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Yu D, Zhu K, Li M, Zhang F, Yang Y, Lu C, Zhong S, Qin C, Lan Y, Yu J, Petersen JD, Jiang J, Liang H, Ye L, Liang B. The origin, dissemination, and molecular networks of HIV-1 CRF65_cpx strain in Hainan Island, China. BMC Infect Dis 2024; 24:269. [PMID: 38424479 PMCID: PMC10905908 DOI: 10.1186/s12879-024-09101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND HIV-1 CRF65_cpx strain carries drug-resistant mutations, which raises concerns about its potential for causing virologic failure. The CRF65_cpx ranks as the fourth most prevalent on Hainan Island, China. However, the origin and molecular epidemiology of CRF65_cpx strains in this area remain unclear. This study aims to estimate the spatial origins and dissemination patterns of HIV-1 CRF65_cpx in this specific region. METHODS Between 2018 and 2021, a total of 58 pol sequences of the CRF65_cpx were collected from HIV-positive patients on Hainan Island. The available CRF65_cpx pol sequences from public databases were compiled. The HIV-TRACE tool was used to construct transmission networks. The evolutionary history of the introduction and dissemination of HIV-1 CRF65_cpx on Hainan Island were analyzed using phylogenetic analysis and the Bayesian coalescent-based approach. RESULTS Among the 58 participants, 89.66% were men who have sex with men (MSM). The median age was 25 years, and 43.10% of the individuals had a college degree or above. The results indicated that 39 (67.24%) sequences were interconnected within a single transmission network. A consistent expansion was evident from 2019 to 2021, with an incremental annual addition of four sequences into the networks. Phylodynamic analyses showed that the CRF65_cpx on Hainan Island originated from Beijing (Bayes factor, BF = 17.4), with transmission among MSM on Hainan Island in 2013.2 (95%HPD: 2012.4, 2019.5), subsequently leading to an outbreak. Haikou was the local center of the CRF65_cpx epidemic. This strain propagated from Haikou to other locations, including Sanya (BF > 1000), Danzhou (BF = 299.3), Chengmai (BF = 27.0) and Tunchang (BF = 16.3). The analyses of the viral migration patterns between age subgroups and risk subgroups revealed that the viral migration directions were from "25-40 years old" to "17-24 years old" (BF = 14.6) and to "over 40 years old" (BF = 17.6), and from MSM to heterosexuals (BF > 1000) on Hainan Island. CONCLUSION Our analyses elucidate the transmission dynamics of CRF65_cpx strain on Hainan Island. Haikou is identified as the potential hotspot for CRF65_cpx transmission, with middle-aged MSM identified as the key population. These findings suggest that targeted interventions in hotspots and key populations may be more effective in controlling the HIV epidemic.
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Affiliation(s)
- Dee Yu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
| | - Kaokao Zhu
- Prevention and Treatment Department, the Fifth People's Hospital of Hainan Province, 3 Xueyuan Road, Haikou, 570102, China
| | - Mu Li
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Fei Zhang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Yuan Yang
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Chunyun Lu
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
| | - Shanmei Zhong
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Cai Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Yanan Lan
- Guangxi medical university oncology school, 22 Shuangyong Road, Nanning, 530021, China
| | - Jipeng Yu
- The First Clinical Medical College, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Jindong Ding Petersen
- International School of Public Health and One Health, Hainan Medical University, 3 Xueyuan Road, Haikou, 571199, China
- Research Unit for General Practice, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Research Unit for General Practice, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
| | - Bingyu Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
- Guangxi Engineering Center for Organoids and Organ-on-chips of Highly Pathogenic Microbial Infections & Biosafety laboratory, Life Science Institute, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, China.
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Alexiev I, Shankar A, Pan Y, Grigorova L, Partsuneva A, Dimitrova R, Gancheva A, Kostadinova A, Elenkov I, Yancheva N, Grozdeva R, Strashimirov D, Stoycheva M, Baltadzhiev I, Doichinova T, Pekova L, Kosmidis M, Emilova R, Nikolova M, Switzer WM. Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012-2020). Viruses 2023; 15:v15040941. [PMID: 37112921 PMCID: PMC10146724 DOI: 10.3390/v15040941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988-2011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012-2020 using polymerase sequences from 1053 of 2010 (52.4%) antiretroviral therapy (ART)-naive individuals. Sequences were analyzed for DRM using the WHO HIV SDRM list implemented in the calculated population resistance tool at Stanford University. Genetic diversity was inferred using automated subtyping tools and phylogenetics. Cluster detection and characterization was performed using MicrobeTrace. The overall rate of SDRMs was 5.7% (60/1053), with 2.2% having resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 1.8% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 2.1% to protease inhibitors (PIs), and 0.4% with dual-class SDRMs. We found high HIV-1 diversity, with the majority being subtype B (60.4%), followed by F1 (6.9%), CRF02_AG (5.2%), A1 (3.7%), CRF12_BF (0.8%), and other subtypes and recombinant forms (23%). Most (34/60, 56.7%) of the SDRMs were present in transmission clusters of different subtypes composed mostly of male-to-male sexual contact (MMSC), including a 14-member cluster of subtype B sequences from 12 MMSC and two males reporting heterosexual contact; 13 had the L90M PI mutation and one had the T215S NRTI SDRM. We found a low SDRM prevalence amid high HIV-1 diversity among ART-naive patients in Bulgaria during 2012-2020. The majority of SDRMs were found in transmission clusters containing MMSC, indicative of onward spread of SDRM in drug-naive individuals. Our study provides valuable information on the transmission dynamics of HIV drug resistance in the context of high genetic diversity in Bulgaria, for the development of enhanced prevention strategies to end the epidemic.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anupama Shankar
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Lyubomira Grigorova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Alexandra Partsuneva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Ivaylo Elenkov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Nina Yancheva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Rusina Grozdeva
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria
| | - Mariana Stoycheva
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Ivan Baltadzhiev
- Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria
| | - Tsetsa Doichinova
- Department of Infectious Diseases, Medical University, 5800 Pleven, Bulgaria
| | - Lilia Pekova
- Clinic of Infectious Diseases, Medical University, 6000 Stara Zagora, Bulgaria
| | - Minas Kosmidis
- Clinic of Infectious Diseases, Medical University, 9002 Varna, Bulgaria
| | - Radoslava Emilova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - Maria Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria
| | - William M Switzer
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Lebedev A, Kuznetsova A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A, Mamatkulov A, Kazakova E, Ibadullaeva N, Brigida K, Musabaev E, Mustafaeva D, Rakhimova V, Bobkova M. Identifying HIV-1 Transmission Clusters in Uzbekistan through Analysis of Molecular Surveillance Data. Viruses 2022; 14:v14081675. [PMID: 36016298 PMCID: PMC9413238 DOI: 10.3390/v14081675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
The CRF02_AG and sub-subtype A6 are currently the predominant HIV-1 variants in the Republic of Uzbekistan, but little is known about their time-spatial clustering patterns in high-risk populations. We have applied molecular evolution methods and network analyses to better understand the transmission patterns of these subtypes by analyzing 316 pol sequences obtained during the surveillance study of HIV drug resistance. Network analysis showed that about one third of the HIV infected persons were organized into clusters, including large clusters with more than 35 members. These clusters were composed mostly of injecting drug users and/or heterosexuals, with women having mainly high centrality within networks identified in both subtypes. Phylogenetic analyses of the 'Uzbek' sequences, including those publicly available, show that Russia and Ukraine played a role as the main sources of the current subtype A6 epidemic in the Republic. At the same time, Uzbekistan has been a local center of the CRF02_AG epidemic spread in the former USSR since the early 2000s. Both of these HIV-1 variants continue to spread in Uzbekistan, highlighting the importance of identifying transmission networks and transmission clusters to prevent further HIV spread, and the need for HIV prevention and education campaigns in high-risk groups.
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Affiliation(s)
- Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
- Correspondence:
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Aleksandr Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Adkhamjon Mamatkulov
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Evgeniya Kazakova
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Nargiz Ibadullaeva
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Krestina Brigida
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Erkin Musabaev
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Dildora Mustafaeva
- Republican AIDS Center, The Ministry of Health, Tashkent 100135, Uzbekistan;
| | - Visola Rakhimova
- Center for Development of Profession Qualification of Medical Workers, Tashkent 100007, Uzbekistan;
| | - Marina Bobkova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
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Brenner BG. Phylogenetic Insights on Patterns of HIV-1 Spread and the Design of Epidemic Control Measures. Viruses 2022; 14:332. [PMID: 35215925 PMCID: PMC8877004 DOI: 10.3390/v14020332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
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Mazrouee S, Little SJ, Wertheim JO. Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment. PLoS Comput Biol 2021; 17:e1009336. [PMID: 34550966 PMCID: PMC8457453 DOI: 10.1371/journal.pcbi.1009336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/09/2021] [Indexed: 12/30/2022] Open
Abstract
HIV molecular epidemiology estimates the transmission patterns from clustering genetically similar viruses. The process involves connecting genetically similar genotyped viral sequences in the network implying epidemiological transmissions. This technique relies on genotype data which is collected only from HIV diagnosed and in-care populations and leaves many persons with HIV (PWH) who have no access to consistent care out of the tracking process. We use machine learning algorithms to learn the non-linear correlation patterns between patient metadata and transmissions between HIV-positive cases. This enables us to expand the transmission network reconstruction beyond the molecular network. We employed multiple commonly used supervised classification algorithms to analyze the San Diego Primary Infection Resource Consortium (PIRC) cohort dataset, consisting of genotypes and nearly 80 additional non-genetic features. First, we trained classification models to determine genetically unrelated individuals from related ones. Our results show that random forest and decision tree achieved over 80% in accuracy, precision, recall, and F1-score by only using a subset of meta-features including age, birth sex, sexual orientation, race, transmission category, estimated date of infection, and first viral load date besides genetic data. Additionally, both algorithms achieved approximately 80% sensitivity and specificity. The Area Under Curve (AUC) is reported 97% and 94% for random forest and decision tree classifiers respectively. Next, we extended the models to identify clusters of similar viral sequences. Support vector machine demonstrated one order of magnitude improvement in accuracy of assigning the sequences to the correct cluster compared to dummy uniform random classifier. These results confirm that metadata carries important information about the dynamics of HIV transmission as embedded in transmission clusters. Hence, novel computational approaches are needed to apply the non-trivial knowledge collected from inter-individual genetic information to metadata from PWH in order to expand the estimated transmissions. We note that feature extraction alone will not be effective in identifying patterns of transmission and will result in random clustering of the data, but its utilization in conjunction with genetic data and the right algorithm can contribute to the expansion of the reconstructed network beyond individuals with genetic data.
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Affiliation(s)
- Sepideh Mazrouee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, United States
| | - Susan J. Little
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, United States
| | - Joel O. Wertheim
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, United States
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Otani M, Shiino T, Kondo M, Hachiya A, Nishizawa M, Kikuchi T, Matano T; Japanese Drug Resistance HIV-1 Surveillance Network. Phylodynamic analysis reveals changing transmission dynamics of HIV-1 CRF01_AE in Japan from heterosexuals to men who have sex with men. Int J Infect Dis 2021; 108:397-405. [PMID: 34082091 DOI: 10.1016/j.ijid.2021.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND HIV-1 circulating recombinant form (CRF) 01_AE is the second major subtype in Japan. Our previous study indicated that CRF01_AE was predominantly circulating in heterosexuals/injecting drug users (IDUs). With implications of increased CRF01_AE infections among men who have sex with men (MSM), this study sought to investigate whether the transmission dynamics of CRF01_AE infections in Japan have changed. METHODS Sequences from 8032 newly diagnosed HIV-1-infected individuals were analysed. For 614 (7.6%) of CRF01_AE cases, clusters were identified and categorised by transmission risks. Median times to the most recent common ancestors (tMRCA) were estimated. RESULTS The individuals were predominantly Japanese (64%) and male (72%). MSM became the predominant transmission risk from 2014. Thirty transmission clusters (TCs) and 48 pairs, including 40% of individuals, were identified. MSM were approximately five times more likely to be in a TC compared to heterosexuals, and were the major contributors to TCs. tMRCA data suggest that MSM TCs emerged from 1996 and became predominant around 2000. CONCLUSIONS CRF01_AE has spread among MSM, with frequent and continuous cluster formations, and MSM has become the predominant transmission risk. Our study suggested that CRF01_AE transmission has shifted from heterosexuals/IDUs to MSM. Prevention measures targeting key populations should be considered for controlling CRF01_AE spread.
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