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Bai C, Tan T, Li L, Lu R, Zhang W, Ouyang L, Wu G, Zhou C. Molecular network characteristics and drug resistance analysis of 392 newly reported MSM HIV/AIDS cases in Chongqing, China. Front Public Health 2024; 12:1308784. [PMID: 38903589 PMCID: PMC11187242 DOI: 10.3389/fpubh.2024.1308784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
To comprehensively investigate the molecular transmission patterns of HIV-1 genotypes among men who have sex with men (MSM) in Chongqing, we employed 392 pol sequences of MSM to construct a phylogenetic tree and gene transmission network. Among the viral subtypes, CRF07_BC accounted for 73.2% (287/392) and CRF01_AE accounted for 20.7% (81/392), emerging as the predominant subtypes in this investigation. Additionally, we observed the presence of CRF55_01B, subtype B, CRF08_BC and other circulating recombinant forms. The HIV-1 molecular network was constructed with a gene distance threshold of 1.5%, resulting in an entry rate of 61.4% (241/392). Within the network, we identified a total of 23 molecular clusters, with the largest cluster being the CRF07_BC molecular cluster comprising 148 node values. Transmitted drug-resistance (TDR) mutations were found in 4.34% of the cases, with 1.79% associated with protease inhibitors (PIs), 0.51% with nucleoside reverse transcriptase inhibitors (NRTIs), and 2.55% with non-nucleoside reverse transcriptase inhibitors (NNRTIs). Statistical analysis indicated a higher enrollment rate in the HIV-1 molecular network among infected individuals with the CRF07_BC subtype, those identifying with same-sex sexual roles as "vers," and individuals with higher education levels. This suggests the need for strengthened investigation and intervention in this population to prevent the formation of larger transmission clusters. Furthermore, continuous monitoring of the HIV-1 molecular dynamics network is necessary to promptly and accurately track changes in molecular epidemic characteristics.
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Affiliation(s)
| | | | | | | | | | | | - Guohui Wu
- Chongqing Center for Disease Control and Prevention, Chongqing, China
| | - Chao Zhou
- Chongqing Center for Disease Control and Prevention, Chongqing, China
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Tan T, Bai C, Lu R, Chen F, Li L, Zhou C, Xiang X, Zhang W, Ouyang L, Xu J, Tang H, Wu G. HIV-1 molecular transmission network and drug resistance in Chongqing, China, among men who have sex with men (2018-2021). Virol J 2023; 20:147. [PMID: 37443039 PMCID: PMC10339625 DOI: 10.1186/s12985-023-02112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Over the past few years, HIV transmission among men who have sex with men (MSM) in China has increased significantly. Chongqing, located in the southwest of China, has the highest prevalence of HIV among MSM in the country. METHODS Blood samples were taken from 894 MSM in Chongqing who had recently been diagnosed with HIV-1 infection and had not yet started getting treatment. In order to determine the distribution of HIV-1 subtypes, transmitted drug resistance, and assessments of molecularly transmitted clusters, we sequenced the Pol genes and employed them in phylogenetic analysis. The genetic distance between molecular clusters was 1.5%. To find potential contributing factors, logistic regression analyses were performed. RESULTS Of the 894 HIV-1 pol sequences acquired from study participants, we discovered that CRF07_BC (73.6%) and CRF01_AE (19.6%) were the two most prevalent HIV-1 genotypes in Chongqing among MSM, accounting for 93.2% of all infections. In addition, CRF08_BC (1.1%), B subtype (1.0%), CRF55_01B (3.4%), and URF/Other subtypes (1.3%) were less frequently observed. Among MSM in Chongqing, transmitted drug resistance (TDR) was reported to be present at a rate of 5.6%. 48 clusters with 600 (67.1%, 600/894) sequences were found by analysis of the molecular transmission network. The distributions of people by age, sexual orientation, syphilis, and genotype were significantly differentially related to being in clusters, according to the multivariable logistic regression model. CONCLUSION Despite the low overall prevalence of TDR, the significance of genotypic drug resistance monitoring needs to be emphasized. CRF07_BC and CRF01_AE were the two main genotypes that created intricate molecular transmission networks. In order to prevent the expansion of molecular networks and stop the virus's spread among MSM in Chongqing, more effective HIV intervention plans should be introduced.
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Affiliation(s)
- Tianyu Tan
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Chongyang Bai
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Rongrong Lu
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Fangfang Chen
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Long Li
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Chao Zhou
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Xu Xiang
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Wei Zhang
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Ling Ouyang
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Jing Xu
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China
| | - Houlin Tang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Guohui Wu
- Chongqing Center for Disease Control and Prevention, 400042, Chongqing, China.
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Pan W, Gao N, Hu B, Yin Y, Shen Y, Yang X, Wei W, Ni J, Dai S, Miao L, Qin Y, Jin L, Guo H, Wu J. The characteristics of HIV-1 subtype B on phylogenetic dynamic and molecular transmission network in Fuyang City, China, 2011 to 2019. Front Public Health 2023; 11:1092376. [PMID: 36935727 PMCID: PMC10015982 DOI: 10.3389/fpubh.2023.1092376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction HIV-1 subtype B, as once one of the earliest strains introduced into mainland China rapidly spread in commercial plasma donors and heterosexuals in 1990s. Here, we aim to investigate the origin and evolutionary history of HIV-1 subtype B in Fuyang city, China. Methods We collected sequences tested from Fuyang in the east of China where higher prevalence of HIV-1 among commercial plasma donors and heterosexuals to construct a phylogenetic tree using the Markov chain Monte Carlo (MCMC) algorithm, infer molecular transmission network using TN93 model and visualize it with Cytoscape software. Results and discussion Our results showed that >99% of subtype B sequences belonged to Thai B. The sequences from Fuyang often cluster closer to those from other its adjacent cities, which clustered together and formed a monophyletic cluster. HIV-1 B circulating in Fuyang dates back to approximately 1990. Among the 1,437 sequences, 166 clustered at a genetic distance of ≤1.2%, resulting in 73 clusters. The degree of clustering with at least one other person was 11.55%. Among the transmission clusters, 50 (80.65%) comprised two individuals. Most clusters consisted of both heterosexual transmission routes and men who have sex with men. Phylogenetic and molecular network analyses revealed a common origin with neighboring regions in mainland China, local onwards transmission after its introduction, and a limited clustering degree. However, at least two co-existing transmission routes in most transmission clusters imply a greater challenge in controlling the spread of HIV-1. Our findings highlight the value on tailoring prevention interventions by combination of molecular surveillance and epidemiology.
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Affiliation(s)
- Wenting Pan
- Anhui No. 2 Provincial People's Hospital, Hefei, China
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
| | - Nannan Gao
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
| | - Bing Hu
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Yueqi Yin
- School of Medicine, Ningbo University, Ningbo, China
| | - Yuelan Shen
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Xiaohui Yang
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Wei Wei
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Jie Ni
- Department of AIDS Prevention and Control, Fuyang Center for Disease Control and Prevention, Fuyang, China
| | - Seying Dai
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Lifeng Miao
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yizu Qin
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Lin Jin
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hongxiong Guo
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
- *Correspondence: Hongxiong Guo
| | - Jianjun Wu
- Department of Health Inspection and Quarantine, School of Public Health, Anhui Medical University, Hefei, China
- Department of AIDS Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Jianjun Wu
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Application of Bayesian networks to identify factors influencing acceptability of HIV pre-exposure prophylaxis in Guilin, China. Sci Rep 2022; 12:20542. [PMID: 36446859 PMCID: PMC9707149 DOI: 10.1038/s41598-022-24965-1] [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: 03/29/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Pre-exposure prophylaxis (PrEP) is an effective strategy to prevent uninfected individuals from contracting human immunodeficiency virus (HIV), however it must be acceptable to stakeholders in order to be effective. This study aimed to assess the acceptability of PrEP and related influencing factors. A cross-sectional survey was conducted among female sex workers (FSW), people who inject drugs (PWID), and men who have sex with men (MSM) using respondent driven sampling. Factors influencing PrEP acceptability were estimated using ordinal logistic regression and Bayesian networks. The survey included 765 eligible participants. The mean score of the perceived acceptability index was 3.9 (SD = 1.97). Multivariable logistic regression analysis revealed a higher acceptance of PrEP was associated with elder age, having other medical insurance, higher perceived utility of PrEP in facilitating prevention of HIV, higher perceived ease of use, higher perceived risk of increased risk behavior, higher perceived privacy problem in using PrEP, higher perceived comparative advantage over condom use, higher perceived comparative advantage of having sex when the urge arises, and higher perceived image of PrEP user as having sexual risky behavior, as public-minded and as health-conscious. The Bayesian network model showed perceived ease of use, perceived image of user as health-conscious, and perceived comparative advantage of having sex when the urge arises were directly associated with acceptability of PrEP. If these three factors were at a high level, 74.6% of the participants would have a high level of acceptability of PrEP. Effective education strategies to promote the acceptance of PrEP are needed. Implementation strategies should incorporate more inclusive messaging and build positive publicity for PrEP to reduce the stigma that PrEP use indicates risky behavior.
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Li QH, Wang JY, Liu SY, Zhang YQ, Li EL, Wang YR, Zhang SL, Zhao WB, Liu SL, Chen XH, Wang FX. Young MSM changed temporal HIV-1 epidemic pattern in Heilongjiang Province, China. Front Microbiol 2022; 13:1028383. [PMID: 36504809 PMCID: PMC9732660 DOI: 10.3389/fmicb.2022.1028383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) epidemic in China is featured by geographical diversity of epidemic patterns. Understanding the characteristics of regional HIV-1 epidemic allows carrying out targeted prevention and controlling measures. This seven-year cross-sectional study was conducted in Heilongjiang, one province of Northeast China, where newly diagnosed infection is fast increasing yearly, but temporal HIV-1 epidemic trend is largely unknown. Methods Information of 1,006 newly diagnosed HIV-1-infected participants were collected before antiretroviral therapy during 2010-2016 in Heilongjiang province. HIV-1 genotype was identified based on the viral gag and env gene sequences. Recent infection was determined by Limiting-Antigen Avidity assays. Comparison analyses on the median ages, CD4 counts, proportions of stratified age groups and CD4 count groups, and rates of recent HIV-1 infection among different population and sampling times were performed to understand temporal HIV-1 epidemic features. Results Homosexual contact among men who have sex with men (MSM) was the main transmission route and CRF01_AE was the most dominant HIV-1 genotype. During 2010-2016, the HIV-1 epidemic showed three new changes: the median age continued to decline, the cases with a CD4 count more than 500 cells/μl (CD4hi cases) disproportionally expanded, and the recent HIV-1 infection rate steadily increased. MSM cases determined the temporal trend of HIV-1 epidemic here. Increase of young MSM cases (aged <30 years) made the main contribution to the younger age trend of MSM cases. These young MSM exhibited a higher median CD4 count, a higher proportion of CD4hi cases, and a higher rate of recent HIV-1 infection than cases aged 30 years and more. MSM infected by CRF01_AE virus mostly affected HIV-1 epidemic patterns among MSM population. Conclusion Young MSM have become a new hotspot and vulnerable group for HIV-1 transmission in Heilongjiang Province, Northeast China. The rapid increase in the number of young MSM cases, mainly those with CRF01_AE infection, changed temporal HIV-1 epidemic pattern here. Measures for prevention and control of HIV-1 infection among this population are urgently needed in the future.
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Affiliation(s)
- Qing-Hai Li
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Si-Yu Liu
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yun-Qi Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - En-Long Li
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yi-Ru Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Shu-Lei Zhang
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Wen-Bo Zhao
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China,Shu-Lin Liu,
| | - Xiao-Hong Chen
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China,Xiao-Hong Chen,
| | - Fu-Xiang Wang
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China,Department of Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China,Department of Infectious Diseases, The Third People’s Hospital of Shenzhen, Shenzhen, China,*Correspondence: Fu-Xiang Wang,
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Zhang D, Wu J, Zhang Y, Shen Y, Dai S, Wang X, Xing H, Lin J, Han J, Li J, Qin Y, Liu Y, Miao L, Su B, Li H, Li L. Genetic characterization of HIV-1 epidemic in Anhui Province, China. Virol J 2020; 17:17. [PMID: 32014042 PMCID: PMC6998069 DOI: 10.1186/s12985-020-1281-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/13/2020] [Indexed: 11/13/2022] Open
Abstract
Background Anhui Province in China is facing a severe HIV epidemic with an increasing number of newly diagnosed cases. Methods In this study, HIV genetic characteristics in the province were investigated. Newly reported HIV-positive individuals from 15 districts of Anhui Province were enrolled and interviewed. Total viral RNA was extracted from plasma isolated from blood samples. We amplified and sequenced an HIV pol fragment of the 1062 bp. The sequences were used for determination of HIV subtypes and the presence of drug resistance mutations. Transmission networks were constructed to explore possible relationships. And all of assembled partial pol genes were submitted to the Stanford HIV Drug Resistance Database website to find the transmitted drug resistance. Results Partial pol gene sequences were obtained from 486 cases. The results showed that MSM was the most dominant transmission route (253, 52.06%), followed by heterosexual transmission (210, 43.21%) and blood-borne transmission (1, 0.21%). Many subtypes were identified, including CRF01_AE (226, 46.50%), CRF07_BC (151, 31.07%), subtype B (28, 5.76%), CRF08_BC (20, 4.12%), CRF55_01B (15, 3.09%), CRF68_01B (7, 1.44%), CRF67_01B (3, 0.62%), CRF57_BC (2, 0.41%), CRF59_01B (2, 0.41%), CRF79_0107 (2, 0.41%), subtype C (2, 0.41%), CRF64_BC (1, 0.21%), and circulating recombinant forms (URFs) (27, 5.55%). Four transmission subnetworks containing high transmission risk individuals (with degree ≥4) were identified based on CRF01_AE and CRF07_BC sequences, including two CRF01_AE transmission subnetworks constituted by elderly people with average ages of 67.9 and 61.5 years. Infection occurred most likely through heterosexual transmission, while the other two CRF07_BC transmission subnetworks consist mainly of MSMs with average ages of 31.73 and 34.15. The level of HIV-transmitted drug resistance is 3.09%. Conclusions The simultaneous spread of multiple HIV subtypes in Anhui province underscores that close surveillance of the local HIV epidemic is necessary. Furthermore, the elderly people were frequently involved, arguing for behaviour intervention in this specific population besides the MSM risk group.
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Affiliation(s)
- Dong Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Sheying Dai
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - 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, 102206, China
| | - Jin Lin
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yizu Qin
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Lifeng Miao
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China.
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
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Wu J, Hu Z, Yao H, Wang H, Lei Y, Zhong P, Feng Y, Xing H, Shen Y, Jin L, Liu A, Qin Y, Miao L, Su B, Zhang Y, Guo H. The inference of HIV-1 transmission direction between HIV-1 positive couples based on the sequences of HIV-1 quasi-species. BMC Infect Dis 2019; 19:566. [PMID: 31253127 PMCID: PMC6599307 DOI: 10.1186/s12879-019-4163-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 06/04/2019] [Indexed: 11/22/2022] Open
Abstract
Background To infer transmission direction of a HIV transmission chain is helpful not only in legal jurisdiction but also in precise intervention to prevent HIV spread. Recently, the direction of transmission is inferred by whether paraphyletic-monophyletic (PM) or a combination of paraphyletic and polyphyletic (PP) topologies is observed or not between the sequences of source and recipient in the phylogenetic tree. However, paraphyly between them often declines over time and may disappear between spouses due to bidirectional transmission after primary infection. In this study, our aim is to test the reliability of inferring HIV transmission direction between epidemiologically linked HIV-1 positive couples using whether or not paraphyly is observed in phylogenetic tree. Methods HIV quasi-species were sequenced using PCR product clones, and then Bayesian analysis of molecular sequences with MCMC was employed to construct phylogenetic relationship of env, gag, pol gene fragments of HIV-1 positive couples using BEAST software. Results Our results showed that all sequences of seven couples except pol sequences of couple 12 and 13 form their own monophyletic cluster in phylogenetic tree including the closest control sequences from GenBank or other studies on local samples, which are supported by significant Bayesian posterior probabilities more than 0.9932. Of seven couples, paraphyly is only observed in phylogenetic tree constructed with env and pol gene sequences of three couples and gag gene sequences of four couples. Paraphyly is not observed in half of HIV positive couples. Pol sequences of couple 13 is separated by Blast selected controls; pol sequences of couple 12 in phylogenetic tree is supported by a lower Bayesian posterior value. Conclusion Paraphyly relationship between sequences of donator and recipient is only observed among partial HIV-1 positive couples with epidemiological link. Phylogenetic relationship is not always the same when various gene regions of HIV are used to conduct phylogenetic analysis. The combination of phylogenetic analysis based on various gene regions of HIV and enough epidemiology investigation is essential when inferring transmission direction of HIV in a transmission chain or in one couple. However, while observed paraphyly can be used to infer transmission direction in HIV-1 positive couple, no observed paraphyly cannot deny it.
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Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Zhongwang Hu
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Hui Yao
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Hai Wang
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Yanhua Lei
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Ping Zhong
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan West Road, Shanghai, China
| | - Yi Feng
- Chinese Center for Disease Control and Prevention, 155 Changbei Road, Beijing, China
| | - Hui Xing
- Chinese Center for Disease Control and Prevention, 155 Changbei Road, Beijing, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Lin Jin
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Aiwen Liu
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Yizu Qin
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Lifeng Miao
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China.
| | - Yibo Zhang
- Department of Hospital Infection Control, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hongxiong Guo
- Jiangsu Provincial Center for Disease Control and Prevention, 172 Jiangsu Road, Nanjing, China.
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Chung YS, Choi JY, Yoo MS, Seong JH, Choi BS, Kang C. Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012. PLoS One 2019; 14:e0217817. [PMID: 31166970 PMCID: PMC6550428 DOI: 10.1371/journal.pone.0217817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/21/2019] [Indexed: 11/29/2022] Open
Abstract
Population-level phylogenetic patterns reflect both transmission dynamics and genetic changes, which accumulate because of selection or drift. In this study, we determined whether a longitudinally sampled dataset derived from human immunodeficiency virus (HIV)-1-infected individuals over a 14-year period (1999–2012) could shed light on the transmission processes involved in the initiation of the HIV-1 epidemic in Korea. In total, 927 sequences were acquired from 1999 to 2012; each sequence was acquired from an individual patient who had not received treatment. Sequences were used for drug resistance and phylogenetic analyses. Phylogenetic and other analyses were conducted using MEGA version 6.06 based on the GTR G+I parameter model and SAS. Of the 927 samples, 863 (93.1%) were classified as subtype B and 64 were classified as other subtypes. Phylogenetic analysis demonstrated that 104 of 927 patient samples (11.2%) were grouped into 37 clusters. Being part of a transmission cluster was significantly associated with subtype-B viruses, infection via sexual contact, and the infection of young males. Of all clusters, three (~8.1%) that comprised 10 individual samples (22.2% of 45 individuals) included at least one member with total transmitted drug resistance (TDR). In summary, HIV transmission cluster analyses can integrate laboratory data with behavioral data to enable the identification of key transmission patterns to develop tailored interventions aimed at interrupting transmission chains.
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Affiliation(s)
- Yoon-Seok Chung
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Ju-Yeon Choi
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Myoung-Su Yoo
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Jae Hyun Seong
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Byeong-Sun Choi
- Division of Viral Diseases Research, Center for Research of Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
| | - Chun Kang
- Division of Viral Diseases, Center for Laboratory Control and Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju, Republic of Korea
- * E-mail:
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Xiao P, Zhou Y, Lu J, Yan L, Xu X, Hu H, Li J, Ding P, Qiu T, Fu G, Huan X, Yang H. HIV-1 genotype diversity and distribution characteristics among heterosexually transmitted population in Jiangsu province, China. Virol J 2019; 16:51. [PMID: 31023323 PMCID: PMC6485170 DOI: 10.1186/s12985-019-1162-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/10/2019] [Indexed: 01/17/2023] Open
Abstract
Background Heterosexual transmission has contributed greatly to the current HIV-1 epidemic in China. However, the HIV-1 genetic characteristics in the heterosexually transmitted population in Jiangsu province remained unclear. Methods A molecular epidemiological investigation on heterosexual transmission of HIV-1 was conducted across Jiangsu province. 301 HIV-1 patients infected through heterosexual transmission were involved in this study. The epidemiological information was investigated by trained staff via face-to-face interviews. Blood samples were taken from each patient, HIV-1 RNA was extracted from the plasma, and used for amplifying the gag and env genes followed by further products sequencing. The genotypes of HIV-1 were determined using phylogenetic tree analyses in the neighbor-joining method. Results A total of 262 samples were successfully taken for genotyping. The main subtypes which accounted for 90.5% of all HIV-1 strains are CRF01_AE (45.4%), CRF07_BC (21.4%), subtype B (12.6%), CRF08_BC (11.1%). Minor subtypes were also detected, such as CRF68_01B, subtype C, CRF55_01B, CRF02_AG and subtype A. Time trend analysis suggested the prevalence of subtype B and CRF08_BC decreased gradually, but the prevalence of CRF01_AE increased over time. A relatively higher prevalence of CRF07_BC in Central Jiangsu and subtype B were detected in South Jiangsu, while a relatively lower prevalence of subtype B and CRF08_BC were detected in Central Jiangsu. Conclusion Complex and unbalanced HIV distribution characteristics suggest that heterosexual transmission of HIV needs to be taken seriously. It is necessary to implement more effective and comprehensive intervention strategies for further control of HIV-1 dissemination.
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Affiliation(s)
- Peipei Xiao
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China
| | - Ying Zhou
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Jing Lu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Li Yan
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China
| | - Xiaoqin Xu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Haiyang Hu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Jianjun Li
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Ping Ding
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Tao Qiu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Gengfeng Fu
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Xiping Huan
- Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China
| | - Haitao Yang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University
- , No.87 Dingjiaqiao, Nanjing, 210009, China. .,Department of HIV/STD Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, No.172 Jiangsu Road, Nanjing, 210009, China. .,Jiangsu Research Institute of Schistosomiasis Control, No.117 Meiyuan Yangxiang, Wuxi, 214064, China.
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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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