{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T18:00:52Z","timestamp":1785348052466,"version":"3.55.0"},"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004772","name":"Natural Science Foundation of Ningxia Province","doi-asserted-by":"publisher","award":["2025AAC020047"],"award-info":[{"award-number":["2025AAC020047"]}],"id":[{"id":"10.13039\/501100004772","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>The CRF01_AE recombinant is the dominant HIV strain in Ningxia, characterized by rapid disease progression and imposing a significant local burden. Current prevention strategies, often based on broad subtype classifications, are insufficient to address the distinct transmission dynamics of such specific recombinants. To delineate the spatiotemporal migration patterns and epidemic trends of CRF01_AE in Ningxia, this study conducted a systematic analysis of 206 local sequences. The results reveal extensive viral spread with clear geographic diffusion routes, particularly strong migration from Yinchuan to other major cities. Key demographic groups driving transmission are individuals aged 20\u201339, retired\/unemployed persons, and those with junior high school education. Although the transmission intensity has fluctuated, the current effective reproductive number remains above 1, indicating ongoing epidemic expansion, while the viral evolutionary rate appears stable. The study demonstrates that the CRF01_AE epidemic in Ningxia is still expanding and evolving, and identifies core transmission hubs and population clusters. These findings not only align with some prior understanding but also uncover more complex transmission networks and demographic patterns, highlighting the necessity for implementing targeted interventions specific to this strain to effectively control its spread.<\/jats:p>","DOI":"10.1371\/journal.pone.0354910","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:34:05Z","timestamp":1785346445000},"page":"e0354910","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Dynamic transmission and evolutionary analysis of the HIV-1 subtype CRF01_AE pol region in Ningxia, China"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-8488-4256","authenticated-orcid":true,"given":"Ziyang","family":"Luo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianxin","family":"Pei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subinuer","family":"Mutalifu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youping","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohong","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3420-1268","authenticated-orcid":true,"given":"Zhonglan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"pone.0354910.ref001","author":"Global HIV"},{"issue":"2","key":"pone.0354910.ref002","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/S1473-3099(18)30647-9","article-title":"Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis","volume":"19","author":"J Hemelaar","year":"2019","journal-title":"Lancet Infect Dis"},{"issue":"11","key":"pone.0354910.ref003","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1093\/infdis\/jiad327","article-title":"Geographic and population distributions of human immunodeficiency virus (HIV)-1 and HIV-2 circulating subtypes: A systematic literature review and meta-analysis (2010-2021)","volume":"228","author":"A Williams","year":"2023","journal-title":"J Infect Dis"},{"issue":"48","key":"pone.0354910.ref004","first-page":"1257","article-title":"National and regional molecular epidemiology of HIV-1 - China, 2004-2023","volume":"6","author":"D Wang","year":"2024","journal-title":"China CDC Wkly"},{"issue":"1","key":"pone.0354910.ref005","doi-asserted-by":"crossref","first-page":"1570","DOI":"10.1038\/s41598-017-01858-2","article-title":"HIV-1 CRF01_AE strain is associated with faster HIV\/AIDS progression in Jiangsu Province, China","volume":"7","author":"M Chu","year":"2017","journal-title":"Sci Rep"},{"issue":"10","key":"pone.0354910.ref006","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1093\/cid\/ciaa380","article-title":"CRF01_AE and CRF01_AE Cluster 4 Are Associated With Poor Immune Recovery in Chinese Patients Under Combination Antiretroviral Therapy","volume":"72","author":"Z Ge","year":"2021","journal-title":"Clin Infect Dis"},{"key":"pone.0354910.ref007","first-page":"1384","article-title":"Analysis of HIV-1 drug resistance and molecular transmission network in Ningxia in 2023","volume":"40","author":"L Yi","year":"2024","journal-title":"Bing Du Xue Bao"},{"issue":"2","key":"pone.0354910.ref008","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1128\/JCM.37.2.333-338.1999","article-title":"Clinical evaluation of an in-house reverse transcription-competitive PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma","volume":"37","author":"M Zazzi","year":"1999","journal-title":"J Clin Microbiol"},{"key":"pone.0354910.ref009","first-page":"1238","article-title":"Occurrence of genotypic drug resistance in HIV-infected\/AIDS patients with virologic failure of antiretroviral therapy and factors influencing it","volume":"41","author":"R Lv","year":"2019","journal-title":"Guangxi Med J"},{"issue":"3","key":"pone.0354910.ref010","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci","volume":"30","author":"MS Gill","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"4","key":"pone.0354910.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"R Bouckaert","year":"2019","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pone.0354910.ref012","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/molbev\/msr217","article-title":"Estimating the basic reproductive number from viral sequence data","volume":"29","author":"T Stadler","year":"2012","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pone.0354910.ref013","doi-asserted-by":"crossref","first-page":"14341","DOI":"10.1038\/s41598-021-93810-8","article-title":"A novel geo-hierarchical population mobility model for spatial spreading of resurgent epidemics","volume":"11","author":"A Top\u00eerceanu","year":"2021","journal-title":"Sci Rep"},{"issue":"5772","key":"pone.0354910.ref014","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1126\/science.1125237","article-title":"Synchrony, waves, and spatial hierarchies in the spread of influenza","volume":"312","author":"C Viboud","year":"2006","journal-title":"Science"},{"issue":"4","key":"pone.0354910.ref015","article-title":"Regional inequality in China\u2019s educational development: An urban-rural comparison","volume":"10","author":"Y Guo","year":"2024","journal-title":"Heliyon"},{"key":"pone.0354910.ref016","author":"Global HIV","year":"2024"},{"issue":"2","key":"pone.0354910.ref017","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jana.2007.01.006","article-title":"Cultural dynamics in HIV\/AIDS prevention research among young people","volume":"18","author":"ML Hare","year":"2007","journal-title":"J Assoc Nurses AIDS Care"},{"issue":"1","key":"pone.0354910.ref018","doi-asserted-by":"crossref","DOI":"10.1016\/S2352-3018(23)00226-6","article-title":"Ageism: the -ism affecting the lives of older people living with HIV","volume":"11","author":"G Guaraldi","year":"2024","journal-title":"Lancet HIV"},{"issue":"2","key":"pone.0354910.ref019","doi-asserted-by":"crossref","first-page":"74","DOI":"10.2174\/1570162X18666200129160723","article-title":"The Emerging of CRF01_AE: A Clinical Story and Future HIV\/AIDS Situation in Thailand","volume":"18","author":"P Winichakoon","year":"2020","journal-title":"Curr HIV Res"},{"issue":"7","key":"pone.0354910.ref020","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1177\/1363460717719240","article-title":"\u201cUnqueer\u201d kinship? Critical reflections on \u201cmarriage fraud\u201d in mainland China","volume":"21","author":"J Zhu","year":"2018","journal-title":"Sexualities"},{"issue":"1","key":"pone.0354910.ref021","doi-asserted-by":"crossref","first-page":"21416","DOI":"10.7448\/IAS.20.1.21416","article-title":"Disclosure of sexual orientation to health professionals in China: results from an online cross-sectional study","volume":"20","author":"W Tang","year":"2017","journal-title":"J Int AIDS Soc"},{"issue":"4","key":"pone.0354910.ref022","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1097\/JNC.0000000000000168","article-title":"\u201cI\u2019ll Change His Sexual Orientation, I Don\u2019t Think About HIV\u201d: A Qualitative Study to Explore Attitudes, Behaviors, and Experiences Among Wives of Men Who Have Sex With Men in Mainland China","volume":"31","author":"F Yan","year":"2020","journal-title":"J Assoc Nurses AIDS Care"},{"issue":"7","key":"pone.0354910.ref023","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1007\/s10508-014-0459-z","article-title":"Neighborhood-level associations with HIV infection among young men who have sex with men in Chicago","volume":"44","author":"2nd Phillips G","year":"2015","journal-title":"Arch Sex Behav"},{"issue":"1","key":"pone.0354910.ref024","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.virol.2009.05.023","article-title":"Phylodynamic analysis of the dissemination of HIV-1 CRF01_AE in Vietnam","volume":"391","author":"H Liao","year":"2009","journal-title":"Virology"},{"issue":"11","key":"pone.0354910.ref025","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1097\/QAD.0b013e328360db2d","article-title":"The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s","volume":"27","author":"Y Feng","year":"2013","journal-title":"AIDS"},{"issue":"10","key":"pone.0354910.ref026","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1002\/jmv.24851","article-title":"Amino acids at positions 3, 168, and 169 are associated with the ability of Nef proteins from HIV-1 CRF01_AE to downmodulate CD4","volume":"89","author":"WD Kuang","year":"2017","journal-title":"J Med Virol"},{"issue":"1","key":"pone.0354910.ref027","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1073\/pnas.1814714116","article-title":"Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade","volume":"116","author":"H Song","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pone.0354910.ref028","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1089\/aid.2021.0211","article-title":"Characterization of Three Novel HIV-1 Second-Generation Recombinants (CRF01_AE\/CRF07_BC) Identified in Shenzhen, China","volume":"38","author":"B Zhu","year":"2022","journal-title":"AIDS Res Hum Retroviruses"},{"key":"pone.0354910.ref029","doi-asserted-by":"crossref","first-page":"1766785","DOI":"10.3389\/fmicb.2026.1766785","article-title":"HIV-1 molecular transmission networks among MSM in Ningxia, China (2018-2024): insights into local transmission dynamics and drug resistance","volume":"17","author":"Z Wu","year":"2026","journal-title":"Front Microbiol"},{"issue":"1","key":"pone.0354910.ref030","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s12985-025-02704-y","article-title":"Divergent transmission dynamics and drug resistance evolution of HIV-1 CRF01_AE and CRF07_BC in Tianjin, China (2013-2022)","volume":"22","author":"Z Minna","year":"2025","journal-title":"Virol J"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354910","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:34:09Z","timestamp":1785346449000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0354910"}},"subtitle":[],"editor":[{"given":"Yury E","family":"Khudyakov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,29]]},"references-count":30,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0354910","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,29]]}}}