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Li X, Trovão NS. The evolutionary and transmission dynamics of HIV-1 CRF08_BC. PLoS One 2024; 19:e0310027. [PMID: 39241052 PMCID: PMC11379155 DOI: 10.1371/journal.pone.0310027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/22/2024] [Indexed: 09/08/2024] Open
Abstract
HIV-1 CRF08_BC is a significant subtype in China, though its origin and spread remain incompletely understood. Previous studies using partial genomic data have provided insights but lack comprehensive analysis. Here, we investigate the early evolutionary and spatiotemporal dynamics of HIV-1 CRF08_BC in China and Myanmar using near-complete genome sequences. We analyzed 28 near-complete HIV-1 CRF08_BC genomes from China and Myanmar (1997-2013). Phylogenetic, molecular clock, and Bayesian discrete trait analyses were performed to infer the virus's origin, spread, and associated risk groups. Based on Bayesian time-scaled inference with the best-fitting combination of models determined by marginal likelihood estimation (MLE), we inferred the time to the most recent common ancestor (TMRCA) and evolutionary rate of HIV-1 CRF08_BC to be at 3 October 1991 (95% HPD: 22 February1989-27 November 1993) and 2.30 × 10-3 substitutions per site per year (95% HPD: 1.96 × 10-3-2.63 × 10-3), respectively. Our analysis suggests that HIV-1 CRF08_BC originated in Yunnan Province, China, among injecting drug users, and subsequently spread to other regions. This study provides valuable insights into the early dynamics of HIV-1 CRF08_BC through combined genomic and epidemiological data, which may inform effective prevention and mitigation efforts. However, the limited genomic data influenced the extent of our findings, and challenges in collecting accurate risk group information during surveillance were evident.
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Affiliation(s)
- Xingguang Li
- Ningbo No.2 Hospital, Ningbo, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, China
| | - Nídia S Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland, United States of America
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2
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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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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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4
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Ge Z, Feng Y, Zhang H, Rashid A, Zaongo SD, Li K, Yu Y, Lv B, Sun J, Liang Y, Xing H, Sönnerborg A, Ma P, Shao Y. HIV-1 CRF07_BC transmission dynamics in China: two decades of national molecular surveillance. Emerg Microbes Infect 2021; 10:1919-1930. [PMID: 34498547 PMCID: PMC8477959 DOI: 10.1080/22221751.2021.1978822] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
By analyzing an unprecedentedly large, longitudinal HIV-1 CRF07_BC sequence dataset collected from China in the past two decades, we sought to build CRF07_BC lengthwise transmission networks, and understand its transmission dynamics. We divided CRF07_BC into two clusters based on phylogenetic analysis and an estimation of the pairwise genetic distance at 0.7%. Of 6213 sequences, 3607 (58.1%) linked to ≥1 other sequence. CRF07_BC was divided into two clusters: 07BC_O and 07BC_N. The 07BC_O is the original CRF07_BC, circulating in people who inject drugs (PWID) and heterosexuals, predominantly in southwestern and northwestern provinces of China. The 07BC_N is a new cluster, identified mostly in men having sex with men (MSM) in the northern provinces of China. Bayesian analysis indicates that CRF07_BC has experienced two phases of exponential growth, which was first driven by 07BC_O then 07BC_N. Compared to 07BC_O, the proportion of the parameter of population transmission risk (TR) of 07BC_N has risen constantly. The power-law function analyses reveal that 07BC_N has increased over years with higher degree. In 07BC_N, only 13.16% of MSM were linked to other risk groups, but these links represent 41.45%, 54.25%, and 55.07% of links among heterosexual females, heterosexual males, and male PWID respectively. This study indicates that CRF07_BC has evolved into two clusters in China, and their distributions are distinct across risk groups and geographical regions. 07BC_N shows a greater risk of transmission, and has gradually replaced 07BC_O. Furthermore, the results show that strengthening the MSM interventions could lower the rapidity of 07BC_N transmission in all risk groups.
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Affiliation(s)
- Zhangwen Ge
- 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, People's Republic of China.,Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Affiliated Hospital of Guizhou University, Guiyang, People's Republic of China.,School of Medicine, Nankai University, Tianjin, People's Republic of 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, People's Republic of China
| | - Hua Zhang
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Affiliated Hospital of Guizhou University, Guiyang, People's Republic of China
| | - Abdur Rashid
- 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, People's Republic of China.,School of Medicine, Nankai University, Tianjin, People's Republic of China
| | - Silvere D Zaongo
- Department of Infectious Diseases, Nankai University Second People's Hospital, Tianjin Second People's Hospital, Tianjin, People's Republic of China
| | - Kang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yueyang Yu
- 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, People's Republic of China.,School of Medicine, Nankai University, Tianjin, People's Republic of China
| | - Bowen Lv
- 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, People's Republic of China
| | - Jia Sun
- 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, People's Republic of China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yanling Liang
- 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, People's Republic of 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, People's Republic of China
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ping Ma
- Department of Infectious Diseases, Nankai University Second People's Hospital, Tianjin Second People's Hospital, Tianjin, People's Republic of China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,School of Medicine, Nankai University, Tianjin, People's Republic of China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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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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6
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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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7
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Chen X, Ye M, Wang Y, Zhang C, Zheng YT. Laos is Affected by HIV CRF01_AE and the Newly Identified CRF97_01B. Virol Sin 2020; 35:538-547. [PMID: 32232730 DOI: 10.1007/s12250-020-00215-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/18/2020] [Indexed: 11/25/2022] Open
Abstract
Laos is the only landlocked country in Southeast Asia and borders Thailand, Myanmar and Cambodia, the three countries in this region that have been hardest hit by human immunodeficiency virus (HIV). Laos has been regarded as a low-HIV-prevalence country for decades. To understand the status of HIV in Laos in recent years, a retrospective study was performed among 2851 patients visiting a hospital in Vientiane, the capital of Laos, from November 2011 to May 2012. Whole blood samples were obtained from the patients, and DNA was extracted. HIV status was determined by HIV gag fragment-specific PCR assay. Sixty-nine samples were detected as HIV proviral DNA positive with a positive rate of 2.4% (69/2851). Sixty-one near full-length genomic sequences were obtained from the positive samples. The results of phylogenetic analysis showed that the vast majority (91.8%) of the HIV strains belonged to CRF01_AE, and the other five (8.2%) strains were identified as a new HIV circulating recombinant form CRF97_01B, which had a CRF01_AE backbone with an insertion of subtype B in the gag-pol region. Phylogeographic analysis revealed that HIV CRF01_AE circulating in Laos were multiply introduced from Thailand. These results indicated that Laos might be suffering a considerably more serious impact of HIV than previously believed. To keep this country from undergoing the same increase in HIV prevalence observed in its neighbors, immediate intervention measures and sufficient epidemiological research are urgently needed.
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Affiliation(s)
- Xin Chen
- 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, 650223, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Mei Ye
- 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, 650223, China
| | - Yu Wang
- KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215006, China
| | - Chiyu Zhang
- Pathogen Discovery and Evolution Unit, Pathogen Discovery and Big Data Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yong-Tang Zheng
- 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, 650223, China.
- KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215006, China.
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8
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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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9
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Molecular evolution of hepatitis C virus in China: A nationwide study. Virology 2018; 516:210-218. [PMID: 29407379 DOI: 10.1016/j.virol.2018.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 12/12/2022]
Abstract
The evolutionary and epidemic history and the regional differences of hepatitis C virus (HCV) are complex and remain unclear in the vast territory China. Here we recruited 1540 HCV-RNA positive patients sampled in 29 provinces across whole China, which is the largest sample capacity and the most comprehensive geographic coverage of China to our knowledge. 1b, 2a, 3b, 6a and 3a were the major subtypes in China. 1b was the most predominant subtype which presented in every province. The second most predominant subtype, 2a, appeared to concentrate in the north of China. Subtypes 3a and 3b were mainly found in the Southwest region, while 6a was restricted in the South region. We further estimated the origins of the dominating subtypes and discovered for the first time that a Chinese-specific transmission pattern for some strains of subtype 2a which was restricted in north China, and Chinese subtype 3b originated from Thailand.
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Pattern of hepatitis C virus genotypes and subtypes circulating in war-stricken Khyber Pakhtunkhwa, Pakistan: Review of published literature. ASIAN PAC J TROP MED 2017; 10:1037-1042. [DOI: 10.1016/j.apjtm.2017.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023] Open
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Wu J, Guo H, Zhang J, Liu X, Ayoupu A, Shen Y, Miao L, Tang J, Lei Y, Su B. The Epidemic History of HIV-1 CRF07_BC in Hetian Prefecture and the Role of It on HIV Spreading in China. AIDS Res Hum Retroviruses 2017; 33:364-367. [PMID: 27824268 DOI: 10.1089/aid.2016.0214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CRF07_BC is one of the most prevalent HIV-1 strains in China, and Xinjiang Uygur Autonomous Region has ever been considered to be a second epidemic center after Yunnan Province in previous studies. Here we use HIV-1 pol gene sequences identified from Hetian Prefecture located in Xinjiang Autonomous Region to reconstruct the epidemic history of HIV CRF07_BC strain circulating in this region. We found that CRF07_BC is the predominant HIV-1 form in Hetian Prefecture, and the estimated tMRCA analysis shows that there is no enough evidence supporting Xinjiang Autonomous Region as a second epidemic center of spreading HIV-1. It may imply that every city may be only a point among the HIV spreading network because of the frequent migration of population in the whole country nowadays.
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Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hongxiong Guo
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Zhang
- Hetian Prefecture Center for Disease Control and Prevention, Hetian, China
| | - Xiaoming Liu
- Hetian Prefecture Center for Disease Control and Prevention, Hetian, China
| | - Aideaierli Ayoupu
- Hetian Prefecture Center for Disease Control and Prevention, Hetian, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Lifeng Miao
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Jihai Tang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yanhua Lei
- Hefei Center for Disease Control and Prevention, Hefei, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
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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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Eybpoosh S, Bahrampour A, Karamouzian M, Azadmanesh K, Jahanbakhsh F, Mostafavi E, Zolala F, Haghdoost AA. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One 2016; 11:e0156499. [PMID: 27280293 PMCID: PMC4900578 DOI: 10.1371/journal.pone.0156499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 01/28/2023] Open
Abstract
HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts.
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Affiliation(s)
- Sana Eybpoosh
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Bahrampour
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Karamouzian
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- School of Population and Public Health, Faculty of Medicine, University of British Colombia, Vancouver, BC, Canada
| | | | | | - Ehsan Mostafavi
- Epidemiology Department, Pasteur Institute of Iran, Tehran, Iran
- Emerging and Reemerging Infectious Diseases Research Centre, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Farzaneh Zolala
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Akbar Haghdoost
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- * E-mail:
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Hser YI, Liang D, Lan YC, Vicknasingam BK, Chakrabarti A. Drug Abuse, HIV, and HCV in Asian Countries. J Neuroimmune Pharmacol 2016; 11:383-93. [PMID: 27000123 DOI: 10.1007/s11481-016-9665-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/10/2016] [Indexed: 02/07/2023]
Abstract
Drug abuse and co-occurring infections are associated with significant morbidity and mortality. Asian countries are particularly vulnerable to the deleterious consequences of these risks/problems, as they have some of the highest rates of these diseases. This review describes drug abuse, HIV, and hepatitis C (HCV) in Asian countries. The most commonly used illicit drugs include opioids, amphetamine-type stimulants (ATS), cannabis, and ketamine. Among people who inject drugs, HIV rates range from 6.3 % in China to 19 % in Malaysia, and HCV ranges from 41 % in India and Taiwan to 74 % in Vietnam. In the face of the HIV epidemics, drug policies in these countries are slowly changing from the traditional punitive approach (e.g., incarcerating drug users or requiring registration as a drug user) to embrace public health approaches, including, for example, community-based treatment options as well as harm reduction approaches to reduce needle sharing and thus HIV transmission. HIV and HCV molecular epidemiology indicates limited geographic diffusion. While the HIV prevalence is declining in all five countries, use of new drugs (e.g., ATS, ketamine) continues to increase, as well as high-risk sexual behaviors associated with drug use-increasing the risk of sexual transmission of HIV, particularly among men who have sex with men. Screening, early intervention, and continued scaling up of therapeutic options (drug treatment and recovery support, ART, long-term HIV and HCV care for drug users) are critical for effective control or continued reduction of drug abuse and co-infections.
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Affiliation(s)
- Yih-Ing Hser
- University of California, Los Angeles, Los Angeles, CA, USA. .,China Medical University, Taichung City, Taiwan.
| | - Di Liang
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Amit Chakrabarti
- Regional Occupational Health Centre (ROHC), Eastern, National Institute of Occupational Health, Ahmedabad, Gujarat, India
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Geographic origin and evolutionary history of China's two predominant HIV-1 circulating recombinant forms, CRF07_BC and CRF08_BC. Sci Rep 2016; 6:19279. [PMID: 26763952 PMCID: PMC4725877 DOI: 10.1038/srep19279] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/09/2015] [Indexed: 11/08/2022] Open
Abstract
To determine the origin and evolutionary history of two predominant and closely-related circulating recombinant forms (CRF07_BC and CRF08_BC), recombinant structures and phylogenies of 7 unique recombinant forms comprised of subtypes of B’ (Thai B linage) and C (designated URFs_BC) from archival specimens of injection drug users (IDUs) collected in 1996 to 1998 from western Yunnan and 4 circulating recombinant forms with B’/C recombinants recently identified (designated nCRFs_BC) in China were compared with those of CRF07_BC and CRF08_BC. The results showed that 5 of 7 URFs_BC and all the nCRFs_BC shared recombination breakpoints with CRF07_BC and/or CRF08_BC. Yunnan URFs_BC consistently occupied the basal branch positions compared with CRF07_BC, CRF08_BC, and nCRFs_BC in phylogenetic trees. The estimated most recent common ancestors (tMRCA) for Yunnan URFs_BC were from ~1987, approximately half a decade earlier than those for CRF07_BC (~1994) and CRF08_BC (~1992). Discrete phylogeographic and spatial diffusion analysis revealed that both CRF07_BC and CRF08 BC came from western Yunnan in the early 1990s. Our results provide compelling evidence for western Yunnan as the geographic origin of CRF07_BC and CRF08_BC, which emerged from a swarm of URFs_BC by a series of recombination events in western Yunnan in the early 1990s.
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Chen M, Ma Y, Chen H, Luo H, Dai J, Song L, Yang C, Mei J, Yang L, Dong L, Jia M, Lu L. Multiple Introduction and Naturally Occuring Drug Resistance of HCV among HIV-Infected Intravenous Drug Users in Yunnan: An Origin of China's HIV/HCV Epidemics. PLoS One 2015; 10:e0142543. [PMID: 26562015 PMCID: PMC4642981 DOI: 10.1371/journal.pone.0142543] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/25/2015] [Indexed: 02/07/2023] Open
Abstract
Background The human immunodeficiency virus 1 (HIV-1) epidemic in China historically stemmed from intravenous drug users (IDUs) in Yunnan. Due to a shared transmission route, hepatitis C virus (HCV)/HIV-1 co-infection is common. Here, we investigated HCV genetic characteristics and baseline drug resistance among HIV-infected IDUs in Yunnan. Methods Blood samples of 432 HIV-1/HCV co-infected IDUs were collected from January to June 2014 in six prefectures of Yunnan Province. Partial E1E2 and NS5B genes were sequenced. Phylogenetic, evolutionary and genotypic drug resistance analyses were performed. Results Among the 293 specimens successfully genotyped, seven subtypes were identified, including subtypes 3b (37.9%, 111/293), 3a (21.8%, 64/293), 6n (14.0%, 41/293), 1b (10.6%, 31/293), 1a (8.2%, 24/293), 6a (5.1%, 15/293) and 6u (2.4%, 7/293). The distribution of HCV subtypes was mostly related to geographic location. Subtypes 3b, 3a, and 6n were detected in all six prefectures, however, the other four subtypes were detected only in parts of the six prefectures. Phylogeographic analyses indicated that 6n, 1a and 6u originated in the western prefecture (Dehong) and spread eastward and showed genetic relatedness with those detected in Burmese. However, 6a originated in the southeast prefectures (Honghe and Wenshan) bordering Vietnam and was transmitted westward. These subtypes exhibited different evolutionary rates (between 4.35×10−4 and 2.38×10−3 substitutions site-1 year-1) and times of most recent common ancestor (tMRCA, between 1790.3 and 1994.6), suggesting that HCV was multiply introduced into Yunnan. Naturally occurring resistance-associated mutations (C316N, A421V, C445F, I482L, V494A, and V499A) to NS5B polymerase inhibitors were detected in direct-acting antivirals (DAAs)-naïve IDUs. Conclusion This work reveals the temporal-spatial distribution of HCV subtypes and baseline HCV drug resistance among HIV-infected IDUs in Yunnan. The findings enhance our understanding of the characteristics and evolution of HCV in IDUs and are valuable for developing HCV prevention and management strategies for this population.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijun Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jingyuan Mei
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- * E-mail: (MJ); (LL)
| | - Lin Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, 650500, China
- * E-mail: (MJ); (LL)
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Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Hubei, Central China. PLoS One 2015; 10:e0137059. [PMID: 26325070 PMCID: PMC4556612 DOI: 10.1371/journal.pone.0137059] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 08/12/2015] [Indexed: 12/20/2022] Open
Abstract
Background Little is known about the molecular epidemiology of hepatitis C virus (HCV) infection in Central China. Methodology/Principal Findings A total of 570 patients from Hubei Province in central China were enrolled. These patients were tested positive for HCV antibody prior to blood transfusion. Among them, 177 were characterized by partial NS5B and/or Core-E1 sequences and classified into five subtypes: 1b, 83.0% (147/177); 2a, 13.0% (23/177); 3b, 2.3% (4/177); 6a, 1.1% (2/177); 3a, 0.6% (1/177). Analysis of genotype-associated risk factors revealed that paid blood donation and transfusion before 1997 were strongly associated with subtypes 1b and 2a, while some subtype 2a cases were also found in individuals with high risk sexual behaviors; subtypes 3b, 6a, and 3a were detected only in intravenous drug users. Phylogeographic analyses based on the coalescent datasets demonstrated that 1b, 2a, 3b, and 6a were locally epidemic in Hubei Province. Among them, subtype 1b Hubei strains may have served as the origins of this subtype in China, and 2a and 3b Hubei strains may have descended from the northwest and southwest of China, respectively, while 6a Hubei strains may have been imported from the central south and southwest. Conclusion/Significance The results suggest that the migration patterns of HCV in Hubei are complex and variable among different subtypes. Implementation of mandatory HCV screening before donation has significantly decreased the incidence of transfusion-associated HCV infection since 1997. More attention should be paid to intravenous drug use and unsafe sexual contact, which may have become new risk factors for HCV infection in Hubei Province.
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Li L, Wei D, Hsu WL, Li T, Gui T, Wood C, Liu Y, Li H, Bao Z, Liu S, Wang X, Li J. CRF07_BC Strain Dominates the HIV-1 Epidemic in Injection Drug Users in Liangshan Prefecture of Sichuan, China. AIDS Res Hum Retroviruses 2015; 31:479-87. [PMID: 25560398 DOI: 10.1089/aid.2014.0120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The Liangshan prefecture in Sichuan province is an area in China severely affected by the HIV epidemic, with intravenous drug use (IDU) as the main risk factor. No reports on HIV subtypes prevalent in IDUs in Liangshan prefecture could be found. In this study, we have characterized the genotypes of HIV-1 in the IDU population in Liangshan prefecture and further determined the phylogenetic relationship of the CRF07_BC strains to HIV-1 sequences from the other regions of China, including Xinjiang and Yunnan provinces, to explore the pattern and possible diffusion pathway of HIV-1 in these regions. HIV-1-seropositive drug-naive IDUs identified in Liangshan prefecture, Sichuan province were enrolled in 2009. Full-length gag and pol genes were amplified by reverse transcription and nested PCR and then sequenced. All of the sequences were subtyped. Phylogenetic trees were constructed using the neighbor-joining and maximum likelihood methods. Divergence times were estimated using a Bayesian molecular clock approach. CRF07_BC was found to be the predominant strain in IDUs in Liangshan prefecture (95.5%). The CRF07_BC strains from Liangshan prefecture were found to be intermixed with those from Yunnan province in phylogenetic trees. The CRF07_BC sequences from Xinjiang province can be grouped into several clusters, suggesting that the expansion of the CRF07_BC epidemic in Xinjiang province was the result of a local epidemic driven by multiple independent introductions in the late 1990s. Only low-level drug-resistant viruses were found in the IDU population. CRF07_BC strains from Liangshan prefecture were more similar to those from Yunnan province than those from Xinjiang province. This finding will contribute to our understanding of the distribution, the evolution, and the potential source of CRF07_BC founder strains, and will also provide useful information for the development of strategies to prevent transmission.
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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
| | - Daying Wei
- Liangshan Center for Disease Control and Prevention, Xichang, Sichuan, China
| | - Wan-Ling Hsu
- Nebraska Center for Virology, School of Biological Sciences and Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Charles Wood
- Nebraska Center for Virology, School of Biological Sciences and Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - 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
| | - Zuoyi Bao
- 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
| | - 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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Migration patterns of hepatitis C virus in China characterized for five major subtypes based on samples from 411 volunteer blood donors from 17 provinces and municipalities. J Virol 2014; 88:7120-9. [PMID: 24719413 DOI: 10.1128/jvi.00414-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED We investigated the migration patterns of hepatitis C virus (HCV) in China. Partial E1 and/or NS5B sequences from 411 volunteer blood donors sampled in 17 provinces and municipalities located in five large regions, the north-northeast, northwest, southwest, central south, and southeast, were characterized. The sequences were classified into eight subtypes (1a, n = 3; 1b, n = 183; 2a, n = 83; 3a, n = 30; 3b, n = 44; 6a, n = 55; 6n, n = 10; 6v, n = 1) and a new subtype candidate. Bayesian evolutionary analysis by sampling trees of the E1 sequences of the five major subtypes revealed distinct migration patterns. Subtype 1b showed four groups: one is prevalent nationwide with possible origins in the north-northeast; two are locally epidemic in the central south and northwest, respectively, and have spread sporadically to other regions; and the fourth one is likely linked to the long-distance dispersion among intravenous drug users from the northwest. Subtype 2a showed two groups: the larger one was mainly restricted to the northwest and seemed to show a trend toward migration via the Silk Road; the smaller one was geographically mixed and may represent descendants of those that spread widely during the contaminated plasma campaign in the 1990s. Subtype 3a exhibited three well-separated geographic groups that may be epidemically unrelated: one showed origins in the northwest, one showed origins in the southwest, and the other showed origins in the central south. In contrast, subtype 3b had a mixture of geographic origins, suggesting migrations from the southwest to the northwest and sporadically to other regions. Structurally resembling the tree for subtype 3a, the tree for subtype 6a showed four groups that may indicate migrations from the central south to southeast, southwest, and northwest. Strikingly, no subtype 6a strain was identified in the north-northeast. IMPORTANCE With a population of greater than 1.3 billion and a territory of >9.6 million square kilometers, China has a total of 34 provinces and municipalities. In such a vast country, the epidemic history and migration trends of HCV are thought to be unique and complex but variable among regions and are unlikely to be represented by those observed in only one or at best a few provinces and municipalities. However, due to the difficulties in recruiting patients, all previous studies for this purpose have been based only on data from limited regions, and therefore, geographical biases were unavoidable. In this study, such biases were greatly reduced because we utilized samples collected from volunteer blood donors in 17 provinces and municipalities. To our knowledge, this is the first study in which the HCV isolates represented such a large portion of the country, and thus, the results should shed light on the current understanding of HCV molecular epidemiology.
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Cao Y, Minhas V, Tan X, Huang J, Wang B, Zhu M, Gao Y, Zhao T, Yang L, Wood C. High prevalence of early childhood infection by Kaposi's sarcoma-associated herpesvirus in a minority population in China. Clin Microbiol Infect 2013; 20:475-81. [PMID: 23992104 DOI: 10.1111/1469-0691.12340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/06/2013] [Accepted: 07/14/2013] [Indexed: 11/30/2022]
Abstract
In China, KSHV seroprevalence varies considerably among different regions and ethnicities. But in Xinjiang province, located in the northwestern China, there is a very high seroprevalence of KSHV in adults of Kazak and Ughur ethnicities. However, KSHV prevalence in children and the risk factors associated with the acquisition of infection are currently not known. The aim of this study was to investigate the prevalence of KSHV infection and identify associated socioeconomic or behavioural risk factors and the humoral immune response among children in this population. This is a cross-sectional study (N = 178) to screen children and their caregivers from Xinjiang for total KSHV antibodies, KSHV neutralizing antibodies and HIV infection. Structured questionnaires were utilized to investigate risk factors associated with KSHV prevalence. KSHV seroprevalence in children and caregivers in Xinjiang was 48.3% and 64.7%, respectively. Neutralizing antibody was detected in most seropositive caregivers (93.8%) but was detected in only 5.8% of the infected children. A significant association was observed between child KSHV seroprevalence and sharing of food among family members. These results suggest that similar to other endemic areas in Africa, KSHV infection in the minority populations of Xinjiang is likely to be occurring during early childhood, probably via horizontal transmission through saliva, and results in high seroprevalence in the adult population.
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Affiliation(s)
- Y Cao
- Nebraska Center for Virology and the School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA; Hangzhou Normal University, Hangzhou, China
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Inference of global HIV-1 sequence patterns and preliminary feature analysis. Virol Sin 2013; 28:228-38. [PMID: 23913180 DOI: 10.1007/s12250-013-3348-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from nonsoutheastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.
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Qi H, Zhao K, Xu F, Zhang X, Zhang Z, Yang L, Li C, Liang X, Guo W, Chen S, Liu Z, Zhang W, Yu XF. HIV-1 diversity, drug-resistant mutations, and viral evolution among high-risk individuals in phase II HIV vaccine trial sites in southern China. PLoS One 2013; 8:e68656. [PMID: 23869225 PMCID: PMC3711821 DOI: 10.1371/journal.pone.0068656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 06/03/2013] [Indexed: 11/21/2022] Open
Abstract
HIV-1 prevalence in Guangxi, China, has been growing since 1996, when the first case was reported. Over half of HIV-1 positive patients in Guangxi Province were injecting drug users (IDUs), possibly because of the province’s location near drug-trafficking routes. Since a phase II HIV vaccine trial is ongoing there, a current characterization of the subtypes of HIV-1 among IDUs in Guangxi would provide critical information for future HIV vaccine trials, as well as further control and prevention of HIV-1 transmission. Thus, we conducted a molecular epidemiological investigation of HIV-1 samples from 2008–2010 among IDUs in multiple cities in Guangxi Province. Our results, based on the gag/pol fragment, indicated a very high proportion (78.47%) of HIV-1 CRF08_BC recombinants, some CRF01_AE (15.38%) recombinants, and a low proportion of CRF07_BC (6.15%) recombinants among the IDUs. The high proportion of CRF08 HIV-1 strains among recent IDUs matches the vaccine candidate constructs. However, future vaccine development should also incorporate CRF01-targeted vaccine candidates. Distinct Env sequence evolution patterns were observed for CRF08_BC and CRF01_AE, indicating that different local selection pressures have been exerted on these two HIV-1 subtypes. Unique drug-resistant mutations were also detected, and our data indicate that HIV treatment programs should consider pre-existing drug-resistant mutations.
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Affiliation(s)
- Haiyan Qi
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Fei Xu
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuzhao Zhang
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiyong Zhang
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Li Yang
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Chunling Li
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xu Liang
- Centers for Disease Control and Prevention, Baise, Guangxi, China
| | - Weigui Guo
- Centers for Disease Control and Prevention, Beihai, Guangxi, China
| | - Shihai Chen
- Centers for Disease Control and Prevention, Nanning, Guangxi, China
| | - Zhihao Liu
- Centers for Disease Control and Prevention, Baise, Guangxi, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiao-Fang Yu
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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Akkarathamrongsin S, Hacharoen P, Tangkijvanich P, Theamboonlers A, Tanaka Y, Mizokami M, Poovorawan Y. Molecular epidemiology and genetic history of hepatitis C virus subtype 3a infection in Thailand. Intervirology 2013; 56:284-294. [PMID: 23838334 DOI: 10.1159/000351621] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 04/22/2013] [Indexed: 10/10/2023] Open
Abstract
OBJECTIVE Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. METHODS Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. RESULTS Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. CONCLUSION The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
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Affiliation(s)
- S Akkarathamrongsin
- Inter-Department of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
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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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Sun Y, Meng S. Evolutionary history and spatiotemporal dynamics of dengue virus type 1 in Asia. INFECTION GENETICS AND EVOLUTION 2013; 16:19-26. [PMID: 23395769 DOI: 10.1016/j.meegid.2013.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 01/07/2013] [Accepted: 01/12/2013] [Indexed: 12/27/2022]
Abstract
Previous studies showed that DENV-1 transmitted from monkeys to humans approximately 125 years ago. However, there is no comprehensive analysis about phylogeography and population dynamics of Asian DENV-1. Here, we adopt a Bayesian phylogeographic approach to investigate the evolutionary history and phylogeography of Asian DENV-1 using envelope (E) protein gene sequences of 450 viruses isolated from 1954 to 2010 throughout 18 Asian countries and regions. Bayesian phylogeographic analyses indicate that the high rates of viral migration possibly follows long-distance travel for humans in Southeast Asia. Our study highlights that Southeast Asian countries have acted as the main viral sources of the dengue epidemics in East Asia. The results reveal that the time to the most recent common ancestor (TMRCA) of Asian DENV-1 is 1906 (95% HPD, years 1897-1915). We show that the spatial dissemination of virus is the major source of DENV-1 outbreaks in the different localities and leads to subsequent establishment and expansion of the virus in these areas.
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Affiliation(s)
- Yan Sun
- Department of Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China.
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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: 55] [Impact Index Per Article: 5.0] [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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Meng Z, Xin R, Zhong P, Zhang C, Abubakar YF, Li J, Liu W, Zhang X, Xu J. A new migration map of HIV-1 CRF07_BC in China: analysis of sequences from 12 provinces over a decade. PLoS One 2012; 7:e52373. [PMID: 23300654 PMCID: PMC3530601 DOI: 10.1371/journal.pone.0052373] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND As one of prevalence HIV-1 strains in IDUs in Asia, the origination and full transmission map of CRF07_BC is of great interested and remains unclear. In the study, we collected 769 CRF07_BC derived sequences (including 45 sequences generated in our laboratory) from 12 provinces in China for reconstructing transmission map. Meanwhile, ample historic epidemic evidences were also reviewed to assist sequences analysis. METHODOLOGY/PRINCIPAL FINDINGS In the study, we collected 769 CRF07_BC derived sequences and identified 138 independent sequences from 12 provinces in China for subsequent phylogeographic tree analysis, Bayes Factor test and the estimation of state tMRCA. The analyses demonstrated that CRF07_BC was originated in 1993 in IDU in Yunnan province and then initially spread to Guangxi (eastern neighbor to Yunnan) in 1994, to Xinjiang (northwest) in 1995 and to Sichuan (northern neighbor to Yunnan) in 1996. The subsequent transmissions occurred from Yunnan to Liaoning (northeast) in 1997 and to Jiangsu in 1998. Interestingly, after the early introduction of CRF07_BC into Guangxi, Xinjiang and Sichuan, these three regions served as secondary epicenters for further spreading into Gansu, Ningxia, Qinghai, Beijing and Hunan during 1999-2001. These analyzed results are in accordance with early epidemic investigations. CONCLUSIONS/SIGNIFICANCE Our data not just reconstructed the migration map of CRF07_BC, but also firstly revealed the active roles of these secondary epicenters in the dynamic migration of CRF07_BC in China.
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Affiliation(s)
- Zhefeng Meng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruolei Xin
- Department of AIDS/STD, Beijing Centers for Disease Control and Prevention, Beijing, China
| | - Ping Zhong
- Department of AIDS/STD, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai, China
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yassir F. Abubakar
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingyun Li
- Institute of Microbiology Epidemiology, Academy of Military Medical Science, Beijing, China
| | - Wei Liu
- Guangxi Provincial Center for Disease Control and Prevention, Nanning, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- * E-mail: (JX); (XZ)
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health at Shanghai Medical College, Fudan University, Shanghai, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- * E-mail: (JX); (XZ)
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Chen S, Cai W, He J, Vidal N, Lai C, Guo W, He H, Chen X, Fu L, Peeters M, Delaporte E, Andrieu JM, Lu W. Molecular epidemiology of human immunodeficiency virus type 1 in Guangdong province of southern China. PLoS One 2012; 7:e48747. [PMID: 23144953 PMCID: PMC3492446 DOI: 10.1371/journal.pone.0048747] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/01/2012] [Indexed: 11/29/2022] Open
Abstract
Background Although the outbreak of human immunodeficiency virus type 1 (HIV-1) in Guangdong has been documented for more than a decade, the molecular characteristics of such a regional HIV-1 epidemic remained unknown. Methodology/Principal Findings By sequencing of HIV-1 pol/env genes and phylogenetic analysis, we performed a molecular epidemiologic study in a representative subset (n = 200) of the 508 HIV-1-seropositive individuals followed up at the center for HIV/AIDS care and treatment of Guangzhou Hospital of Infectious Diseases. Of 157 samples (54.1% heterosexual acquired adults, 20.4% needle-sharing drug users, 5.7% receivers of blood transfusion, 1.3% men who have sex with men, and 18.5% remained unknown) with successful sequencing for both pol and env genes, 105 (66.9%) HIV-1 subtype CRF01_AE and 24 (15.3%) CRF07_BC, 9 (5.7%) B’, 5 (3.2%) CRF08_BC, 5 (3.2%) B, 1 (0.6%) C, 3 (1.9%) CRF02_AG, and 5 (3.2%) inter-region recombinants were identified within pol/env sequences. Thirteen (8.3%) samples (3 naïves, 6 and 5 received with antiretroviral treatment [ART] 1–21 weeks and ≥24 weeks respectively) showed mutations conferring resistance to nucleoside/nonnucleoside reverse transcriptase inhibitors or protease inhibitors. Among 63 ART-naïve patients, 3 (4.8%) showed single or multiple drug resistant mutations. Phylogenetic analysis showed 8 small clusters (2–3 sequences/cluster) with only 17 (10.8%) sequences involved. Conclusion/Significance This study confirms that sexual transmission with dominant CRF01_AE strain is a major risk for current HIV-1 outbreak in the Guangdong’s general population. The transmission with drug-resistant variants is starting to emerge in this region.
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Affiliation(s)
- Song Chen
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- Laboratoire d’Oncologie et Virologie Moléculaire, Université Paris Descartes, Paris, France
| | - Weiping Cai
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Jingyang He
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Nicole Vidal
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Chunhui Lai
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weizhong Guo
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haolan He
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Xiejie Chen
- Guangzhou Hospital of Infectious Diseases, Guangzhou, China
| | - Linsheng Fu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Martine Peeters
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Eric Delaporte
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
| | - Jean-Marie Andrieu
- Laboratoire d’Oncologie et Virologie Moléculaire, Université Paris Descartes, Paris, France
| | - Wei Lu
- Sino-French Collaborative Laboratory, Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
- UMI 233, Institut de Recherche pour le Développement and Université de Monpellier 1, Monpellier, France
- * E-mail:
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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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Extensive and complex HIV-1 recombination between B', C and CRF01_AE among IDUs in south-east Asia. AIDS 2012; 26:1121-9. [PMID: 22333750 DOI: 10.1097/qad.0b013e3283522c97] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
OBJECTIVE To investigate the subtype characterization of HIV-1 among IDUs in northern Myanmar. DESIGN A molecular epidemiological investigation was conducted among IDUs in Laza and Maizayang cities of northern Myanmar. METHODS A total of 83 HIV-1-positive serums were collected from consenting IDUs during June to August 2009. HIV-1 p17, pol, vif-env, C2V3 fragments were amplified and sequenced. Phylogenetic and bootscanning analyses were performed. RESULTS A very high proportion (86.1%) of HIV-1 intersubtype recombinants and very low proportion of subtypes B' (3.8%), C (7.6%) and CRF01_AE (1.3%) were found in this HIV-infected IDUs cohort. These recombinants cover all four kinds of recombination forms formed among CRF01_AE, B and C. The B/C and CRF01_AE/B/C recombinants are the two most dominant recombinants, accounting for 54.4 and 42.6% of all cases, respectively, and indicating the ongoing generation of extensive and complex HIV-1 recombination among CRF01_AE, B' and C in northern Myanmar. Intriguingly, most recombinants have different chimeric patterns from each other, forming 64 unique recombination forms (URFs) that are quite distinct from any previously identified circulating recombinant forms (CRFs) and URFs in Asia. CONCLUSION The extremely high proportion of intersubtype recombinants, especially CRF01_AE/B'/C recombinants (42.6%), strongly suggests that northern Myanmar is a big forge for HIV-1 recombination among CRF01_AE, B' and C.
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Complex patterns of HCV epidemic in Suzhou: evidence for dual infection and HCV recombination in East China. J Clin Virol 2012; 54:207-12. [PMID: 22595306 DOI: 10.1016/j.jcv.2012.04.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/24/2012] [Accepted: 04/18/2012] [Indexed: 01/22/2023]
Abstract
BACKGROUND HCV transmission is closely associated with injection drug use (IDU), and co-circulation of multiple subtypes has been found among injection drug users (IDUs) in China. OBJECTIVES To investigate HCV subtype characterizations among IDUs and general population (GP) in Suzhou, a city at the important "Hu-ning" transportation line. STUDY DESIGN During January 2010 to May 2011, 123 HCV positive plasma from IDUs and 131 stored HCV positive sera from general individuals were collected in Suzhou. HCV C/E2 and NS5B fragments were amplified using a new multiple RT-nested PCR strategy and subsequent sequenced. Genotypes were characterized by phylogenetic analyses. RESULTS Eight HCV subtypes (1a, 1b, 2a, 3a, 3b, 6a, 6n, and 6u) were detected among Suzhou IDUs, and six subtypes (1b, 2a, 3a, 3b, 6a and 6n) among GP. HCV subtype distribution is distinct between IDUs and GP. Interestingly, we detected discrepancy of genotyping results between C/E2 and NS5B regions in one general individual, indicating the presence of HCV intersubtype recombinant in China. The recombinant belongs to a 3a/1b recombinant. We also detected dual infections in one general individual and two IDUs. They include dual infections between 1b and 3a, 3a and 6a, and two distinct lineages of 3b. CONCLUSIONS Complex patterns of HCV epidemic among IDUs, as well as GP, in Suzhou, might imply a spread of HCV from IDUs to GP. The finding of one HCV 3a/1b intersubtype recombinant might represent the first report of HCV recombination in China.
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Tee KK, Kamarulzaman A, Matano T, Takebe Y. Phylodynamic inference of infectious diseases caused by HIV, enterovirus 71 and the 2009 swine-origin human influenza virus. Future Virol 2012. [DOI: 10.2217/fvl.12.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rapidly evolving nature of viruses, particularly RNA viruses, exhibit complex phylodynamic behaviors, accumulating mutations across the genome on a timescale observable by humans. Phylodynamic investigations provide unique and quantitative evolutionary data on the origin, progression in terms of time and space, and epidemic and transmission history of pathogens. This review describes recent phylodynamic conjectures on three distinct categories of human viruses, including HIV, enterovirus 71 and the swine-origin pandemic influenza virus H1N1, which are of enormous importance to public health.
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Affiliation(s)
- Kok Keng Tee
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yutaka Takebe
- Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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