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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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Li Y, Chang W, Liang J, Liu Y, Li L, Liu L, Wang JY, Feng RL, Liao B, Feng Y. Characterization of a new HIV-1 second-generation circulating recombinant form (CRF170_0107) among men who have sex with men in Yunnan, China. J Infect 2024; 88:206-209. [PMID: 38135162 DOI: 10.1016/j.jinf.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Affiliation(s)
- Yi Li
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Wei Chang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Liang
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Yang Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li Li
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jing-Ying Wang
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Rui-Lin Feng
- Kunming Center for Disease Control and Prevention, Kunming, China
| | - Bin Liao
- Kunming Center for Disease Control and Prevention, Kunming, China.
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
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He M, Li C, Chang W, Tian B, Liu Y, Liu L, Liu J, Feng Y. Genomic characterization of a newly emerging circulating recombinant form of HIV-1, CRF143_cpx, involving subtypes B, C and CRF01_AE, identified in Yunnan, China. J Infect 2023; 87:e58-e60. [PMID: 37355049 DOI: 10.1016/j.jinf.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Affiliation(s)
- Meilan He
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Chongxi Li
- Department of Infectious Diseases I, Kunming Third People's Hospital, Kunming, China
| | - Wei Chang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Bo Tian
- Department of Infectious Diseases I, Kunming Third People's Hospital, Kunming, China
| | - Yang Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Liu
- Department of Infectious Diseases I, Kunming Third People's Hospital, Kunming, China.
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
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Cao R, Lei S, Chen H, Ma Y, Dai J, Dong L, Jin X, Yang M, Sun P, Wang Y, Zhang Y, Jia M, Chen M. Using molecular network analysis to understand current HIV-1 transmission characteristics in an inland area of Yunnan, China. Epidemiol Infect 2023; 151:e124. [PMID: 37462024 PMCID: PMC10540185 DOI: 10.1017/s0950268823001140] [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: 02/27/2023] [Revised: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023] Open
Abstract
HIV-1 molecular surveillance provides a new approach to explore transmission risks and targeted interventions. From January to June 2021, 663 newly reported HIV-1 cases were recruited in Zhaotong City, Yunnan Province, China. The distribution characteristics of HIV-1 subtypes and HIV-1 molecular network were analysed. Of 542 successfully subtyped samples, 12 HIV-1 strains were identified. The main strains were CRF08_BC (47.0%, 255/542), CRF01_AE (17.0%, 92/542), CRF07_BC (17.0%, 92/542), URFs (8.7%, 47/542), and CRF85_BC (6.5%, 35/542). CRF08_BC was commonly detected among Zhaotong natives, illiterates, and non-farmers and was mostly detected in Zhaoyang County. CRF01_AE was frequently detected among married and homosexual individuals and mostly detected in Weixin and Zhenxiong counties. Among the 516 pol sequences, 187 (36.2%) were clustered. Zhaotong natives, individuals aged ≥60 years, and illiterate individuals were more likely to be found in the network. Assortativity analysis showed that individuals were more likely to be genetically associated when stratified by age, education level, occupation, and reporting area. The genetic diversity of HIV-1 reflects the complexity of local HIV epidemics. Molecular network analyses revealed the subpopulations to focus on and the characteristics of the risk networks. The results will help optimise local prevention and control strategies.
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Affiliation(s)
- Rui Cao
- School of Public Health, Kunming Medical University, Kunming, China
| | - Shouxiong Lei
- Division for AIDS/STD Control and Prevention, Zhaotong Center for Disease Control and Prevention, Zhaotong, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Xiaomei Jin
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Min Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Pengyan Sun
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yawen Wang
- School of Public Health, Kunming Medical University, Kunming, China
| | - Yuying Zhang
- School of Public Health, Kunming Medical University, Kunming, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Min Chen
- Health Laboratory Center, Yunnan Center for Disease Control and Prevention, Kunming, China
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Chen M, Ma Y, Chen H, Lei S, Jia M. Identification of a new HIV-1 second-generation circulating recombinant form (CRF134_0185) in Yunnan, China. J Infect 2023; 87:e12-e15. [PMID: 37100174 DOI: 10.1016/j.jinf.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023]
Affiliation(s)
- Min Chen
- Health Laboratory Center, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China.
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Shouxiong Lei
- Division for AIDS/STD Control and Prevention, Zhaotong Center for Disease Control and Prevention, Zhaotong, Yunnan, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China.
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Focosi D, Maggi F. Second-Generation SARS-CoV-2 Recombinants: Lessons from Other Viruses. Viruses 2023; 15:v15051063. [PMID: 37243149 DOI: 10.3390/v15051063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
RNA viruses have developed notable strategies to evolve and escape host immunity [...].
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani", 00149 Rome, Italy
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Fan W, Jia J, Shi H, Su M, Meng J, An W. Identification of the Near Full-length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant with a Complex Genomic Structure Isolated in Hebei Province, China. Curr HIV Res 2023; 21:268-276. [PMID: 37642005 DOI: 10.2174/1570162x21666230828122711] [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: 04/17/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND During HIV genotypic drug resistance testing of patient samples in Baoding, Hebei Province, China, in 2022, a recombinant fragment was detected in the pol region of an HIV-1 strain. OBJECTIVE The objective of the study was to analyze the near full-length genome of a novel HIV-1 CRF01_AE/CRF07_BC recombinant with a complex genomic structure. METHODS Viral RNA was extracted from the blood of the infected individual and reverse transcribed to cDNA. Two overlapping segments of the HIV-1 genome were amplified using a nearendpoint dilution method and sequenced. Recombinant breakpoints were determined using RIP, jpHMM, and SimPlot 3.5.1 software. MEGA 6.0 software was used to construct a neighbor-joining phylogenetic tree. RESULTS We obtained the near full-length genome sequence (8680 bp) of a novel HIV-1 CRF01_AE/CRF07_BC recombinant. Recombination analysis showed that the genome comprised at least 12 overlapping segments, including six CRF07_BC and six CRF01_AE segments, with CRF07_BC as the backbone. The emergence of CRF01_AE/CRF07_BC recombinant strains indicated that HIV-1 co-infection is common. However, the increasing genetic complexity of the HIV-1 epidemic in China warrants continued investigation. CONCLUSION The increase in CRF01_AE/CRF07_BC recombinant viruses suggests that HIV-1 has a high genetic mutation rate in Hebei, China. This highlights the need for close monitoring of HIV-1 molecular epidemiologic changes to provide accurate, up-to-date information for effective disease control.
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Affiliation(s)
- Weiguang Fan
- Clinical Laboratory, The People's Hospital of Baoding, Baoding, Hebei, China
| | - Jianru Jia
- Infection Division, The People's Hospital of Baoding, Baoding, Hebei, China
| | - Haoxi Shi
- Clinical Laboratory, The People's Hospital of Baoding, Baoding, Hebei, China
| | - Miaomiao Su
- Infection Division, The People's Hospital of Baoding, Baoding, Hebei, China
| | - Juan Meng
- Infection Division, The People's Hospital of Baoding, Baoding, Hebei, China
| | - Weina An
- Clinical Laboratory, The People's Hospital of Baoding, Baoding, Hebei, China
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Maksimenko LV, Sivay MV, Totmenin AV, Shvalov AN, Skudarnov SE, Ostapova TS, Yaschenko SV, Maksutov RA, Gashnikova NM. Novel HIV-1 A6/B recombinant forms (CRF133_A6B and URF_A6/B) circulating in Krasnoyarsk region, Russia. J Infect 2022; 85:702-769. [DOI: 10.1016/j.jinf.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
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