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Shi H, Li X, Wang S, Dong X, Qiao M, Wu S, Wu R, Yuan X, Wang J, Xu Y, Zhu Z. Molecular transmission network analysis of newly diagnosed HIV-1 infections in Nanjing from 2019 to 2021. BMC Infect Dis 2024; 24:583. [PMID: 38867161 PMCID: PMC11170874 DOI: 10.1186/s12879-024-09337-6] [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: 11/23/2023] [Accepted: 04/21/2024] [Indexed: 06/14/2024] Open
Abstract
OBJECTIVE The objective of this study was to conduct a comprehensive analysis of the molecular transmission networks and transmitted drug resistance (TDR) patterns among individuals newly diagnosed with HIV-1 in Nanjing. METHODS Plasma samples were collected from newly diagnosed HIV patients in Nanjing between 2019 and 2021. The HIV pol gene was amplified, and the resulting sequences were utilized for determining TDR, identifying viral subtypes, and constructing molecular transmission network. Logistic regression analyses were employed to investigate the epidemiological characteristics associated with molecular transmission clusters. RESULTS A total of 1161 HIV pol sequences were successfully extracted from newly diagnosed individuals, each accompanied by reliable epidemiologic information. The analysis revealed the presence of multiple HIV-1 subtypes, with CRF 07_BC (40.57%) and CRF01_AE (38.42%) being the most prevalent. Additionally, six other subtypes and unique recombinant forms (URFs) were identified. The prevalence of TDR among the newly diagnosed cases was 7.84% during the study period. Employing a genetic distance threshold of 1.50%, the construction of the molecular transmission network resulted in the identification of 137 clusters, encompassing 613 nodes, which accounted for approximately 52.80% of the cases. Multivariate analysis indicated that individuals within these clusters were more likely to be aged ≥ 60, unemployed, baseline CD4 cell count ≥ 200 cells/mm3, and infected with the CRF119_0107 (P < 0.05). Furthermore, the analysis of larger clusters revealed that individuals aged ≥ 60, peasants, those without TDR, and individuals infected with the CRF119_0107 were more likely to be part of these clusters. CONCLUSIONS This study revealed the high risk of local HIV transmission and high TDR prevalence in Nanjing, especially the rapid spread of CRF119_0107. It is crucial to implement targeted interventions for the molecular transmission clusters identified in this study to effectively control the HIV epidemic.
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Affiliation(s)
- Hongjie Shi
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Xin Li
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Sainan Wang
- Department of Laboratory Medicine, Jiangning Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xiaoxiao Dong
- Department of Microbiology Laboratory, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Mengkai Qiao
- Department of Microbiology Laboratory, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Sushu Wu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Rong Wu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Xin Yuan
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Jingwen Wang
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Yuanyuan Xu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China.
| | - Zhengping Zhu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China.
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Zhou Y, Lu J, Zhang Z, Sun Q, Xu X, Hu H. Characteristics of the different HIV-1 risk populations based on the genetic transmission network of the newly diagnosed HIV cases in Jiangsu, Eastern China. Heliyon 2023; 9:e22927. [PMID: 38125421 PMCID: PMC10730745 DOI: 10.1016/j.heliyon.2023.e22927] [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: 07/05/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The HIV-1 prevalence has been steadily increasing in Jiangsu, China. HIV-1 genetic transmission network can be used to explore the transmission kinetics and precision intervention in high-risk populations. Thus, we generated an HIV-1 genetic transmission network, explored key risk populations based on different risk factors and found out the risk factors for HIV-1 prevention and control among the newly-diagnosed HIV-1 cases from 2017 to 2018. Method We amplified the HIV-1 pol sequences from the plasma samples of the newly-diagnosed HIV-1 cases from 2017 to 2018 and obtained the infection data from The National HIV/AIDS Surveillance System. HIV-Trace and Cytoscape Software were both used to construct the HIV-1 genetic network with a gene distance of <0.005. The R software was used to analyze the risk factors for inclusion into the network. Results We obtained 3362 sequences with the pol gene region, of which 3316 contained detailed individual information. CRF01_AE accounted for 42.3 % of the HIV-1 subtypes in the samples. The median CD4+T lymphocyte count was 329 cells/μL in 2017 and 313 cells/μL in 2018. At the gene distance threshold of 0.005, 481 sequences were incorporated into the HIV-1 gene network, constructing 202 clusters. Age over 60 years old, heterosexual transmission route, subtype (CRF105_0107, CRF55_01 B, and CRF67_01 B) and CD4+T lymphocyte count (>200) were the risk factors influencing inclusion into the HIV-1 gene network. Moreover, south Jiangsu cities had higher inclusion in the network. Thus, key risk populations in the clusters with different transmission routes, new emerging subtypes, drug resistance nodes, and individuals above 60 years of age in the network represented the critical risk populations that should be focused more on for intervention. Conclusion The HIV-1 genetic transmission network is adept at discovering undiagnosed HIV-infected cases and linking all diagnosed cases for determination of risk infections. Therefore we should pay more attention to these risk infections with further investigation and intervention, helping to achieve the goal of 95 % use combination prevention from the World Health Organization, and push to end AIDS epidemic.
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Affiliation(s)
- Ying Zhou
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Jing Lu
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Zhi Zhang
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Qi Sun
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Xiaoqin Xu
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Haiyang Hu
- Institute of AIDS/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, 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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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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Ge Y, Liu Y, Fu G, Lu J, Li X, Du G, Fei G, Wang Z, Li H, Li W, Wei P. The Molecular Epidemiological and Immunological Characteristics of HIV-1 CRF01_AE/B Recombinants in Nanjing, China. Front Microbiol 2022; 13:936502. [PMID: 35910646 PMCID: PMC9335199 DOI: 10.3389/fmicb.2022.936502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-type 1 (HIV-1) CRF01_AE/B recombinants are newly emerging strains that are spreading rapidly in Southern and Eastern China. This study aimed to elucidate the molecular epidemiological characteristics of HIV-1 CRF01_AE/B recombinants in Nanjing and to explore the impact of these novel strains on the immunological status. A total of 1,013 blood samples from newly diagnosed HIV-1-infected patients were collected in Nanjing from 2015 to 2019, among which 958 partial Pol sequences were sequenced successfully. We depicted the molecular epidemiological characteristics of CRF01_AE/B recombinants by the molecular evolutionary analysis, Bayesian system evolution analysis, and transmission network analysis. The generalized additive mixed model was applied to evaluate the CD4+ T-cell count change of CRF01_AE/B recombinants. The Kaplan–Meier analysis was performed to assess the time from combined antiretroviral therapy (cART) initiation to immune reconstruction. We have identified 102 CRF01_AE/B recombinants (102/958, 10.65%) in Nanjing, including CRF67_01B (45/102, 44.12%), CRF68_01B (35/102, 34.31%), and CRF55_01B (22/102, 12.57%). According to the Bayesian phylogenetic inference, CRF55_01B had a rapid decline stage during 2017–2019, while CRF67_01B and CRF68_01B have experienced a fast growth phase during 2014–2015 and then remained stable. We have constructed 83 transmission networks, in which three larger clusters were composed of CRF67_01B and CRF68_01B. CRF01_AE/B recombinants manifested a faster decrease rate of CD4+ T-cell count than CRF_07BC but similar to CRF01_AE. The probability of achieving immune reconstruction in CRF01_AE/B recombinants was lower than CRF07_BC in the subgroup of baseline CD4+ T-cell count at cART initiation <300 cells/μl. In summary, CRF67_01B and CRF68_01B were the major strains of CRF01_AE/B recombinants in Nanjing, which have formed large transmission clusters between Nanjing and other provinces. CRF01_AE/B recombinants might be associated with rapid disease progression and poor immune reconstruction. The continuous epidemiological monitoring of CRF01_AE/B recombinants should be highly emphasized.
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Affiliation(s)
- You Ge
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yangyang Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Gengfeng Fu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Jing Lu
- Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, China
| | - Xiaoshan Li
- Department of Lung Transplant Center, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, China
| | - Guoping Du
- Department of Southeast University Hospital, Southeast University, Nanjing, China
| | - Gaoqiang Fei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Zemin Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Han Li
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Quality Management, Children's Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Pingmin Wei
| | - Pingmin Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
- Wei Li
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Yueqi Y, Ying Z, Jing L, Hongxiong G, Jianshuang C, Yan X, Hao C, Defu Y, Haiyang H, Xiaoqin X, Bei W, Gengfeng F. The Identification of A Novel HIV-1 Second-Generation Recombinant form (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Jiangsu, China. Curr HIV Res 2021; 19:188-194. [PMID: 33106145 DOI: 10.2174/1570162x18666201026143200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/12/2020] [Accepted: 09/25/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recent years. OBJECTIVE This study aimed to report on novel HIV-1 recombinants. METHODS We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination breakpoints using SimPlot 3.5.1. RESULTS We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_ AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints in the virus, which differed from any previously identified CRF and URF around the world. CONCLUSION Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.
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Affiliation(s)
- Yin Yueqi
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Zhou Ying
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Lu Jing
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Guo Hongxiong
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Chen Jianshuang
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Xuan Yan
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Cheng Hao
- Wuxi Xinwu District Center for Disease Control and Prevention, Wuxi 214028, China
| | - Yuan Defu
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hu Haiyang
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Xu Xiaoqin
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Wang Bei
- Department of Epidemiology and Health Statistics, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Fu Gengfeng
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Li W, Li X, He Y, Ge Y, Ong JJ, Li X, Dong X, Chu J, Musa TH, Cao S, Qian N, Zhang L, Wei P. The evolutionary and transmission characteristic of HIV-1 CRF07_BC in Nanjing, Jiangsu. J Med Virol 2020; 92:3237-3245. [PMID: 32275071 DOI: 10.1002/jmv.25854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/24/2020] [Accepted: 04/05/2020] [Indexed: 11/11/2022]
Abstract
To understand the epidemiology, evolutionary and transmission characteristics of HIV-1 CRF07_BC in Nanjing, China. One hundred and fifty-nine patients with HIV-1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV-1-infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV-1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1-178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV-1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36-2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12-2.65] × 10-3 per site per year with the relaxed exponential clock model. HIV-1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before.
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Affiliation(s)
- Wei Li
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Xiaoshan Li
- Department of Lung Transplant Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yan He
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - You Ge
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Jason J Ong
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
| | - Xin Li
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Xiaoxiao Dong
- Nanjing Municipal Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Jinjin Chu
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Taha Hussein Musa
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Shang Cao
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Ni Qian
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
| | - Lei Zhang
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Pingmin Wei
- Key Laboratory of Environmental Medicine Engineering, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Ministry of Education, Nanjing, Jiangsu, China
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