCV subtype 3b was the most predominant subtype in both Yingjiang and Kaiyuan prefectures. The dominant circulating HIV-1 subtypes for drug users among the two areas were CRF08_BC and URF_BC. Maximum clade credibility trees revealed that both HIV-1 and HCV were transmitted from Yingjiang to Kaiyuan. CONCLUSIONS The spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected drug users seem to have high consistency, providing theoretical evidence for the prevention of HIV-1 and HCV simultaneously.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China.,KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Wuzhong District, Suzhou, 215000, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Si-Dong Xiong
- KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Wuzhong District, Suzhou, 215000, China. .,Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, China. .,KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Wuzhong District, Suzhou, 215000, China.
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10
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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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11
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Li Y, Chen X, Zhao Y, Wan Z, Zeng Y, Ma Y, Zhou L, Xu G, Reboud J, Cooper JM, Zhang C. A rapid variant-tolerant reverse transcription loop-mediated isothermal amplification assay for the point of care detection of HIV-1. Analyst 2021; 146:5347-5356. [PMID: 34323889 DOI: 10.1039/d1an00598g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human immunodeficiency virus (HIV) continues to be a major burden on public health globally with on-going increases in the number of new infections each year. Rapid and sensitive point-of-care tests allow timely interventions and are essential to control the spread of the disease. However the highly variable nature of the virus, resulting in the evolution of many subtypes and inter-subtype recombinants, poses important challenges for its diagnosis. Here we describe a variant-tolerant reverse-transcription RT-LAMP amplification of the virus's INT gene, providing a simple to use, rapid (<30 min) in vitro point-of-care diagnostic test with a limit of detection <18 copies/reaction. The assay was first validated in clinical studies of patient samples, using both established RT-LAMP and RT-qPCR assays for reference, with results showing that this new variant-tolerant HIV-1 RT-LAMP diagnostic test is highly sensitive without compromising its high specificity for HIV-1 subtypes. The diagnostic test was subsequently configured within an easy-to-read paper microfluidic lateral flow test and was validated clinically using patient samples, demonstrating its future potential for use in timely, effective, low cost HIV diagnostics in global regions where healthcare resources may be limited.
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Affiliation(s)
- Yingxue Li
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
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Xie YN, Li SL, Yang RR, Huang J, Peng X, Xu W, Cheng SW, Zhou YH, Chen X, Li H. Genetic Characteristics of Three Unique Recombinant Forms of HIV-1 in Yunnan, China. AIDS Res Hum Retroviruses 2021; 37:580-584. [PMID: 33287633 DOI: 10.1089/aid.2020.0234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To explore the molecular epidemiological status of human immunodeficiency virus type 1 (HIV-1) in Yunnan, China, three HIV-1 near full-length genomes were amplified and sequenced from plasma samples that were collected from Burmese patients newly diagnosed with HIV-1 in Dehong Prefecture in Yunnan Province in 2017. Phylogenetic and bootscanning analyses revealed that all the sequences might be HIV-1 second-generation recombinant forms of circulating recombinant forms (CRF07_BC and CRF83_cpx) and unique recombinant forms. One of the sequences contained six CRF01_AE fragments, five subtype C fragments, and two subtype B fragments, which were separated by 12 breakpoints. These results revealed that the second-generation recombination of HIV-1 within different strains is still ongoing in Dehong, China. Systematic surveys and immediate interventions are urgently needed to prevent the formation of increasingly complex HIV-1 recombinant forms.
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Affiliation(s)
- Ying-Na Xie
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Si-Le Li
- Yunnan Cancer Hospital and the Third Affiliated Hospital of Kunming Medical University and Yunnan Cancer Center, Kunming, China
| | - Rong-Rong Yang
- Ganzhou Center for Disease Control and Prevention, Ganzhou, China
| | - Jin Huang
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Xia Peng
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Si-Wei Cheng
- Department of Zoology, School of Life Sciences, Yan'an University, Yan'an, China
| | - Yan-Heng Zhou
- Department of Zoology, School of Life Sciences, Yan'an University, Yan'an, China
| | - Xin Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Hong Li
- Yunnan Center for Disease Control and Prevention, Kunming, China
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Ding Y, Chen M, Wang J, Yang Y, Feng Y, Wang L, Duan S, Lin Q, Xing H, Ma Y, Han M, Ma L. Increase in HIV-1-transmitted drug resistance among ART-naïve youths at the China-Myanmar border during 2009 ~ 2017. BMC Infect Dis 2021; 21:93. [PMID: 33478415 PMCID: PMC7818912 DOI: 10.1186/s12879-021-05794-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Background HIV-transmitted drug resistance (TDR) is found in antiretroviral therapy (ART)-naïve populations infected with HIV-1 with TDR mutations and is important for guiding future first- and second-line ART regimens. We investigated TDR and its effect on CD4 count in ART-naïve youths from the China-Myanmar border near the Golden Triangle to better understand TDR and effectively guide ART. Methods From 2009 to 2017, 10,832 HIV-1 infected individuals were newly reported along the Dehong border of China, 573 ART-naïve youths (16 ~ 25 y) were enrolled. CD4 counts were obtained from whole blood samples. HIV pol gene sequences were amplified from RNA extracted from plasma. The Stanford REGA program and jpHMM recombination prediction tool were used to determine genotypes. TDR mutations (TDRMs) were analyzed using the Stanford Calibrated Population Resistance tool. Results The most common infection route was heterosexuals (70.51%), followed by people who inject drugs (PWID, 19.20%) and men who have sex with men (MSM) (8.90%). The distribution of HIV genotypes mainly included the unique recombinant form (URF) (44.08%), 38.68% were CRFs, 13.24% were subtype C and 4.04% were subtype B. The prevalence of TDR increased significantly from 2009 to 2017 (3.48 to 9.48%) in ART-naïve youths (4.00 to 13.16% in Burmese subjects, 3.33 to 5.93% in Chinese subjects), and the resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) were 3.49, 2.62, and 0.52%, respectively. Most (94.40%, n = 34) of HIV-1-infected patients with TDRM had mutation that conferred resistance to a single drug class. The most common mutations Y181I/C and K103N, were found in 7 and 9 youths, respectively. The mean CD4 count was significantly lower among individuals with TDRMs (373/mm3 vs. 496/mm3, p = 0.013). Conclusions The increase in the prevalence of HIV-1 TDR increase and a low CD4 count of patients with TDRMs in the China-Myanmar border suggests the need for considering drug resistance before initiating ART in HIV recombination hotspots. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05794-5.
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Affiliation(s)
- Yibo Ding
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - 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
| | - Jibao Wang
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Yuecheng Yang
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Yi Feng
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Lijie Wang
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Song Duan
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Mangshi, 678400, China
| | - Qianru Lin
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Hui Xing
- 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, 155 Changbai Road, Changping District, Beijing, 102206, 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
| | - Mengjie Han
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China.
| | - Liying Ma
- 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, 155 Changbai Road, Changping District, Beijing, 102206, China.
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Su L, Feng Y, Liang S, Zeng Y, Li Y, Yang H, Ye L, Wang Q, Wei D, Yuan D, Lai W, Zhang L. The origin and spread of CRF85_BC, driven by heterosexual transmission among older people in Sichuan, China. BMC Infect Dis 2020; 20:772. [PMID: 33076868 PMCID: PMC7574430 DOI: 10.1186/s12879-020-05488-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/08/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND CRF_BC recombinants, including CRF07_BC and CRF08_BC, were considered the predominant subtypes in China. Since the discovery of HIV-1 circulating recombinant form CRF 85_BC in Southwest China in 2016, this BC recombinant forms had been reported in different regions of China. However, the history and magnitude of CRF85_BC transmission were still to be investigated. METHOD We conducted the most recent molecular epidemiology of HIV-1 among newly reported HIV-1 infected patients in Sichuan in 2019 by sequencing and phylogenetic analysis of 1291 pol sequences. Then, we used maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of pol sequences to reconstruct the phylogeographic and demographic dynamics of the CRF85_BC. RESULTS HIV-1 CRF85_BC (68/1291, 5.27%) became the fourth most prevalent strain revealing a significant increase in local population. CRF85_BC were only found in heterosexually infected individuals and the majority of CRF85_BC (95.45%) were circulating among the people living with HIV aged 50 years and over (PLHIV50+), suggesting a unique prevalent pattern. The founder lineages of CRF85_BC were likely to have first emerged in Yunnan, a province of Southwest China bordering Sichuan, in the early 2000s. It then spread exponentially to various places (including Guangxi, Sichuan, et al) and became endemic around 2008.6 (2006.7-2010.2) in Sichuan. CONCLUSION Taken together, our findings on HIV-1 subtype CRF85_BC infections provided new insights into the spread of this virus and extended the understanding of the HIV epidemic in China.
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Affiliation(s)
- Ling Su
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yi Feng
- Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), China CDC, Beijing, China
| | - Shu Liang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yali Zeng
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yiping Li
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Hong Yang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Li Ye
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Qiushi Wang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Dongbin Wei
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Dan Yuan
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Wenhong Lai
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Linglin Zhang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China.
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Jiang Y, Zhang L, Hou Z, Tu A, Qiao R, Dai C, Yao N, Du X, Xu Y, Tan J. Prevalence of Different Genotypes of HIV-1 in Injection Drug Users in China: A Systematic Review and Meta-Analysis. Curr HIV Res 2020; 17:240-257. [PMID: 31538898 DOI: 10.2174/1570162x17666190919115036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Since 1981, an increasing trend in HIV has been observed for transmission via injection drug users (IDUs), sexual transmission and mother-to-child transmission. The IDUs are blamed for early increases in HIV-positive cases in China. OBJECTIVE HIV genotypes of IDUs were comprehensively analysed to trace the source and relationships of the AIDS epidemic in China. METHODS Relevant databases written in English and Chinese were searched. Overall, 7,149 publications were identified in six databases. After screening 7,104 articles according to the inclusion and exclusion criteria, 45 studies consisting of 2,765 cases were finally identified. A meta-analysis was conducted using R MATLAB software, RevMan and SPSS. Subgroup analyses focused on time frame, region, and location of different genotypes of IDUs in China. RESULTS There were five dominant HIV-1 genotypes among the 2,765 IDU cases. The proportions of CRF07_BC, CRF01_AE, CRF08_BC, subtype B/B', and subtype C were 45.18% (95% CI: 33.55-57.08%), 16.00% (95% CI: 9.39-23.82%), 13.43% (95% CI: 7.32-20.84%), 3.58% (95% CI: 1.52-6.24%), and 0.90% (95% CI: 0.04-2.43%), respectively. HIV genotypes transmitted among IDUs in China are primarily CRF07-BC, followed by CRF01-AE and CRF08-BC. Across the different time frames and regions, CRF07_BC was the most prevalent HIV-1 genotype among IDUs, while CRF08_BC was the most prevalent genotype in the southwest region. CONCLUSION Our study reveals that CRF07-BC was the dominant prevalent strain among IDUs from 1991 to 2015 in China, while CRF08-BC was the dominant prevalent strain among IDUs in southwestern China. This systematic review and meta-analysis shows evidence of the comprehensive prevalence of different genotypes, data and characteristics of HIV among IDUs in China.
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Affiliation(s)
- Yu Jiang
- Department of Immunology, School of Basic Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Lincai Zhang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - Zongjie Hou
- Department of Immunology, School of Basic Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Aixia Tu
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - Ruijuan Qiao
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - Chen Dai
- Department of Immunology, School of Basic Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Ning Yao
- Department of Ophthalmology, Gansu Gem Flower Hospital, Lanzhou, 730060, China
| | - Xiufen Du
- Department of Immunology, School of Basic Medicine, Lanzhou University, Lanzhou, 730000, China
| | - Yaning Xu
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - Jiying Tan
- Department of Immunology, School of Basic Medicine, Lanzhou University, Lanzhou, 730000, China
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The Examination of Viral Characteristics of HIV-1 CRF07_BC and Its Potential Interaction with Extracellular Galectin-3. Pathogens 2020; 9:pathogens9060425. [PMID: 32485969 PMCID: PMC7350312 DOI: 10.3390/pathogens9060425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 11/16/2022] Open
Abstract
HIV-1 CRF07_BC is a B’ and C subtype recombinant emerging virus and many of its viral characteristics remain unclear. Galectin-3 (Gal3) is a β-galactose binding lectin that has been reported as a pattern recognition receptor (PRR) and is known to mediate adhesion between cells and microbes. This study aims to examine the viral characteristics of HIV-1 CRF07_BC virus and the role of extracellular galectin-3 in HIV-1 CRF07_BC infection. A total of 28 HIV-1+ injecting drug users (IDUs) were recruited and 24 (85.7%) were identified as HIV-1 CRF07_BC. Results indicate that significant higher serum galectin-3 was measured in CRF07_BC infected patients and CRF07_BC infection triggered significant galectin-3 expression (p < 0.01). Viral characteristics demonstrate that CRF07_BC virions display a higher level of envelope gp120 spikes. The virus infectivity assay demonstrated that co-treatment with galectin-3 significantly promoted CRF07_BC attachment and internalization (p < 0.01). A co-immunoprecipitation assay showed that pulldown galectin-3 co-precipitated both CD4 and gp120 proteins. Results from an enzyme-linked immunosorbent assay (ELISA) indicate that the galectin-3 promoting effect occurs through enhancement of the interaction between gp120 and CD4. This study suggests that CRF07_BC was predominant in HIV-1+ IDUs and CRF07_BC utilized extracellular galectin-3 to enhance its infectivity via stabilization of the gp120-CD4 interaction.
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Amino Acid Deletions in p6 Gag Domain of HIV-1 CRF07_BC Ameliorate Galectin-3 Mediated Enhancement in Viral Budding. Int J Mol Sci 2020; 21:ijms21082910. [PMID: 32326345 PMCID: PMC7216183 DOI: 10.3390/ijms21082910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/13/2020] [Accepted: 04/19/2020] [Indexed: 01/04/2023] Open
Abstract
HIV-1 CRF07_BC is a recombinant virus with amino acid (a.a.) deletions in p6Gag, which are overlapped with the Alix-binding domain. Galectin-3 (Gal3), a β-galactose binding lectin, has been reported to interact with Alix and regulate HIV-1 subtype B budding. This study aims to evaluate the role of Gal3 in HIV-1 CRF07_BC infection and the potential effect of a.a. deletions on Gal3-mediated regulation. A total of 38 HIV-1+ injecting drug users (IDUs) were enrolled in the study. Viral characterization and correlation of Gal3 were validated. CRF07_BC containing 7 a.a. deletions and wild-type in the p6Gag (CRF07_BC-7d and -wt) were isolated and infectious clones were generated. Viral growth kinetic and budding assays using Jurkat-CCR5/Jurkat-CCR5-Gal3 cells infected with CRF07_BC were performed. Results indicate that 69.4% (25/38) of the recruited patients were identified as CRF07_BC, and CRF07_BC-7d was predominant. Slow disease progression and significantly higher plasma Gal3 were noted in CRF07_BC patients (p < 0.01). Results revealed that CRF07_BC infection resulted in Gal3 expression, which was induced by Tat. Growth dynamic and budding assays indicated that Gal3 expression in Jurkat-CCR5 cells significantly enhanced CRF07_BC-wt replication and budding (p < 0.05), while the promoting effect was ameliorated in CRF07_BC-7d. Co-immunoprecipitation found that deletions in the p6Gag reduced Gal-3-mediated enhancement of the Alix–Gag interaction.
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Chen X, Zhou YH, Ye M, Wang Y, Duo L, Pang W, Zhang C, Zheng YT. Burmese injecting drug users in Yunnan play a pivotal role in the cross-border transmission of HIV-1 in the China-Myanmar border region. Virulence 2018; 9:1195-1204. [PMID: 30001176 PMCID: PMC6086311 DOI: 10.1080/21505594.2018.1496777] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Injecting drug users (IDUs) are the major risk group for HIV-1 infection in the China-Myanmar border area. There are a large number of Burmese IDUs living in Yunnan (Yunnan-mIDUs) who might be associated with the cross-border transmission of HIV-1. From 2010 to 2013, 617 Yunnan-mIDUs were recruited from three counties of Yunnan, 19.0% of whom were detected to be HIV-1 positive by serological testing. Partial HIV-1 p17, pol, vif-env, and env genes were amplified from the positive samples and were sequenced. Phylogenetic and HIV-1 subtyping analyses revealed that HIV-1 recombinant forms (RFs), including RF_BC (36.4%), RF_01BC (26.1%), RF_01C (9.1%) and RF_01B (1.1%), were predominant among this cohort. Of the identified HIV-1 strains, 14.8%, 9.1% and 3.4% belonged to subtype C, CRF01_AE and subtype B, respectively. Transmission cluster analysis showed that sequences from the Yunnan-mIDUs formed transmission clusters not only with those from Burmese IDUs but also with those from Chinese IDUs, indicating that Yunnan-mIDUs might acquire HIV-1 infection from or spread HIV-1 to both Burmese and Chinese IDUs. Phylogeographic analyses revealed three cross-border transmission patterns associated with Yunnan-mIDUs, in which Yunnan-mIDUs served as the crucial nodes linking the Burmese and Chinese IDUs. These results suggest that Yunnan-mIDUs are a potential viral reservoir for the diffusion of HIV-1 in Yunnan and play a pivotal role in the bidirectional cross-border transmission of HIV-1 in the China-Myanmar border region. More intervention efforts that focus on Yunnan-mIDUs are recommended in Yunnan’s campaign against HIV/AIDS.
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Affiliation(s)
- Xin Chen
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, National Kunming High Level Biosafety Research Center for Non-human Primate, Kunming Institute of Zoology , Chinese Academy of Sciences , Kunming , China
| | - Yan-Heng Zhou
- b College of Life Sciences , Yan'an University , Yan'an , China
| | - Mei Ye
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, National Kunming High Level Biosafety Research Center for Non-human Primate, Kunming Institute of Zoology , Chinese Academy of Sciences , Kunming , China
| | - Yu Wang
- c KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences , Soochow University , Suzhou , China
| | - Lin Duo
- d Section of Science and Education, The Second People's Hospital of Yunnan Province , Kunming , China
| | - Wei Pang
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, National Kunming High Level Biosafety Research Center for Non-human Primate, Kunming Institute of Zoology , Chinese Academy of Sciences , Kunming , China
| | - Chiyu Zhang
- e Pathogen Discovery and Evolution Unit, Pathogen Discovery and Big Data Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai , Chinese Academy of Sciences , Shanghai , China
| | - Yong-Tang Zheng
- a Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, National Kunming High Level Biosafety Research Center for Non-human Primate, Kunming Institute of Zoology , Chinese Academy of Sciences , Kunming , China.,c KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences , Soochow University , Suzhou , China
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Das S, Bansal M, Bhattacharya J. Characterization of the membrane-bound form of the chimeric, B/C recombinant HIV-1 Env, LT5.J4b12C. J Gen Virol 2018; 99:1438-1443. [PMID: 30129918 DOI: 10.1099/jgv.0.001141] [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: 12/15/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) diversity is a significant challenge in developing a vaccine against the virus. B/C recombinants have been found in India and other places but are the predominant clade prevalent in China. HIV-1 envelopes (Envs) are the target of broadly neutralizing antibodies (bNAbs) which develop spontaneously in some HIV-1 infected patients. It has been previously reported with efficiently cleaved clade A, B and C Envs that preferential binding of Envs to bNAbs as opposed to non-NAbs, a desirable property for immunogens, is correlated with efficient cleavage of the Env precursor polypeptide into constituent subunits. These Envs are suitable for designing immunogens as soluble proteins, virus-like particles or for delivery by viral vectors/plasmid DNA. However, a B/C recombinant Env with similar properties has not been reported. Here we show that the chimeric, recombinant B/C clade Env LT5.J4b12C is efficiently cleaved on the plasma membrane and selectively binds to bNAbs.
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Affiliation(s)
- Supratik Das
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Manish Bansal
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Jayanta Bhattacharya
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India.,2International AIDS Vaccine Initiative, New York, USA
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Chen ZW, Liu L, Chen G, Cheung KW, Du Y, Yao X, Lu Y, Chen L, Lin X, Chen Z. Surging HIV-1 CRF07_BC epidemic among recently infected men who have sex with men in Fujian, China. J Med Virol 2018; 90:1210-1221. [PMID: 29574774 DOI: 10.1002/jmv.25072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/15/2018] [Indexed: 12/18/2022]
Abstract
A rapidly increasing number of HIV-1 infections have been identified among men who have sex with men (MSM) in Fujian province of China since 2010. We aimed to investigate the causative factors underlying this surging epidemic. Using immunoassays for HIV-1 diagnosis and phylogenetic analysis for viral genotyping, we found that the number of MSM infections doubled from 171 in 2011 to 340 in 2013 with a significantly increased prevalent rate from 4.1% to 5.2%. Majority of these increased infections took place in Fuzhou, Xiamen, and Quanzhou, three large cities in Fujian, mainly among youth, unemployed, business, and well-educated MSMs. Phylogenetic analysis revealed three major HIV-1 genotypes including CRF01_AE, CRF07_BC, and B/B' yet the surging MSM infections were primarily associated with the rapid sexual spread of CRF07_BC in addition to CRF01_AE. In particular, there was a significant proportional expansion of CRF07_BC infections among recently infected MSMs from 19% in 2012 to 41.9% in 2013. This increase was accompanied by emergence of complex patterns of viral recombination including multiple hybrid variants derived from CRF01_AE and CRF07_BC. Full-genome analysis indicated that CRF07_BC in Fujian was likely originated from similar strains previously found among IDUs in Yunnan province but with unique recombination break points. Our findings indicated that HIV-1 CRF07_BC has adapted for rapid sexual transmission, resulting in the surging HIV-1 epidemic and the emergence of new recombinant strains among MSMs in Fujian. Our findings have implications to vaccine and passive immunization trials in Fujian with emphasis on the induction of cross-subtype protective immunity.
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Affiliation(s)
- Zhi-Wei Chen
- Fujian Medical University, Fuzhou, Fujian Province, P.R. China.,AIDS Institute and Department of Microbiology, State Key laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Li Liu
- AIDS Institute and Department of Microbiology, State Key laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China.,HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, P.R. China
| | - Guozhong Chen
- Fujian Center for Disease Control and Prevention, Fujian Province, P.R. China
| | - Ka-Wai Cheung
- AIDS Institute and Department of Microbiology, State Key laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Yanhua Du
- AIDS Institute and Department of Microbiology, State Key laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China
| | - Xu Yao
- Fuzhou Center for Disease Control and Prevention, Fuzhou, Fujian Province, P.R. China
| | - Yuan Lu
- Fuzhou Center for Disease Control and Prevention, Fuzhou, Fujian Province, P.R. China
| | - Liang Chen
- Fujian Center for Disease Control and Prevention, Fujian Province, P.R. China
| | - Xinhua Lin
- Fujian Medical University, Fuzhou, Fujian Province, P.R. China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, State Key laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, P.R. China.,HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases and Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, P.R. China
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21
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Ren L, Wang B, Gong K, Liu P, Zhou S, Zhang L, Xia X, Wang K. Epidemiology reveals Zhaotong City as the hub of human immunodeficiency virus type 1 transmission from the Yunnan province to other regions in China. J Gen Virol 2017; 98:3093-3100. [PMID: 29091580 DOI: 10.1099/jgv.0.000961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Yunnan province in China has a high incidence of human immunodeficiency virus-1 (HIV-1) infection. Zhaotong City is located in the Yunnan province, a neglected 'important region'. In this study, we evaluated the unique molecular epidemiological characteristics of HIV-1 infection in Zhaotong City. We collected 305 serum samples from HIV-infected patients in Zhaotong City between May 2015 and April 2016. A total of 122 samples were selected for HIV-1 gag-pol gene amplification, of which 88 were successfully amplified and sequenced for phylogenetic and phylogeographic analysis. Circulating recombinant forms 07_BC (CRF07_BC, 23 cases, 26.14 %) and CRF08_BC (49 cases, 55.68 %) were the predominant subtypes; the high proportions of these two subtypes differed from those elsewhere in the Yunnan province. The other subtypes were CRF01_AE (11 cases, 12.5 %), B (one case, 1.14 %) and unique recombinant forms (four cases, 4.55 %). Phylogeographic analysis of the CRF07_BC and CRF08_BC subtype strains revealed that Zhaotong was one of the regions in which CRF07_BC and CRF08_BC entered initially. The CRF08_BC strain originated from this region closer to the 'root' position of the phylogenetic tree. Thus, Zhaotong City may have been an important channel in the transmission route of HIV-1 from Yunnan to other parts of the country. Based on this unique distribution of HIV-1 subtypes in Zhaotong City, the epidemic outbreak in this area may have played an important role in the spread of CRF07_BC and CRF08_BC subtypes.
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Affiliation(s)
- Li Ren
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan Province, PR China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650031, Yunnan Province, PR China.,Medical Faculty of Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Bingbui Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Kunmei Gong
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan Province, PR China
| | - Pan Liu
- Yan'an Hospital of Kunming Chenggong Hospital, Kunming 650501, Yunnan Province, PR China
| | - Shiyi Zhou
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, PR China
| | - Li Zhang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Kunming 650093, Yunnan Province, PR China
| | - Kunhua Wang
- Yunnan Institute of Digestive Disease, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, PR China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650031, Yunnan Province, PR China
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22
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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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23
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Zhang L, Wang B, Liang Y, Feng Y, Dong S, Wang Y, Li Y, Zhang AM, Liu L, Qin W, Xia X. Phylogenetic characteristics of HIV-1 among travelers entering China from Myanmar: A retrospective study. J Med Virol 2017; 89:1404-1411. [PMID: 28198547 DOI: 10.1002/jmv.24786] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/25/2017] [Indexed: 11/11/2022]
Abstract
Due to the open policy of the Chinese government, a large number of Burmese individuals enter China at land ports in Yunnan province for travel or business. However, the situation of HIV-1 infection and its phylogenetic characteristics among these travelers remains unclear, which is a potential threat to public health. From January 2003 to December 2012, a total of 1,961 travelers were detected to be positive for HIV-1 infection at land ports between Myanmar and Yunnan province, China. From 1153 (58.8%) Burmese of them, we randomly collected 489 serum samples for HIV-1 subtype/recombinant analysis. Based on successfully obtained 223 gag-RT sequences, 187 of them were genotyped as 2 subtypes and 3 CRFs. CRF01_AE was showed to be the most prevalent genotype (54.3%), followed by subtypes C (13.5%) and B (10.8%). Notably, CRF07_BC (1.3%) and CRF08_BC (4.0%) were mainly distributed in travelers from Shan state and Kachin (91.7%, 11/12), but was not found in travelers from the capital city of Yangon (0/16). Additionally, there were 36 samples (16.1%) were preliminary determined as unique recombinant forms (URFs). The higher HIV-1 infection among entering travelers from Myanmar and its diverse and complex genotypes distribution suggest this bridge population may facilitate the transmission of HIV-1. It is necessary to have the strict monitoring on this population for prevention of HIV-1 cross-border transmission.
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Affiliation(s)
- Li Zhang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Binhui Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yaobo Liang
- Care Center for International Travel Health in Yunnan, Kunming, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shuwei Dong
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yajuan Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yaping Li
- Care Center for International Travel Health in Yunnan, Kunming, Yunnan, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Liu
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Weihong Qin
- Care Center for International Travel Health in Yunnan, Kunming, Yunnan, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan, China
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24
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Chen X, Ye M, Pang W, Smith DM, Zhang C, Zheng YT. First Appearance of HIV-1 CRF07_BC and CRF08_BC Outside China. AIDS Res Hum Retroviruses 2017; 33:74-76. [PMID: 27392826 DOI: 10.1089/aid.2016.0169] [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: 11/12/2022] Open
Abstract
Neither full length genomic sequence of CRF07_BC nor that of CRF08_BC was found in any other countries since they originated in Yunnan, China, in early 1990s. Here, we first report that CRF07_BC and CRF08_BC appeared among intravenous drug users in Shan state of Myanmar bordering Yunnan, and confirmed that they spread from China to Myanmar. The introduction of CRF07_BC and CRF08_BC in northern Myanmar may forebode a changing subtype epidemic in Southeast Asia.
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Affiliation(s)
- Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, San Diego, California
- Veterans Affairs Healthcare System San Diego, San Diego, California
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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25
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Qin C, Zhang P, Zhu W, Hao F, Gu A, Fen P, Zhu X, Du H. HIV-1 diversity in infected individuals in Suzhou and Suqian, China. SPRINGERPLUS 2016; 5:886. [PMID: 27386334 PMCID: PMC4920801 DOI: 10.1186/s40064-016-2378-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/20/2016] [Indexed: 11/29/2022]
Abstract
Jiangsu is one province with severe HIV-1 epidemic in China. However, the molecular epidemiological characterizations of HIV-1 in many cities of Jiangsu remain unclear. A molecular epidemiological investigation was performed based on 38 HIV-positive samples collected from Suzhou and Suqian during 2011–2013. Five HIV-1 genomic fragments, p17, pol, vif-vpr, vpr-env, and C2V3 were amplified and sequenced from these samples. HIV-1 group M subtype of each sample was determined by phylogenetic analyses with the standard reference sequences. Among these infected individuals, 81.6 % (31/38) self-reported to be infected via sexual contacts, including 50.0 % (19/38) via heterosexual contact and 31.6 % (12/38) via homosexual contact. Among 34 samples with available pol or vif-env sequence, 19 (55.9 %) CRF01_AE, 7 (20.6 %) CRF07_BC, 3 (8.8 %) CRF08_BC, and 5 (14.7 %) inter-subtype recombinants were identified. No pure B, B′ and C subtypes were found in this cohort. The five recombinants contain one B/C, three CRF01/B and one CRF01/B/C recombinants. These results suggest that CRF01_AE was the most predominant HIV-1 group M subtype and CRF01_AE-involved recombinants were the major recombinant forms. Comparison showed that there was no obvious difference in HIV-1 group M subtype distribution between Jiangsu (including Suzhou and Suqian) and the surrounding provinces (e.g., Shanghai, Anhui, and Shandong). CRF01_AE and CRF07_BC were the top two predominant HIV-1 genotypes in Jiangsu, and less and/or no pure subtype B and C was currently circulating here. We predicted that more CRF01/CRF07 recombinants, but fewer B/C recombinants will be generated in Jiangsu in future.
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Affiliation(s)
- Chenhao Qin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
| | - Ping Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
| | - Weiguang Zhu
- Department of Clinical Laboratory, Suqian Center of Disease Control and Prevention, Suqian, Jiangsu China
| | - Fangyuan Hao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu China
| | - Aiping Gu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
| | - Ping Fen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
| | - Xueming Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, 215004 Jiangsu China
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26
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Li J, Li L, Li H, Li J, Yang S, Zhang M, Ouyang H. Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant Form Originated from CRF01_AE and CRF08_BC in Dali Prefecture of Yunnan Province, China. AIDS Res Hum Retroviruses 2016; 32:607-11. [PMID: 26885777 DOI: 10.1089/aid.2015.0383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Yunnan seems to be a "hot spot" region of HIV-1 recombination. CRF01_AE and subtype CRF08_BC are two main HIV-1 clades circulating in Yunnan. We report here a novel HIV-1 second-generation recombinant form originated from CRF01_AE and CRF08_BC. The strain (12YN10551) was isolated from a HIV-positive male infected through heterosexual contact in Dali prefecture of Yunnan province, China. This is the first report of HIV-1 near full-length genomic sequence in Dali. Recombinant analysis shows that 12YN10551 was composed of two well-established circulating recombinant forms (CRF01_AE and CRF08_BC). Two CRF01_AE recombinant fragments were inserted into the CRF08_BC backbone genome in the pol/vif/vpr/tat/rev and nef gene regions, respectively. The discovery and characterization of this new recombinant indicate that intersubtype recombination is continuously generating new forms of HIV-1. More work is needed to better monitor the genetic diversity of HIV-1 in this region.
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Affiliation(s)
- Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiqin Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaomin Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Mi Zhang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Hongmei Ouyang
- First People's Hospital of Yunnan Province, Kunming University of Science and Technology Affiliated Kun Hua Hospital, Kunming, China
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27
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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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28
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Li J, Li L, Yang S, Li J, Zhang M, Yang C, Liu J, Li H. The Identification of a Novel HIV-1 CRF01_AE/B Recombinant Based on Near Full-Length Genomic Analysis in Yunnan Province, China. AIDS Res Hum Retroviruses 2016; 32:467-70. [PMID: 26678279 DOI: 10.1089/aid.2015.0245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombination contributes substantially to the genetic diversity of HIV-1. Recently, many kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in China, especially in areas with multiple subtypes of HIV-1 circulating. Yunnan, which borders the "Golden triangle" region of South China, is an epicenter of HIV-1 infections in China. Multiple subtypes, including subtypes B, CRF01_AE, CRF07_BC, and CRF08_BC, were found epidemic in the area. Many URFs composed of subtypes B and C genomes were identified in Yunnan; however, CRF01_AE/B recombinant form is relatively rare. In this study, we identified a novel recombinant form of CRF01_AE/B, which was isolated from a heterosexual transmitted individual. The genomic structure of the strain is distinctly different from any previously reported URFs. Three CRF01_AE segments were inserted into the subtype B backbone genome. In the past few years, many kinds of URFs and CRFs have emerged and spread quickly in China, which implies that coinfection or super infection of more than one HIV-1 subtype might be common in China, especially in Yunnan. Therefore, more work is needed to monitor the appearance of URFs and survey the epidemiologic significance of the new recombination.
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Affiliation(s)
- Jianjian Li
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shaomin Yang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mi Zhang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Cuixian Yang
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Jiafa Liu
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
| | - Huiqin Li
- Department of HIV/AIDS Clinical Research, Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, China
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29
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Li J, Li L, Yang S, Li J, Zhang M, Yang C, Liu J, Li H. Identification and characterization of two human immunodeficiency virus type 1 unique recombinant forms from Yunnan, China. Virol Sin 2016; 31:184-7. [PMID: 26847649 PMCID: PMC8193385 DOI: 10.1007/s12250-015-3671-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Shaomin Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Mi Zhang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Cuixian Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Jiafa Liu
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China
| | - Huiqin Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming, 650301, China.
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30
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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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Zhou YH, Chen X, Liang YB, Pang W, Qin WH, Zhang C, Zheng YT. Near Full-Length Identification of a Novel HIV-1 CRF01_AE/B/C Recombinant in Northern Myanmar. AIDS Res Hum Retroviruses 2015; 31:845-50. [PMID: 25970165 DOI: 10.1089/aid.2015.0021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Myanmar-China border appears to be the "hot spot" region for the occurrence of HIV-1 recombination. The majority of the previous analyses of HIV-1 recombination were based on partial genomic sequences, which obviously cannot reflect the reality of the genetic diversity of HIV-1 in this area well. Here, we present a near full-length characterization of a novel HIV-1 CRF01_AE/B/C recombinant isolated from a long-distance truck driver in Northern Myanmar. It is the first description of a near full-length genomic sequence in Myanmar since 2003, and might be one of the most complicated HIV-1 chimeras ever detected in Myanmar, containing four CRF01_AE, six B segments, and five C segments separated by 14 breakpoints throughout its genome. The discovery and characterization of this new CRF01_AE/B/C recombinant indicate that intersubtype recombination is ongoing in Myanmar, continuously generating new forms of HIV-1. More work based on near full-length sequence analyses is urgently needed to better understand the genetic diversity of HIV-1 in these regions.
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Affiliation(s)
- Yan-Heng Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yue-Bo Liang
- Yunnan International Travel Healthcare Center, Kunming, Yunnan, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei-Hong Qin
- Yunnan International Travel Healthcare Center, Kunming, Yunnan, China
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Yang C, Yang S, Li J, Yang B, Liu J, Li H, Bian Z. Genetic Diversity and Drug Resistance Among Antiretroviral Treatment-Failed Individuals from 2010 to 2012 in Honghe, China. AIDS Res Hum Retroviruses 2015; 31:822-9. [PMID: 25919896 DOI: 10.1089/aid.2014.0348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The most common antiretroviral treatment (ART) received by individuals infected with HIV-1 in China is the combination therapy, comprised of nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs). To assess the prevalence of HIV-1 drug resistance and subtypes in Honghe of Yunnan, China, patient plasmas from ART-failed individuals were collected from January 2010 to December 2012. Genotyping was conducted using an in-house assay on patient plasmas. A total of 254 pol sequences were obtained. The prevalence of drug resistance was 47.2% in ART-failed individuals. Of these drug-resistant individuals, 51.7% harbored HIV strains dually resistant to NRTIs and NNRTIs or protease inhibitors (PIs) (34.2% for NNRTIs and 14.2% for NRTIs). Mutations such as M184V, A62V, T69Ins, K103N, Y181C, and G190A were common among the ART-failed individuals. The frequencies of M184V, A62V, and K103N were 20.5%, 11.0%, and 23.6%, respectively. The most common subtypes in Honghe were CRF08_BC (68.50%) and CRF07_BC (12.20%). The subtypes were almost consistent in different time points for one individual. When receiving ART for 6-12 months, the frequency of HIV-1 drug-resistant variants ranked first. This study shows that the high prevalence of HIV drug resistance observed among the ART-failed individuals should be of increasing concern (monitoring of resistance mutations) in ART regions and facilitate developing novel strategies for prevention and control of HIV infection in China.
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Affiliation(s)
- Cuixian Yang
- The Third Military Medical School, Chongqing, China
- Center for Infectious Diseases, CPLA Kunming General Hospital, Kunming, China
| | - Shaomin Yang
- Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Bihui Yang
- Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Jiafa Liu
- Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Huiqin Li
- Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Zhongqi Bian
- The Third Military Medical School, Chongqing, China
- Center for Infectious Diseases, CPLA Kunming General Hospital, Kunming, China
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The sexually driven epidemic in youths in China's southwestern border region was caused by dynamic emerging multiple recombinant HIV-1 strains. Sci Rep 2015; 5:11323. [PMID: 26133091 PMCID: PMC4489098 DOI: 10.1038/srep11323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/01/2015] [Indexed: 11/25/2022] Open
Abstract
Dehong prefecture, Yunnan province on China’s southwestern border was the gateway of the country’s AIDS epidemic. Studies on HIV-1 molecular epidemiology will provide key information on virus transmission dynamics and help to inform HIV prevention strategies. HIV-1 infected youths (age 16–25 years) diagnosed in the continuous 3 months in 2009 to 2012 were enrolled. By means of phylogenetic and statistical analyses, It was showed that two thirds (133/205) of youths in Dehong, of which 74.1% were infected sexually, were infected by uncharacterized recombinant HIV-1 strains. Among them about 59.4% (79/131) were unique recombinant forms (URFs) and 40.6% (54/131) formed 11 transmission clusters, termed potential circulating recombinant forms (pCRFs). The emergence of recombinants was statistically significant related with people of low education, residents outside the capital city of Dehong and being Myanmar residents. It was the first report with ongoing HIV-1 recombinant strains in a sexually driven epidemic area in China. Great efforts should be put on reducing multiple risk exposures behavior in local young people, containing the spread of pCRFs to other regions, and preventing the URFs from evolving into future CRFs. Collaborative prevention across border is needed to better control the local AIDS epidemic.
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Wang Y, Liang Y, Feng Y, Wang B, Li Y, Wu Z, Zhang J, Baloch Z, Zhang AM, Liu L, Qin W, Xia X. HIV-1 prevalence and subtype/recombinant distribution among travelers entering China from Vietnam at the HeKou port in the Yunnan province, China, between 2003 and 2012. J Med Virol 2015; 87:1500-9. [PMID: 25865741 DOI: 10.1002/jmv.24202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 11/09/2022]
Abstract
The aim of this study was to assess HIV-1 prevalence and the distribution of HIV-1 subtypes among travelers crossing the border at the HeKou land port. Between 2003 and 2012, 22,799 persons were randomly recruited from people entering China from Vietnam. In this crossing border population, a total of 161 (0.71%) travelers were determined as HIV-1-positive. From them, 140 HIV-1-positive serum samples were collected for RNA extraction and subsequent RT-nested PCR amplification of the group-specific antigen (gag)-RT with a length of 2.6 kb. The DNA sequences were analyzed to determine the HIV-1 subtypes/recombinants. We found that the circulating recombinant form 01_AE (CRF01_AE) was the most common HIV-1 subtype, accounting for 49.4% (41/83) of the subtyped 83 samples, followed by CRF08_BC (26.5%, 22/83) and CRF07_BC (7.2%, 6/83). Only 1 sample was classified as subtype C. Thirteen cases could not be clustered into any known subtypes or CRFs and presented as unique recombinant forms (URFs). Of them, 6 recombination patterns were identified. They had distinct structures consisting of fragments of subtypes B, C, CRF01_AE, CRF07_BC and CRF08_BC. Between 2003 and 2012, CRF01_AE and CRE08_BC were shown to be the most prevalent recombinant forms identified each year. But yearly change of each subtype is uncertain regular among in these travelers during the past decade. Understanding the distribution of HIV-1 subtypes/recombinants and how it changes across time among individuals entering China from Vietnam through this land port is crucial to establish strategies for the prevention of HIV cross-border transmission.
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Affiliation(s)
- Yajuan Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - Yaobo Liang
- Care Center for International Travel Health in Yunnan, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - Yaping Li
- Care Center for International Travel Health in Yunnan, Yunnan, China
| | - Zhikun Wu
- HeKou Entry-Exit Inspection and Quarantine Bureau, Yunnan, China
| | - Jianchun Zhang
- HeKou Entry-Exit Inspection and Quarantine Bureau, Yunnan, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - Li Liu
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
| | - Weihong Qin
- Care Center for International Travel Health in Yunnan, Yunnan, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Center for Molecular Medicine in Yunnan province, Kunming University of Science and Technology, Yunnan, China
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Chabria SB, Gupta S, Kozal MJ. Deep Sequencing of HIV: Clinical and Research Applications. Annu Rev Genomics Hum Genet 2014; 15:295-325. [DOI: 10.1146/annurev-genom-091212-153406] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shiven B. Chabria
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
| | - Shaili Gupta
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
| | - Michael J. Kozal
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
- Section of Infectious Diseases, Department of Internal Medicine, VA Connecticut Healthcare System, West Haven, Connecticut 06516
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Diverse forms of HIV-1 among Burmese long-distance truck drivers imply their contribution to HIV-1 cross-border transmission. BMC Infect Dis 2014; 14:463. [PMID: 25158600 PMCID: PMC4152572 DOI: 10.1186/1471-2334-14-463] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The China-Myanmar border is a particularly interesting region that has very high prevalence of and considerable diversity of HIV-1 recombinants. Due to the transient nature of their work, long-distance truck drivers (LDTDs) have a comparatively high potential to become infected with HIV-1 and further spread virus to other individuals in the area they travel within. In this study, we hypothesized that Burmese LDTDs crossing the China-Myanmar border frequently may potentially be involved in the cross-border transmission of HIV, and contribute to the extremely high prevalence of HIV-1 inter-subtype recombinants in this border region. METHODS A molecular epidemiology study was conducted among 105 Burmese LDTDs between 2008 and 2010. HIV-1 genetic fragments including p17, pol, vif-vpr, vpr-env, and C2V3 were amplified and sequenced. The subtype characterization and HIV-1 transmission were determined by both phylogenetic and phylogeographic analyses. RESULTS Diverse forms of HIV-1, including subtypes CRF01_AE (41.9%), C (8.6%), B (4.8%), CRF02_AG (1.0%), and inter-subtype recombinants (33.3%), as well as dual infection (10.5%), were detected among the tested LDTDs. Phylogeographic analyses based on pure subtype revealed that 77.8% Burmese LDTDs acquired HIV-1 infection in Yunnan, and the others in Myanmar. Both the C-related and CRF01_AE-related recombinants from these LDTDs appeared to have close genetic relationship with those from IDUs in Myanmar and Dehong. CONCLUSIONS Burmese LDTDs may contribute to HIV-1 transmission along the China-Myanmar border. The results may provide some new perspective for understanding the on-going generation and prevalence of HIV-1 recombinants in the border region.
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Wang B, Feng Y, Li Z, Duan H, Zhao T, Zhang A, Liu L, Baloch Z, Xia X. Distribution and diversity of hepatitis B virus genotypes in Yunnan, China. J Med Virol 2014; 86:1675-82. [PMID: 24992445 PMCID: PMC4255792 DOI: 10.1002/jmv.24002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2014] [Indexed: 12/17/2022]
Abstract
Hepatitis B virus (HBV) is one of the most prevalent pathogens in the world, and infection with this virus is a serious threat for public health. Yunnan is considered as an important endemic center for blood-borne viruses such as human immunodeficiency virus and hepatitis C virus, in China. However, the distribution and diversity of HBV subgenotypes remain unclear in Yunnan province. In the current study, HBV positive samples were collected from different prefectures of Yunnan province and their molecular epidemiological characters were determined. Phylogenetic analysis on the pre-S/S gene (865 bps) showed the prevalence of four HBV genotypes, including genotype B (24 cases, 33.3%), genotype C (45 cases, 62.5%), genotype I (two cases, 2.78%) and C/D recombinants (one case, 1.39%). The most prevalent genotypes B and C could be sub classified into subgenotype B2 and C1, C2, C5, and C7, respectively. Clusters of subgenotype B2 and C2 consisted of strains from China and other East Asian countries, while subgenotype C1, C5, and C7 and genotype I formed a cluster together with strains from Southeast Asia. Using Bayesian inference from phylogenetic, HBV genotypes B and C were estimated to have originated in 1860s and 1910s with an evolutionary rate of 3.26 and 8.01 × 10(-4) substitutions/site/year, respectively. These findings indicate that the distribution of HBV genotypes in Yunnan was influenced by strains from the rest of China and the neighboring countries.
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Affiliation(s)
- Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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Feng Y, Wei H, Hsi J, Xing H, He X, Liao L, Ma Y, Ning C, Wang N, Takebe Y, Shao Y. Identification of a novel HIV Type 1 circulating recombinant form (CRF65_cpx) composed of CRF01_AE and subtypes B and C in Western Yunnan, China. AIDS Res Hum Retroviruses 2014; 30:598-602. [PMID: 24279591 DOI: 10.1089/aid.2013.0233] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A novel HIV-1 circulating recombinant form (CRF) designated CRF65_cpx was recently characterized from three epidemiologically unlinked individuals infected through heterosexual contact in western Yunnan province of China. This is the first complex mosaic HIV-1 CRF, consisting of contributions from three or more different subtypes, identified in China. An additional full-length genome sequence with identical recombinant breakpoints was found among a previously reported recombinant strain from a man who had sex with a man in Anhui province of East Central China. The breakpoint analysis of the recombinants showed a complex genome organization composed of parental subtypes B' (Thailand variant of subtype B), C, and CRF01_AE, with 13 recombination breakpoints observed in almost all structure genes of HIV-1. The generation of complex recombinant forms is likely due to cocirculation of multiple lineages of HIV-1 strains in high-risk populations in western Yunnan.
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Affiliation(s)
- 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
| | - Huamian Wei
- 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
| | - Jenny Hsi
- 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
| | - Xiang He
- 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
- Guangdong Provincial Institute of Public Health, Guangdong, China
| | - Lingjie Liao
- 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
| | - Yanling Ma
- Yunnan Center for Disease Control and Prevention, Yunnan, China
| | - Chuanyi Ning
- 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
| | - Nidan Wang
- 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
| | - Yutaka Takebe
- 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
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - 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
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Dey SK, Zahan N, Afrose S, Islam T, Shajahan M, Saha S, Mahmud SA, Talukder AA, Mizuguchi M, Ushijima H. Molecular epidemiology of HIV in Asia. HIV & AIDS REVIEW 2014. [DOI: 10.1016/j.hivar.2014.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Abstract
One of the major characteristics of HIV-1 is its high genetic variability and extensive heterogeneity. This characteristic is due to its molecular traits, which in turn allows it to vary, recombine, and diversify at a high frequency. As such, it generates complex molecular forms, termed recombinants, which evade the human immune system and so survive. There is no sequence constraint to the recombination pattern as it appears to occur at inter-group (between groups M and O), as well as interand intra-subtype within group M. Rapid emergence and active global transmission of HIV-1 recombinants, known as circulating recombinant forms (CRFs) and unique recombinant forms (URFs), requires urgent attention. To date, 55 CRFs have been reported around the world. The first CRF01_AE originated from Central Africa but spread widely in Asia. The most recent CRF; CRF55_01B is a recombinant form of CRF01_AE and subtype B, although its origin is yet to be publicly disclosed. HIV-1 recombination is an ongoing event and plays an indispensable role in HIV epidemics in different regions. Africa, Asia and South America are identified as recombination hot-spots. They are affected by continual emergence and cocirculation of newly emerging CRFs and URFs, which are now responsible for almost 20% of HIV-1 infections worldwide. Better understanding of recombinants is necessary to determine their biological and molecular attributes.
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Affiliation(s)
- Katherine A Lau
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute , Westmead Hospital, The University of Sydney
| | - Justin J L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute , Royal Prince Alfred Hospital, The University of Sydney, Sydney, Australia
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Han X, An M, Zhao B, Duan S, Yang S, Xu J, Zhang M, McGoogan JM, Takebe Y, Shang H. High prevalence of HIV-1 intersubtype B'/C recombinants among injecting drug users in Dehong, China. PLoS One 2013; 8:e65337. [PMID: 23741489 PMCID: PMC3669332 DOI: 10.1371/journal.pone.0065337] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Objective To examine the distribution of HIV-1 genotypes among injecting drug users (IDUs) from Dehong, Yunnan province. Materials and Methods Blood samples from a total of 95 HIV-positive IDUs were retrospectively analyzed. Samples were collected between 2005 and 2009 from four cities in Dehong prefecture, western Yunnan province, the geographical origin of the HIV epidemic in China. HIV-1 gag, partial pol, vpr-env fragment, half-genome, or near-full-length sequences were analyzed to determine the HIV-1 genotypes of each subject. Results were compared with findings from past studies of IDUs in Dehong and in neighboring Myanmar. Results We observed a high prevalence of B′/C recombinants (82.4%) among IDUs in Dehong, the structural profiles of which do not match those previously reported in Dehong or in Myanmar. Furthermore, statistically significant differences in geographical and temporal distributions of HIV-1 genotypes were characterized by a predominance of HIV-1 B′/C recombinant forms among older subjects(p = 0.034), subjects from Longchuan district (p = 0.022), and subjects diagnosed between 2000 and 2004 (p = 0.004). Conclusions The increasing prevalence of multiple, new B′/C recombinant forms suggest that HIV-1 intersubtype recombination is substantial and ongoing in western Yunnan. This reflects the high-risk behavior of IDUs in this region and argues the need for stronger monitoring and prevention measures in Dehong and other high-prevalence areas around China.
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Affiliation(s)
- Xiaoxu Han
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Minghui An
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Bin Zhao
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Song Duan
- Dehong Prefecture Center for Disease Control and Prevention, Mangshi, Yunnan Province, China
| | - Shaomin Yang
- AIDS Care Center, Yunnan Provincial Hospital Infectious Disease, Kunming, Yunnan, China
| | - Junjie Xu
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Min Zhang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jennifer M. McGoogan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yutaka Takebe
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hong Shang
- Key Laboratory of AIDS Immunology of Ministry of Health, Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
- * E-mail:
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Chen M, Yang L, Ma Y, Su Y, Yang C, Luo H, Chen H, Chen L, Yan W, Shi Y, Jia M, Lu L. Emerging variability in HIV-1 genetics among recently infected individuals in Yunnan, China. PLoS One 2013; 8:e60101. [PMID: 23555898 PMCID: PMC3608604 DOI: 10.1371/journal.pone.0060101] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
Background Yunnan has the longest endured Human Immunodeficiency Virus-1 (HIV-1) epidemic in China, and the genetic diversity of HIV-1 constitutes an essential characteristic of molecular epidemiology in this region. To obtain a more comprehensive picture of the dynamic changes in Yunnan’s HIV-1 epidemic, a cross-sectional molecular epidemiological investigation was carried out among recently infected individuals. Methodology/Principal Findings We sequenced partial gag (HXB2∶781–1861) and env (HXB2∶7002–7541) genes from 308 plasma samples of recently infected patients. With phylogenetic analysis, 130 specimens generated interpretable genotyping data. We found that the circulating genotypes included: CRF08_BC (40.8%), unique recombinant forms (URFs, 27.7%), CRF01_AE (18.5%), CRF07_BC (9.2%), subtype B (2.3%) and C (1.5%). CRF08_BC was the most common genotype, and was predominant in both intravenous drug users (IDUs) and heterosexually transmitted populations. CRF08_BC and CRF07_BC still predominated in eastern Yunnan, but CRF08_BC showed increasing prevalence in western Yunnan. Strikingly, the URFs raised dramatically in most regions of Yunnan. Seven different types of URFs were detected from 12 prefectures, suggesting that complicated and frequent recombination is a salient feature of Yunnan’s HIV-1 epidemic. Among URFs, two BC clusters with distinctive recombination patterns might be potential new CRF_BCs. CRF01_AE was no longer confined to the prefectures bordering Myanmar, and had spread to the eastern part of Yunnan, especially the capital city of Kunming, with a large number of infections in the transient population. The ratios of the main genotypes showed no statistical differences between infected IDUs and heterosexually transmitted infections. Conclusions/Significance The changing patterns of the dominant HIV-1 genotypes in Yunnan indicate the complex evolving dynamic nature of the epidemic. Understanding new trends in molecular epidemiology of HIV-1 infection is critical for adjusting current prevention strategies and vaccine development in Yunnan.
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Affiliation(s)
- Min Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Li Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yanling Ma
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yingzhen Su
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Chaojun Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Hongbing Luo
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Ling Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Wenyun Yan
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yuhua Shi
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Manhong Jia
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MJ); (LL)
| | - Lin Lu
- Center 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
- * E-mail: (MJ); (LL)
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Abstract
The aim of this study was to characterize updated HIV subtypes in Yunnan to determine their origins and distribution within the population. RT-PCR of both the gag and env genes were sequenced from Yunnan province inhabitants newly diagnosed with HIV-1. Sequence data from 290 samples were used for statistical analysis of subtype distribution and phylogenetic tree construction. Distribution data were adjusted to account for different geographical distributions of HIV-1 subtypes in the population. Phylogenetic analysis revealed six HIV-1 subtypes in Yunnan, including eight types of unique recombination forms (URFs). The most prevalent subtypes in this province, CRF07_BC (18·9%), CRF08_BC (39·1%), CRF01_AE (22·4%), and URFs (subtype C, 5·9% and subtype B, 4·5%), were all recombinants. We found significant differences in the distribution of these HIV-1 subtypes not only geographically, but also between various ethnic groups and with respect to transmission routes. Our findings indicate a complex population of HIV-1 subtypes, URFs, and recombinant subtypes in Yunnan province. This diversity could make the prevention and control of HIV infection in Yunnan more difficult due to the possibility of virus recombination or infection by multiple subtypes.
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Wu J, Meng Z, Xu J, Lei Y, Jin L, Zhong P, Han R, Su B. New emerging recombinant HIV-1 strains and close transmission linkage of HIV-1 strains in the Chinese MSM population indicate a new epidemic risk. PLoS One 2013; 8:e54322. [PMID: 23372706 PMCID: PMC3553145 DOI: 10.1371/journal.pone.0054322] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/10/2012] [Indexed: 11/18/2022] Open
Abstract
In recent years, the population of men who have sex with men (MSM) have become the most significant increasing group of HIV-1 transmission in China. To identify new recombinant strains and transmission patterns of HIV-1 in Chinese MSM population, a cross-sectional investigation of MSM in Anhui Province (in south-eastern China) was performed in 2011. The diagnosed AIDS case rate, CD4 T-cell counts, HIV subtypes, and origin of the recombinant strains were investigated in 138 collected samples. The phylogenetic and bootscan analyses demonstrated that, apart from three previously reported circulating strains (CRF07_BC, CRF01_AE, subtype B), various recombinant strains among subtype B, subtype C, CRF01_AE, and CRF07_BC were simultaneously identified in Chinese MSM for the first time. The introducing time of B subtype in Chinese MSM populations was estimated in 1985, CRF01_AE in 2000, and CRF07_BC in 2003; the latter two account for more than 85% of MSM infections. Notably, in comparison with B subtype infections in Anhui MSM, CRF01_AE, with the highest prevalence rate, may accelerate AIDS progression. Over half of patients (56%) infected with new recombinant strains infection are diagnosed as progression into AIDS. Both Bayes and phylogenetic analyses indicated that there was active HIV transmission among MSM nationwide, which may facilitate the transmission of the new 01B recombinant strains in MSM. In conclusion, new recombinant strains and active transmission were identified in the Chinese MSM population, which may lead to a new alarming HIV pandemic in this population due to the increased pathogenesis of the newly emerging strains.
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Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Zhefeng Meng
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanhua Lei
- Hefei Center for Disease Control and Prevention, Hefei, China
| | - Lin Jin
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Ping Zhong
- Department of AIDS/STD, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai, China
| | - Renzhi Han
- Department of Cell and Molecular Physiology, Loyola University Chicago Health Science Division, Maywood, Illinois, United States of America
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
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Discordant genotypic resistance and HIV-1 genetic diversity from paired plasma and cerebrospinal fluid samples in Chinese settings. J Neurovirol 2013; 19:131-6. [DOI: 10.1007/s13365-013-0148-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 11/30/2012] [Accepted: 01/07/2013] [Indexed: 10/27/2022]
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Chen M, Ma Y, Duan S, Xing H, Yao S, Su Y, Luo H, Yang L, Chen H, Fu L, Qu A, Ou CY, Jia M, Lu L. Genetic diversity and drug resistance among newly diagnosed and antiretroviral treatment-naive HIV-infected individuals in western Yunnan: a hot area of viral recombination in China. BMC Infect Dis 2012; 12:382. [PMID: 23270497 PMCID: PMC3552723 DOI: 10.1186/1471-2334-12-382] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background The emergence of an HIV-1 epidemic in China was first recognized in Dehong, western Yunnan. Due to its geographic location, Dehong contributed greatly in bridging HIV-1 epidemics in Southeast Asia and China through drug trafficking and injection drug use; and also extensively to the HIV genetic diversity in Yunnan and China. We attempt to monitor HIV-1 in this area by studying the HIV-1 genetic distribution and transmitted drug resistance (TDR) in various at-risk populations. Methods Blood samples from a total of 320 newly HIV-1 diagnosed individuals, who were antiretroviral therapy (ART)-naive, were collected from January 2009 to December 2010 in 2 counties in Dehong. HIV-1 subtypes and pol gene drug resistance (DR) mutations were genotyped. Results Among 299 pol sequences successfully genotyped (93.4%), subtype C accounted for 43.1% (n=129), unique recombinant forms (URFs) for 18.4% (n=55), CRF01_AE for 17.7% (n=54), B for 10.7% (n=32), CRF08_BC for 8.4% (n=25) and CRF07_BC for 1.7% (n=5). Subtype distribution in patients infected by different transmission routes varied. In contract to the previous finding of CRF01_AE predominance in 2002-2006, subtype C predominated in both injecting drug users (IDUs) and heterosexually transmitted populations in this study. Furthermore, we found a high level of BC, CRF01_AE/C and CRF01_AE/B/C recombinants suggesting the presence of active viral recombination in the area. TDR associated mutations were identified in 4.3% (n=13) individuals. A total of 1.3% of DR were related to protease inhibitors (PIs), including I85IV, M46I and L90M; 0.3% to nucleoside reverse transcriptase inhibitors (NRTIs), including M184I; and 2.7% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), including K103N/S, Y181C, K101E and G190A. Conclusion Our work revealed diverse HIV-1 subtype distributions and intersubtype recombinations. We also identified a low but significant TDR mutation rate among ART-naive patients. These findings enhance our understanding of HIV-1 evolution and are valuable for the development and implementation of a comprehensive public health approach to HIV-1 DR prevention and treatment in the region.
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Affiliation(s)
- Min Chen
- Yunnan Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
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Rutvisuttinunt W, Sirivichayakul S, Oota S, Assawadarachai V, Poltavee K, Savadsuk H, Pattanachaiwit S, Chaemchuen S, Arroyo MA, Paris RM, Michael NL, Kim JH, Ruxrungtham K, de Souza M, Phanuphak P, Tovanabutra S. Two unique recombinant forms identified in incident HIV type 1 infections in Thai blood donors. AIDS Res Hum Retroviruses 2012; 28:1703-11. [PMID: 22587412 DOI: 10.1089/aid.2011.0339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 genetic diversity of recently seroconverting (<12 months) Thai repeated blood donors attending the National Blood Centre, Thai Red Cross Society (NBC, TRCS) from September 2007 until March 2008 was assessed. Ten HIV-1 recent seroconvertors (10/239,134 donations) were identified during the study period. The estimated median time to seroconversion was 67.3 days (range: 45.5-102.0 days), and viral load ranged from 307 to 341,805 copies HIV-1 RNA/ml. MHAbce, a real-time-based PCR genotyping assay, identified six CRF01_AE, two CRF01_AE/B recombinants, one subtype B, and one CRF01_AE/B dual infection. Nine samples were further characterized by full genome sequencing, identifying CRF01_AE (N=6), unique CRF01_AE/B recombinants (N=2), and subtype B (N=1). One recombinant contained 13 breakpoints located in gag, pol, vif, vpr, env, and nef while the other recombinant contained 10 breakpoints located in pol, vif, env, and nef. This study found two unique CRF01B recombinants circulating in 10 recent HIV-1-positive subjects from a blood donor population in Thailand.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sineenart Oota
- National Blood Centre, Thai Red Cross Society, Bangkok, Thailand
| | | | - Kultida Poltavee
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Hathairat Savadsuk
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Suwittra Chaemchuen
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Miguel A. Arroyo
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Robert M. Paris
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Kiat Ruxrungtham
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Mark de Souza
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Praphan Phanuphak
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
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Li L, Chen L, Yang S, Li T, Li J, Liu Y, Jia L, Yang B, Bao Z, Li H, Wang X, Zhuang D, Liu S, Li J. Recombination form and epidemiology of HIV-1 unique recombinant strains identified in Yunnan, China. PLoS One 2012; 7:e46777. [PMID: 23056447 PMCID: PMC3467292 DOI: 10.1371/journal.pone.0046777] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for phylogenetic analysis. Recombinant breakpoints and genomic schematics were identified with online software jpHMM. 63 (10.2%) unique recombinant strains were identified from 617 strains with subtypes. The URFs distributed significantly differently among prefectures (Pearson chi-square test, P<0.05). IDUs contained more URFs than sexual transmitted population (Pearson chi-square test, P<0.05). Two main recombinant forms were identified by considering the presence of CRF01_AE segments in full length gag-pol genes, which were B′/C and B′/C/CRF01-AE recombinants. Three clusters were identified in the ML tree which contained more than three sequences and supported by high bootstrap values. One CRF was identified. Many of URFs contained identical breakpoints. The results will contribute to our understanding on HIV recombination and provide clues to the identification of potential CRFs in China.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lili Chen
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Urumqi General Hospital of Lanzhou Military Area Command, Urumqi, Xinjiang, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianjian Li
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yongjian Liu
- 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
| | - Bihui Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Zuoyi Bao
- 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
| | - Daomin Zhuang
- 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
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * E-mail:
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Liu Y, Li L, Bao Z, Li H, Zhuang D, Liu S, Wang X, Li T, Jia L, Yang S, Li J. Identification of a novel HIV type 1 circulating recombinant form (CRF52_01B) in Southeast Asia. AIDS Res Hum Retroviruses 2012; 28:1357-61. [PMID: 22269007 DOI: 10.1089/aid.2011.0376] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thirty HIV-1 URF_01AE/ B' complete or nearly full-length genome sequences sampled within Southeast Asia were obtained from the Los Alamos HIV Sequence Database. Phylogenetic and recombinant analyses revealed that three sequences indeed displayed the identical recombinant structure. Of note, the three subjects, harboring novel CRF01_AE/B recombinants, did not have apparent epidemiological linkage. They fulfilled the criteria for the designation of a new circulating recombinant form (CRF) and constituted the 52nd CRF identified in the worldwide HIV-1 pandemic. In this chimera, two short subtype B segments were inserted into a backbone of CRF_01AE. The breakpoints corresponded to HXB2 nucleotide positions 2930, 3251, 8521, and 9004 approximately. This CRF is the first one identified by neatening and analyzing the sequences already presented in the Los Alamos HIV Sequence Database. This indicates that we should pay attention not only to explicit subtype sequences but also to those classified as a unique recombinant form (URF) so far.
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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, China
| | - Lin 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
| | - Hanping Li
- 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
| | - Siyang Liu
- 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
| | - Tianyi 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
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Liu J, Jia Y, Xu Q, Zheng YT, Zhang C. Phylodynamics of HIV-1 unique recombinant forms in China-Myanmar border: implication for HIV-1 transmission to Myanmar from Dehong, China. INFECTION GENETICS AND EVOLUTION 2012; 12:1944-8. [PMID: 22917657 DOI: 10.1016/j.meegid.2012.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 07/18/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
China-Myanmar border plays a crucial role in HIV-1 transmission in Asia. Here, we performed Bayesian phylodynamics analyses on p17 gene using BEAST to investigate HIV-1 transmission in this region. Maximum clade credibility trees of subtype C and CRF01_AE show that majority of unique recombinant forms (URFs) and pure subtype strains from Dehong and Myanmar cluster together, forming large clades with ancestral geographical states of Dehong. Bayes factor tests support the statistically significant geographic diffusion link between Dehong and Myanmar. The estimated time to the most recent common ancestor of Myanmar URFs_BC (1999.2) was later than that of Dehong URFs_BC (1998.0), but earlier than that of Myanmar URFs_01BC (2004.3). Since 1998, HIV-1 recombination between subtypes B, C and CRF01_AE has been continuously occurring in China-Myanmar border region. These results suggest that HIV-1 subtypes B, C and CRF01_AE were most likely transmitted from Dehong to Myanmar, and predict that URFs_01BC should be also prevalent in Dehong, Yunnan.
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Affiliation(s)
- Jun Liu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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