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Lan C, Zhu B, Zhuo H, Shi Y, Sun Z, Zhang L, Jia L, Li H, Liu Y, Wang X, Li J, Zhang B, Han J, Jiang J, Li L. Near Full-Length Genome Characterization of Two Novel Unique Recombinants (CRF01_AE/CRF07_BC) in Beijing, China. AIDS Res Hum Retroviruses 2024. [PMID: 38517080 DOI: 10.1089/aid.2023.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
With the prevalence of human immunodeficiency virus type 1 (HIV-1) CRF01_AE and CRF07_BC subtypes in China, the co-circulation of multiple subtypes in the HIV-1-positive population may result in dual infection or superinfection in the population, leading to the emergence of unique recombinant forms (URFs) of the HIV-1 virus. In this study, two second-generation unique recombinant strains, BI0114 and BI0116, were identified, and their near full-length genome sequences were obtained. Recombination analysis showed that both sequences were isoforms of URF_0107, and they were second-generation unique recombinant strains formed by the recombination of CRF01_AE and CRF07_BC, with the isoforms being CRF01_AE and CRF0107_BC, respectively. The continued emergence of novel CRF01_AE/CRF07_BC recombinant strains suggests that the epidemiological, preventive, and control situation of HIV-1 is complex and that the relevant health authorities urgently need to establish responses to the challenges posed by changes in the pattern of strain recombination.
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Affiliation(s)
- Chunlin Lan
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Zhu
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hailong Zhuo
- Department of Transfusion Medicine, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Yuting Shi
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zixuan Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lixuan Zhang
- 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
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - 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
| | - Bohan Zhang
- 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
| | - Junjun Jiang
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, 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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2
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Feng Y, Lu J, Wang L, Wang Y, Li J, Li H, Li L, Dai E. Near-full-length genome analysis of two novel HIV second recombinant forms in Hebei, China. Arch Virol 2024; 169:76. [PMID: 38494576 DOI: 10.1007/s00705-024-06007-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
The number of individuals infected with HIV-1 among men who have sex with men (MSM) has risen rapidly in recent years in China, and the subtypes CRF01_AE, CRF07_BC, and B, as well as many novel unique recombinant forms (URFs) are prevalent among them. Co-circulation of strains among MSM populations allows the generation of circulating recombinant forms (CRFs) and URFs. In this study, we identified two new URFs from two HIV-1-positive subjects who were infected through homosexual contact in Hebei, China. Analysis of near-full-length genome sequences, using phylogenetic and recombination analysis showed that the two URFs originated from CRF01_AE, CRF07_BC, and B, and CRF01_AE segments in the backbone of the URFs were derived from cluster 4 of CRF01_AE. The CRF07_BC segments of two URFs were clustered with 07BC_N in a phylogenetic tree. The identification of novel URFs with complex genomic structures shows that it is necessary to strengthen surveillance of HIV-1 variants in MSM populations in this region.
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Affiliation(s)
- Yuxin Feng
- School of Public Health, Department of Public Health Laboratory Medicine, North China University of Science and Technology, No. 21 Bohai Road, Caofeidian District, 063210, Tangshan, Hebei, China
- Hebei Key Laboratory of Immune Mechanism of Major Infectious Diseases and New Technology of Diagnosis and Treatment, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jianhua Lu
- Hebei Key Laboratory of Immune Mechanism of Major Infectious Diseases and New Technology of Diagnosis and Treatment, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Lijing Wang
- Hebei Key Laboratory of Immune Mechanism of Major Infectious Diseases and New Technology of Diagnosis and Treatment, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Yuling Wang
- Hebei Key Laboratory of Immune Mechanism of Major Infectious Diseases and New Technology of Diagnosis and Treatment, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Erhei Dai
- School of Public Health, Department of Public Health Laboratory Medicine, North China University of Science and Technology, No. 21 Bohai Road, Caofeidian District, 063210, Tangshan, Hebei, China.
- Hebei Key Laboratory of Immune Mechanism of Major Infectious Diseases and New Technology of Diagnosis and Treatment, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China.
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, North China University of Science and Technology, No.42 Ta'nan Road, Yuhua District, 050021, Shijiazhuang, Heibei, China.
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Dong S, Lu X, Wang Y, An N, Liu M, Li Y, Li Q. Near-Full-Length Genome Analysis of a HIV-1 CRF01_AE/B Recombinant Strain Among Men Who Have Sex with Men in Chengde City, China. AIDS Res Hum Retroviruses 2023. [PMID: 37981835 DOI: 10.1089/aid.2023.0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
The unique recombinant form (URF) of HIV is formed by multiple subtypes which are cocirculating in some area, and the number of HIV recombinants is on the increase worldwide. In this study, we identified a URF named 2019638, composed of CRF01_AE and subtype B, in a man who has sex with men in Qinhuangdao, Hebei province, China. The near-full-length genome (NFLG) sequence was confirmed to be a novel URF. Within this NFLG, two CRF01_AE fragments were inserted into the pol and vif regions, respectively, using subtype B as the backbone. Moreover, the presence of the V106M and V179D point mutations in the reverse transcriptase (RT) region rendered the high-level resistance to efavirenz and nevirapine and intermediate resistance to doravirine. Our findings suggest that the HIV epidemic is evolving toward a high degree of recombination, and we need to continuously monitor HIV genetic diversity to control the further development of the AIDS epidemic.
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Affiliation(s)
- Shuofan Dong
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
- School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xinli Lu
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
| | - Yingying Wang
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
| | - Ning An
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
| | - Meng Liu
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
| | - Yan Li
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
| | - Qi Li
- Hebei Key Laboratory of Pathogen and Epidemiology of Infectious Disease, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
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Li Z, Kang Q, Liu Y, Jia L, Li T, Wang X, Li J, Zhang B, Han J, Li H, Li L. Identification of Two Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/CRF07_BC) in Men Who Have Sex with Men in Hebei, China. AIDS Res Hum Retroviruses 2023; 39:681-687. [PMID: 36943286 DOI: 10.1089/aid.2022.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
In recent years, men who have sex with men (MSM) have been identified as the primary source of HIV-1 transmission in Hebei Province, China. Co-circulation of multiple subtypes in HIV-1 positive MSM populations may contribute to the emergence of the second generation of recombinant HIV-1 strains, indicating the occurrence of dual infections or superinfections in MSM populations. Thus, the discovery of new recombinant strains is important to indicate the appearance of multiple infected individuals and the prevalence caused by changes in the parent strains. In this study, we present two new unique recombinant forms (URFs) from two HIV-1-positive subjects (HB070052 and HB070056) infected through homosexual contact in Hebei Province, China. The near full-length genome of the two URFs revealed that HB070052 was divided into seven segments by six breakpoints in the gag, pol, vif, and vpr genes; HB070056 was separated into five fragments by four breakpoints, with two regions of CRF07_BC inserted into a CRF01_AE backbone's gag, pol regions. The subregion tree showed CRF01_AE segments were traced back to the cluster 4 and 6 of the CRF01_AE phylogenetic tree, which were prevalent among HIV-1 infections through MSM in China. The continued emergence of the novel CRF01_AE/CRF07_BC recombinant forms indicates the HIV-1 epidemic is complex and long-term surveillance of recombinant strains is necessary among MSM in this region.
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Affiliation(s)
- Zhengyang Li
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qian Kang
- 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
| | - Lei Jia
- 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
| | - Bohan Zhang
- 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
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Nchinda N, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, Hemelaar J. Global associations of key populations with HIV-1 recombinants: a systematic review, global survey, and individual participant data meta-analysis. Front Public Health 2023; 11:1153638. [PMID: 37575094 PMCID: PMC10420084 DOI: 10.3389/fpubh.2023.1153638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 06/28/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Global HIV infections due to HIV-1 recombinants are increasing and impede prevention and treatment efforts. Key populations suffer most new HIV infections, but their role in the spread of HIV-1 recombinants is unknown. We conducted a global analysis of the associations between key populations and HIV-1 recombinants. Methods We searched PubMed, EMBASE, CINAHL, and Global Health for HIV-1 subtyping studies published from 1/1/1990 to 31/12/2015. Unpublished data was collected through a global survey. We included studies with HIV-1 subtyping data of key populations collected during 1990-2015. Key populations assessed were heterosexual people (HET), men who have sex with men (MSM), people who inject drugs (PWID), vertical transmissions (VERT), commercial sex workers (CSW), and transfusion-associated infections (BLOOD). Logistic regression was used to determine associations of key populations with HIV-1 recombinants. Subgroup analyses were performed for circulating recombinant forms (CRFs), unique recombinant forms (URFs), regions, and time periods. Results Eight hundred and eighty five datasets including 77,284 participants from 83 countries were included. Globally, PWID were associated with the greatest odds of recombinants and CRFs (OR 2.6 [95% CI 2.46-2.74] and 2.99 [2.83-3.16]), compared to HET. CSW were associated with increased odds of recombinants and URFs (1.59 [1.44-1.75] and 3.61 [3.15-4.13]). VERT and BLOOD were associated with decreased odds of recombinants (0.58 [0.54-0.63] and 0.43 [0.33-0.56]). MSM were associated with increased odds of recombinants in 2010-2015 (1.43 [1.35-1.51]). Subgroup analyses supported our main findings. Discussion As PWID, CSW, and MSM are associated with HIV-1 recombinants, increased preventative measures and HIV-1 molecular surveillance are crucial within these key populations. Systematic review registration PROSPERO [CRD42017067164].
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Affiliation(s)
- Nkazi Nchinda
- Nuffield Department of Population Health, Infectious Disease Epidemiology Unit, National Perinatal Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Ramyiadarsini Elangovan
- Nuffield Department of Population Health, Infectious Disease Epidemiology Unit, National Perinatal Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Jason Yun
- Nuffield Department of Population Health, Infectious Disease Epidemiology Unit, National Perinatal Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Leslie Dickson-Tetteh
- Nuffield Department of Population Health, Infectious Disease Epidemiology Unit, National Perinatal Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Shona Kirtley
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Botnar Research Centre, Oxford, United Kingdom
| | - Joris Hemelaar
- Nuffield Department of Population Health, Infectious Disease Epidemiology Unit, National Perinatal Epidemiology Unit, University of Oxford, Oxford, United Kingdom
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Li Y, Zhu B, Han J, Li J, Jia L, Wang X, Li H, Li L. Identification of Two Novel HIV-1 Unique Recombinant Forms in Shenzhen, China. AIDS Res Hum Retroviruses 2022; 38:497-501. [PMID: 35172615 DOI: 10.1089/aid.2021.0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Homosexual contact is one of the main transmission routes of the HIV-1 epidemic in Shenzhen. Several subtypes of HIV-1 are prevalent among men who have sex with men simultaneously, which provides favorable conditions for the formation of a unique recombinant form (URF). In this study, we reported two URFs of HIV-1 (LS10525 and LS13740) infected through homosexual contact in Shenzhen. Phylogeny and recombination analyses based on the nearly full-length genome indicated that LS10525 was a second-generation recombinant strain composed of circulating recombinant form (CRF)07_BC and CRF59_01B, and LS13740 was a second-generation recombinant strain composed of CRF07_BC and CRF55_01B. The emergence of the novel structure of URFs urgently needs to surveil the HIV-1 epidemic in the population.
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Affiliation(s)
- Yang Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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7
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Zhu B, Zhao J, Wang X, Li H, Liu Y, Zheng C, Jia L, Li T, Wang X, Chen L, Li J, Zhang B, Han J, Li L. Characterization of Three Novel HIV-1 Second-Generation Recombinants (CRF01_AE/CRF07_BC) Identified in Shenzhen, China. AIDS Res Hum Retroviruses 2022; 38:242-247. [PMID: 35044246 DOI: 10.1089/aid.2021.0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prevalence of recombinant forms has greatly enhanced HIV-1 genetic diversity. Under co-circulation of major epidemic HIV-1 strains (CRF01_AE and CRF07_BC) in China, more CRF01_AE and CRF07_BC as the backbone of HIV-1 second-generation recombinants (SGRs) are also emerging. In this study, we identified three similar novel HIV-1 SGR strains composed of CRF01_AE and CRF07_BC from HIV-1 positive individuals in Shenzhen, China. Near full-length genome phylogenetic and recombinant analysis confirmed that these unique recombination forms were CRF01_AE and CRF07_BC strains recombined. Further subregion phylogenetic analysis indicated that all CRF01_AE fragments were from CRF01_AE cluster 4 prevalent among men who have sex with men, and all subtype B and C fragments derived from CRF07_BC. The emergence of novel recombinants of CRF01_AE/CRF07_BC indicates the increased genetic diversity of the HIV epidemic in Shenzhen. It is necessary to monitor HIV-1 SGR strains among high-risk populations for the epidemic dynamics of HIV-1 in Shenzhen, China.
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Affiliation(s)
- Bo Zhu
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaorui Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohan Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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8
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Xing Y, Guo Y, Wang L, Li H, Han J, Wang X, Liu Y, Jia L, Li J, Bai H, Li C, Li B, Li L, Dai E. Identification of Two Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/CRF07_BC) in Hebei, China. AIDS Res Hum Retroviruses 2021; 37:967-972. [PMID: 33926207 DOI: 10.1089/aid.2021.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Homosexual contact is one of the main transmission routes of HIV-1 epidemic in Hebei, China. Several subtypes of HIV are prevalent simultaneously in the population, which always lead to the emergency of unique recombinant forms (URFs). In this study, we reported two new URFs from two HIV-1 positive subjects infected through homosexual contact route in Hebei, China. Phylogenetic and recombinant analyses based on the near full-length genome of the two URFs both revealed the two URFs are the second generation of recombinant strains originated from CRF01_AE and CRF07_BC. The CRF01_AE segments of two URFs located in cluster 4 of CRF01_AE strains in the phylogenetic tree. The emergence of the novel CRF01_AE/CRF07_BC recombinant forms with complicated genomic structures indicated the importance of the continuous monitoring of the HIV-1 epidemic and new URFs among the men who have sex with men populations.
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Affiliation(s)
- Ying Xing
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, China
- Department of Laboratory medicine, the Fifth Hospital of Shijiazhuang, Hebei Medicine University, Shijiazhuang, China
| | - Yaolin Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijing Wang
- Department of Laboratory medicine, the Fifth Hospital of Shijiazhuang, Hebei Medicine University, Shijiazhuang, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- 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
| | - Lei Jia
- 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
| | - Haijun Bai
- Department of Dermatology and Venereal Disease, Handan infectious Disease Hospital, Handan, China
| | - Chen Li
- Department of Laboratory medicine, the Fifth Hospital of Shijiazhuang, Hebei Medicine University, Shijiazhuang, China
| | - Beilei Li
- Department of Laboratory medicine, the Fifth Hospital of Shijiazhuang, Hebei Medicine University, Shijiazhuang, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Erhei Dai
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, China
- Department of Laboratory medicine, the Fifth Hospital of Shijiazhuang, Hebei Medicine University, Shijiazhuang, China
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Kusagawa S, Tatsumi M, Sakamoto-Umeki Y, Takekawa N, Matsubayashi K, Ishimaru K, Kawana-Tachikawa A. Nucleotide Sequence of HIV-1-Positive Specimen Reference Panel for Evaluation of HIV In Vitro Diagnostics in Japan. AIDS Res Hum Retroviruses 2021; 37:994-997. [PMID: 34652965 DOI: 10.1089/aid.2021.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 subtype/circulating recombinant form (CRF) distribution of HIV-1-positive specimens for evaluating HIV in vitro diagnostics (IVDs) was examined and compared with the HIV-1 epidemic in Japan. The nucleotide sequences of the gag-pol region of 173 plasma specimens (84, provided in 2007, and 89 in 2013-2015) were determined. HIV-1 subtype/CRF classification was performed based on the phylogenetic analyses of the sequences. The subtype/CRF distribution resulting in this study was similar to that of a previous epidemiological report. Three CRF02_AG and one unique recombinant form, including subtype G and A regions, were observed in the 2013 and 2014 specimens, except in the 2007 specimens. The reference panel consisting of these specimens was practical for the evaluation of HIV IVDs in Japan.
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Affiliation(s)
- Shigeru Kusagawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masashi Tatsumi
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Sakamoto-Umeki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Naho Takekawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keiji Matsubayashi
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Ken Ishimaru
- Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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10
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Han L, Li H, Wang L, Jia L, Han J, Li T, Wang X, Liu Y, Li J, Lu J, Qu X, He X, Liu H, Li L, Dai E. Near Full-Length Genomic Characterization of Two Novel HIV-1 Unique Recombinant Forms (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Shijiazhuang City, Hebei Province, China. AIDS Res Hum Retroviruses 2021; 37:978-984. [PMID: 34465138 DOI: 10.1089/aid.2021.0100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unique recombinant forms (URFs) are more likely developed among HIV-1 infections through men who have sex with men (MSM) because of cocirculation of multiple subtypes. In this study, two novel URFs deriving from two HIV-positive subjects (HB010014, HB010063) were identified in Shijiazhuang, Hebei province, China, and two sequences formed a distinct monophyletic cluster. Further recombination analysis showed that of two new URFs were consisted of circulating recombinant form (CRF)01_AE and CRF07_BC. The subregion phylogenetic analysis indicated that CRF01_AE segments were traced back to cluster 4 of CRF01_AE strains, which were prevalent among HIV-1 infections through MSM in China. New URFs being developing gradually and spreading released that more and more novel recombinant strains of HIV-1 could be developed, which means that the past prevention strategies need to be adjusted.
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Affiliation(s)
- Leilei Han
- School of Public Health, North China University of Science and Technology, Tangshan, China
- Department of Laboratory Medicine, North China University of Science and Technology, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijing Wang
- Department of Laboratory Medicine, North China University of Science and Technology, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianhua Lu
- Department of Laboratory Medicine, North China University of Science and Technology, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Xiaojing Qu
- Department of Laboratory Medicine, North China University of Science and Technology, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Xuhui He
- Clinical Laboratory, The Second Hospital of Xingtai, Xingtai, China
| | - Haichun Liu
- Clinical Laboratory, Zhangjiakou Infectious Disease Hospital, Zhangjiakou, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Erhei Dai
- School of Public Health, North China University of Science and Technology, Tangshan, China
- Department of Laboratory Medicine, North China University of Science and Technology, The Fifth Hospital of Shijiazhuang, Shijiazhuang, China
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11
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Elangovan R, Jenks M, Yun J, Dickson-Tetteh L, Kirtley S, Hemelaar J. Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study. Front Microbiol 2021; 12:690647. [PMID: 34335516 PMCID: PMC8320730 DOI: 10.3389/fmicb.2021.690647] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
Global HIV-1 genetic diversity forms a major obstacle to the development of an HIV vaccine. It may be necessary to employ subtype-specific HIV-1 vaccines in individual countries according to their HIV-1 subtype distribution. We estimated the global and regional need for subtype-specific HIV-1 vaccines. We took into account the proportions of different HIV-1 variants circulating in each country, the genetic composition of HIV-1 recombinants, and the different genome segments (gag, pol, env) that may be incorporated into vaccines. We modeled different scenarios according to whether countries would employ subtype-specific HIV-1 vaccines against (1) the most common subtype; (2) subtypes contributing more than 5% of HIV infections; or (3) all circulating subtypes. For therapeutic vaccines targeting the most common HIV-1 subtype in each country, 16.5 million doses of subtype C vaccine were estimated globally, followed by subtypes A (14.3 million) and B (4.2 million). A vaccine based on env required 2.6 million subtype E doses, and a vaccine based on pol required 4.8 million subtype G doses. For prophylactic vaccines targeting the most common HIV-1 subtype in each country, 1.9 billion doses of subtype A vaccine were estimated globally, followed by subtype C (1.1 billion) and subtype B (1.0 billion). A vaccine based on env required 1.2 billion subtype E doses, and a vaccine based on pol required 0.3 billion subtype G doses. If subtype-specific HIV-1 vaccines are also directed against less common subtypes in each country, vaccines targeting subtypes D, F, H, and K are also needed and would require up to five times more vaccine doses in total. We conclude that to provide global coverage, subtype-specific HIV-1 vaccines need to be directed against subtypes A, B, and C. Vaccines targeting env also need to include subtype E and those targeting pol need to include subtype G.
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Affiliation(s)
| | - Michael Jenks
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jason Yun
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Leslie Dickson-Tetteh
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Shona Kirtley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Joris Hemelaar
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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12
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Yueqi Y, Ying Z, Jing L, Hongxiong G, Jianshuang C, Yan X, Hao C, Defu Y, Haiyang H, Xiaoqin X, Bei W, Gengfeng F. The Identification of A Novel HIV-1 Second-Generation Recombinant form (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Jiangsu, China. Curr HIV Res 2021; 19:188-194. [PMID: 33106145 DOI: 10.2174/1570162x18666201026143200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/12/2020] [Accepted: 09/25/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recent years. OBJECTIVE This study aimed to report on novel HIV-1 recombinants. METHODS We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination breakpoints using SimPlot 3.5.1. RESULTS We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_ AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints in the virus, which differed from any previously identified CRF and URF around the world. CONCLUSION Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.
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Affiliation(s)
- Yin Yueqi
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Zhou Ying
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Lu Jing
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Guo Hongxiong
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Chen Jianshuang
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xuan Yan
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Cheng Hao
- Wuxi Xinwu District Center for Disease Control and Prevention, Wuxi 214028, China
| | - Yuan Defu
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hu Haiyang
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Xu Xiaoqin
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Wang Bei
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Fu Gengfeng
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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13
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Hemelaar J, Loganathan S, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S; WHO-UNAIDS Network for HIV Isolation and Characterization. Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015. J Virol 2020; 95:e01580-20. [PMID: 33087461 DOI: 10.1128/JVI.01580-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country level HIV-1 diversity globally between 1990 and 2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from 1 January 1990 to 31 December 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected between 1990 and 2015 were included. This resulted in a database with 383,519 subtyped HIV-1 samples from 116 countries over four time periods (1990 to 1999, 2000 to 2004, 2005 to 2009, and 2010 to 2015). We analyzed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analyzed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon diversity index for each country. Finally, we analyzed global temporal trends in each of these measures of HIV-1 diversity. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola, and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (United States) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in Southeast Asia (>95% of infections in Viet Nam, Cambodia, and Thailand), China, and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (>75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (>30%) were found in Myanmar, Republic of the Congo, and Argentina. Global temporal analysis showed consistent increases over time in country level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country level HIV-1 diversity. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved.IMPORTANCE This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.
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14
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Yao T, Wu J, Zhang Y, Shen Y, Wang X, Xing H, Liu Y, Yang X, Ding X, Hu B, Han J, Li J, Li H, Li L. Near Full-Length Genomic Characterization of a Novel Unique Recombinant (CRF01_AE/CRF07_BC) in Fuyang City of China. AIDS Res Hum Retroviruses 2020; 36:527-532. [PMID: 32079407 DOI: 10.1089/aid.2020.0002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombinant forms contribute substantially to the genetic diversity of HIV-1. Recent studies have also revealed that three major viral strains (CRF07_BC, CRF01_AE, and subtype B) have been cocirculating among men who have sex with men (MSM) in Anhui, suggesting a high probability of generating new recombinants. In this study, we reported a novel CRF01_AE and CRF07_BC HIV-1 recombinant form in MSM in Fuyang city of China. Two near full-length genome (NFLG) named FY184 and FY208 were successfully obtained. The genomic composition analysis of the NFLG reveals that it was divided into four segments by three breakpoints, with two regions of CRF07_BC inserted into a CRF01_AE backbone's gag and pol regions. The CRF01_AE regions were originated from a subcluster lineage of CRF01_AE, which is mainly circulating among MSM in China. The emergence of a novel recombinant of CRF01_AE/CRF07_BC is indicative of the increasing genetic diversity of the HIV epidemic in MSM in Anhui.
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Affiliation(s)
- Tengchong Yao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jianjun Wu
- Department of AIDS Confirmation Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuelan Shen
- Department of AIDS Confirmation Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 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
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaohui Yang
- Department of AIDS Confirmation Laboratory, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Xinping Ding
- Department of AIDS Confirmation Laboratory, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Bing Hu
- Department of AIDS Confirmation Laboratory, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Jingwan Han
- 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
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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15
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Liang B, Wei Q, Yang Y, Yang Y, Liu J, Chu J, Chen R, Liang H, Ye L. Identification of a Novel HIV-1 CRF55_01B/B Recombinant Isolate in Guangxi, China. AIDS Res Hum Retroviruses 2020; 36:434-439. [PMID: 31775514 DOI: 10.1089/aid.2019.0222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dynamic recombination is the driving force in the genetic diversity of human immunodeficiency virus type 1 (HIV-1). When multiple subtypes are circulating in the same area of a population, new HIV-1 strains are likely to be generated through recombination. In this study, we report a novel recombinant strain (2018GXQZLSHET001) of HIV-1, isolated from a HIV-1-positive heterosexual individual infected in Guangdong province, who recently lived in Guangxi province, China. Phylogenetic analysis of the near full-length genome suggested that 2018GXQZLSHET001 was a recombinant of strains CRF55_01B and subtype B. Similarity plotting and bootscaning showed that a subtype B segment was inserted into the CRF55_01B genome with one breakpoint in the nef and 3' long terminal repeat regions. Further subregion phylogenetic analysis demonstrated that the CRF55_01B segment originated from Guangdong. The subtype B segment was similar to a Thai B lineage. This indicated that the strain might be a novel recombinant, comprising sequences of both CRF55_01B and B. The emergence of this unique recombinant strain illustrated the complexity of the HIV-1 epidemic, and the need to strengthen molecular epidemiological surveillance and measures to reduce its spread.
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Affiliation(s)
- Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Qiuyu Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yao Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yuan Yang
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jie Liu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Jiemei Chu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Rongfeng Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
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16
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Liang B, Yang Y, Zhang F, Li K, Yang Y, Ou W, Huang J, Ning C, Ye L, Liang H. Characterization of a Novel HIV-1 Recombinant Form (CRF01_AE/CRF07_BC/CRF08_BC) Identified from Guangxi, China. AIDS Res Hum Retroviruses 2020; 36:143-152. [PMID: 31482724 DOI: 10.1089/aid.2019.0185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, more and more kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in the population in China. A novel HIV-1 recombinant virus (2016GXNNIDU016) was identified in this study, which was isolated from an HIV-1 infected intravenous drug user in Nanning, the capital of Guangxi, China. Phylogenetic analysis of the near full-length genome (NFLG) indicated that the sequence (2016GXNNIDU016) was a monophyletic branch that did not cluster with any previously identified genotype. Recombinant analysis showed that the NFLG of 2016GXNNIDU016 is composed of CRF07_BC, CRF01_AE, and CRF08_BC, including nine mosaic segments. Differing from previously documented CRF01_AE and CRF07/08_BC recombinant forms, 2016GXNNIDU016 increases the genetic complexity of HIV-1 in Guangxi. The constant emergence of novel recombinant forms should draw our attention to make more efforts in supervising and preventing the spread of HIV infection.
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Affiliation(s)
- Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yao Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Kang Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yuan Yang
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Weidong Ou
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
| | - Chuanyi Ning
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, School of Public Health, Guangxi Medical University, Nanning, China
- Guangxi Collaborative Innovation Center for Biomedicine, Life Science Institute, Guangxi Medical University, Nanning, China
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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18
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Zhou Z, Ma P, Feng Y, Ou W, Shao Y, Wei M. Another Near Full-Length Sequence of an HIV-1 CRF01_AE/CRF07_BC Recombinant Virus from a Man Who Has Sex with Men in Tianjin, China. AIDS Res Hum Retroviruses 2019; 35:865-869. [PMID: 31154808 DOI: 10.1089/aid.2019.0071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Surprisingly, more new unique recombinant forms (URFs) of CRF01_AE/CRF07_BC recombinant viruses were found in Tianjin, China, recently. Here we identified another novel HIV-1 recombinant virus (TJ20170315) isolated from an HIV-1 positive man who has sex with men in Tianjin, China. Phylogenetic analysis of the near full-length genome of TJ20170315 showed that it formed a monophyletic branch within the cluster of CRF01_AE reference sequences. Recombinant analysis showed that the virus kept the CRF01_AE parental backbone, and one CRF07_BC segment was inserted into gag, pol genes of the CRF01_AE backbone. Nowadays, multiple kinds of circulating recombinant forms (CRFs) and URFs were identified among men who has sex with men in China. The emergency of URFs highlights the complexity of HIV-1 infection in Tianjin, China, and implies that the next new CRF and HIV-1 epidemic are coming on the road.
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Affiliation(s)
- Zehua Zhou
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Ping Ma
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weidong Ou
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Min Wei
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
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19
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Karade S, Sen S, Sashindran VK. Absence of Integrase Strand Transfer Inhibitor Associated Resistance in Antiretroviral Therapy Naïve and Experienced Individuals from Western India. AIDS Res Hum Retroviruses 2019; 35:567-571. [PMID: 30793915 DOI: 10.1089/aid.2018.0272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Indian national AIDS control program heavily relies on low cost nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI). With global increase in resistance to these, alternative antiretroviral combinations need to be explored. Owing to higher potency, better efficacy and tolerability, recently WHO recommended integrase strand transfer inhibitor (INSTI) based first-line antiretroviral therapy (ART). There is lack of INSTI resistance surveillance data from India. Thus, there is a need to analyze integrase (IN) gene from primarily HIV-1 subtype C infected Indian population, before widespread introduction of INSTI in first-line ART. Plasma samples were collected from INSTI naïve individuals reporting to ART centre of Pune, India. RNA was extracted and IN gene was amplified by nested polymerase chain reaction (PCR) using prior published primers. PCR product of 867 bp was bi-directionally sequenced and resistance associated mutation were analyzed using Stanford University HIV drug resistance algorithm. A total of 58 HIV-1 sequences from 62 INSTI naïve individuals were successfully genotyped. Of these 58, 40 were ART naïve, newly diagnosed and remaining individuals were on NRTI, NNRTI, or protease inhibitors based failing regimen. The commonest subtype identified in the study was C (93%) followed by A1 (3.5%). A total of 191 (66.31%) fully conserved amino acid (aa) positions were observed in IN gene. Overall there was absence of major INSTI resistance mutation, however, E157Q (13.79%) emerged as common polymorphic mutation. Other accessory mutations were L74IM (34.48%), Q95K (1.72%), and T97A (1.72%). To conclude, this first Indian study on primarily HIV-1 subtype C sequences characterized aa variations in IN gene and indicated absence of major INSTI resistance associated mutations.
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Affiliation(s)
- Santosh Karade
- Department of Microbiology, Armed Forces Medical College, Pune, India
| | - Sourav Sen
- Department of Microbiology, Armed Forces Medical College, Pune, India
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20
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Zhou Z, Ma P, Feng Y, Ou W, Qian J, Gao L, Zhang D, Shao Y, Wei M. Characterization of a New HIV-1 CRF01_AE/CRF07_BC Recombinant Virus in Tianjin, China. AIDS Res Hum Retroviruses 2018; 34:705-708. [PMID: 29724117 DOI: 10.1089/aid.2018.0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV is notorious for its rapid evolution since its transmissions from monkey to human. Currently, HIV contains multiple subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs). Here, from an HIV-positive mother and her child in Tianjin, China, we identified a novel HIV-1 second-generation recombinant virus (TJ20170316 and TJ20170317) between CRF01_AE and CRF07_BC. Near full-length genomes (NFLGs) were obtained from both samples, and they shared very close sequences, except some point mutations. Phylogenetic analyses of the NFLGs showed that they consist of CRF01_AE backbone and part CRF07_BC sequences. Recombinant Identification Program and Simplot software identified four breakpoints in gag, pol, vif, and tat genes in TJ20170316, totally different from other reported CRFs and URFs. The emergence of such URFs in Tianjin, China, highlights the complexity of HIV-1 epidemic and more measures should be taken to prevent HIV transmissions.
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Affiliation(s)
- Zhehua Zhou
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Ping Ma
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weidong Ou
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Qian
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Liying Gao
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Defa Zhang
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Min Wei
- Nankai University Second People's Hospital, School of Medicine, Nankai University, Tianjin, China
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21
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Wang X, Zhang M, Li J, Li T, Sun C, Li H, Liu Y, Liu S, Zhuang D, Bao Z, Han J, Li J, Li L. Genetic Characterization of a Unique Recombinant Strain Identified in Yunnan with Genome Comprising B and C. AIDS Res Hum Retroviruses 2017; 33:614-620. [PMID: 28398773 DOI: 10.1089/aid.2017.0013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since the first identification of HIV-1 outbreak in Dehong, Yunnan province has been the epidemic center of HIV in China. Owing to the special geographic location and the frequent population mobility, Yunnan province contained complex HIV subtype distribution. Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) have been found in recent years. In this study, a unique HIV-1 recombinant strain genome (YN10134) was characterized from an HIV-positive female in Yunnan, China. This virus genome had a complex intersubtype recombinant structure with eight breakpoints, composed of subtypes B and C. Although the sequence had a similar breakpoint with CRF07_BC in the start position in Env, the phylogenetic analysis showed that the segment was not originated from CRF07_BC. The identification of the URF indicated the severity of the HIV epidemic in Yunnan province and the urgent need for epidemiological surveillance of the new recombination.
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Affiliation(s)
- Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Min Zhang
- Anhui Medical University, Anhui, China
| | - Jianjian Li
- AIDS Care Center (YNACC), Yunnan Provincial Hospital of Infectious Disease, Kunming, China
| | - Tianyi Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changrong Sun
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang H, Luo P, Zhu H, Wang N, Hu J, Mo Q, Yang Z, Feng Y. Near Full-Length Genomic Characterization of a Novel HIV-1 Unique Recombinant (CRF55_01B/CRF07_BC) from a Malaysian Immigrant Worker in Zhejiang, China. AIDS Res Hum Retroviruses 2017; 33:275-278. [PMID: 27460422 DOI: 10.1089/aid.2016.0100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombinant forms contribute substantially to the genetic diversity of human immunodeficiency virus type 1 (HIV-1). Here we report a novel HIV-1 recombinant detected from a comprehensive HIV-1 molecular epidemiologic study among cross-border populations in China. Near full-length genome (NFLG) phylogenetic analysis showed that the novel HIV-1 recombinant ZJCIQ15005, which was isolated from a Malaysian immigrant worker in Zhejiang, China, clustered with CRF55_01B reference sequences but set up a distinct branch. Recombinant analysis showed that the NFLG of ZJCIQ15005 composed of CRF55_01B (as the backbone) and CRF07_BC, with 12 recombinant break points observed in the pol, vif, vpr, tat, rev, env, nef, and 3'LTR regions. This is the first detection of a novel HIV-1 recombinant (CRF55_01B/CRF07_BC) in immigrant workers in China. The emergence of this recombinant may increase the complexity of the HIV-1 epidemic in China and suggests the importance of continuous surveillance of the dynamic changes of HIV-1.
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Affiliation(s)
- Haibo Wang
- Zhuhai International Travel Healthcare Center, Zhuhai, China
| | - Peng Luo
- Zhejiang International Travel Healthcare Center, Hangzhou, China
| | - Hong Zhu
- Beijing International Travel Healthcare Center, Beijing, China
| | - Ningli Wang
- Yunnan International Travel Healthcare Center, Kunming, China
| | - Jing Hu
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiuhua Mo
- Zhuhai International Travel Healthcare Center, Zhuhai, China
| | - Ze Yang
- Zhuhai International Travel Healthcare Center, Zhuhai, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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24
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Jia D, Zhao J, Li T, Sun C, Li H, Zheng C, Chen L, Liu Y, Liu S, Zhuang D, Wang X, Bao Z, Li J, Li L. Near Full-Length Genomic Sequences of Two Novel HIV-1 Recombinant Forms Identified in Shenzhen, China. AIDS Res Hum Retroviruses 2017; 33:82-86. [PMID: 27460636 DOI: 10.1089/aid.2016.0162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most HIV subtypes prevalent in China can be found in Shenzhen, including CRF07_BC, CRF01_AE, CRF08_BC, CRF55_01B, and subtype B. Multiple subtypes spreading in the same population always lead to the emergence of unique recombinant strains. Here, we report two unique recombinant forms (SZ44LS7251 and SZ95LS8027) of HIV-1 identified in a heterosexual population. Recombinant analyses were fulfilled based on the near full-length genomes. Both strains comprise subtypes B, C, and CRF01_AE. Phylogenetic analysis reveals that SZ44LS7251 is the second generation recombination originated from CRF55_01B andCRF07_BC, whereas SZ95LS8027 comprises CRF01_AE and CRF07_BC.The emergence of second generation recombination of HIV with complicated genomic structures supposed that high ratio of super infections or coinfections might happen in the Shenzhen area.
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Affiliation(s)
- Dijing Jia
- Graduate School, Anhui Medical University, Anhui, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Changrong Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chenli Zheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lin Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Daomin Zhuang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Graduate School, Anhui Medical University, Anhui, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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