{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T18:13:59Z","timestamp":1791656039178,"version":"4.3.4"},"reference-count":27,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chongqing Medical Scientific Research Project","award":["2026MSXM090"],"award-info":[{"award-number":["2026MSXM090"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"\n Background<\/jats:title>\n The emergence of drug resistance poses a major challenge to the long-term efficacy of antiretroviral therapy (ART) in managing HIV-1 infection. A comprehensive understanding of the prevalence and determinants of HIV-1 drug resistance mutations (DRMs) among patients with treatment failure in Chongqing, China, remains limited.<\/jats:p>\n <\/jats:sec>\n \n Objectives<\/jats:title>\n This study sought to characterize the prevalence of HIV-1 DRMs and to identify factors associated with drug resistance in patients experiencing ART failure in Chongqing between 2019 and 2023.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n We conducted a retrospective analysis of individuals living with HIV\/AIDS who had received ART for at least six months and exhibited virologic failure(VF) (viral load(VL) > 1000 copies\/mL). Genotypic resistance testing was performed on plasma samples. Associations between potential risk factors and the presence of DRMs were evaluated using univariate and multivariate logistic regression models.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Of the 1,522 patients with ART failure included in the study, amplifiable partial pol and integrase (INT) gene sequences were obtained from 1,426 and 653 specimens, respectively. DRMs were identified in 66.55% (949\/1,426) of the patients. The predominant HIV-1 subtype was CRF07_BC (50.14%). Class-specific DRM prevalence was highest for non-nucleoside reverse transcriptase inhibitors (NNRTIs) at 61.15%, followed by nucleoside reverse transcriptase inhibitors (NRTIs) at 44.60%, integrase strand transfer inhibitors (INSTIs) at 6.13%, and protease inhibitors (PIs) at 5.39%. The most commonly observed mutations were M184V\/I (38.00%) for NRTIs, K103N\/S\/H (24.96%) for NNRTIs, and M46I (1.54%) for PIs. Multivariate analysis confirmed that lower baseline CD4\u2009+\u2009T-cell counts and initiation of treatment with an NNRTI-based regimen were independently associated with the development of DRMs.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n Our study reveals a high prevalence of HIV-1 drug resistance among patients with treatment failure in Chongqing, with low baseline CD4\u2009+\u2009T-cell counts and NNRTI-based initial regimens identified as key risk factors. These findings underscore the urgency of optimizing first-line therapy by prioritizing dolutegravir (DTG)-based regimens, with protease inhibitor (PI)-based regimens as a practical alternative. Furthermore, we recommend implementing timely genotypic resistance testing, ideally within 4 weeks upon confirmed virologic failure, to guide effective regimen switching and curb the spread of drug resistance.<\/jats:p>\n <\/jats:sec>","DOI":"10.1371\/journal.pone.0342301","type":"journal-article","created":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T18:30:16Z","timestamp":1771957816000},"page":"e0342301","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["HIV-1 drug resistance and associated risk factors in patients with antiretroviral therapy failure in Chongqing, China, 2019\u20132023"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6000-8440","authenticated-orcid":true,"given":"Huizheng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-0499-8131","authenticated-orcid":true,"given":"Ping","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,2,24]]},"reference":[{"key":"pone.0342301.ref001","volume-title":"Fact sheet 2025: global HIV statistics","author":"UNAIDS","year":"2025"},{"key":"pone.0342301.ref002","article-title":"The Chinese free antiretroviral treatment program: challenges and responses","author":"F Zhang","year":"2007","journal-title":"AIDS"},{"key":"pone.0342301.ref003","volume-title":"National free antiretroviral treatment manual","author":"National Center for AIDS\/STD Control and Prevention CC","year":"2023","edition":"5"},{"key":"pone.0342301.ref004","volume-title":"Joint Programme Results in China: 2022-2023","author":"UNAIDS","year":"2023"},{"issue":"3","key":"pone.0342301.ref005","first-page":"225","article-title":"National AIDS and STD epidemic in December 2023","volume":"30","author":"Chinese Center for Disease Control and Prevention NCfASCaP","year":"2024","journal-title":"Chinese Journal of AIDS & STD"},{"issue":"9","key":"pone.0342301.ref006","article-title":"Predictors of HIV virological failure and drug resistance in Chinese patients after 48 months of antiretroviral treatment, 2008-2012: a prospective cohort study","volume":"7","author":"W Kan","year":"2017","journal-title":"BMJ Open"},{"key":"pone.0342301.ref007","volume-title":"HIV drug resistance report 2021","author":"World Health Organization","year":"2021"},{"issue":"9","key":"pone.0342301.ref008","doi-asserted-by":"crossref","DOI":"10.1016\/S2352-3018(20)30172-7","article-title":"Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study","volume":"7","author":"A Gupta-Wright","year":"2020","journal-title":"Lancet HIV"},{"issue":"1","key":"pone.0342301.ref009","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1186\/s12879-022-07894-2","article-title":"Virological failure among people living with HIV receiving second-line antiretroviral therapy in Pune, India","volume":"22","author":"S Salvi","year":"2022","journal-title":"BMC Infect Dis"},{"issue":"9","key":"pone.0342301.ref010","article-title":"Virological failure and acquired genotypic resistance associated with contemporary antiretroviral treatment regimens","volume":"7","author":"S-Y Rhee","year":"2020","journal-title":"Open Forum Infect Dis"},{"key":"pone.0342301.ref011","article-title":"The effect of pretreatment potential resistance to NNRTIs on antiviral therapy in patients With HIV\/AIDS","volume":"91","author":"C-L Li","year":"2022","journal-title":"J Acquir Immune Defic Syndr"},{"key":"pone.0342301.ref012","volume-title":"Overview of HIV\/AIDS Epidemic in Chongqing","author":"Prevention CMCfDCa","year":"2024"},{"issue":"11","key":"pone.0342301.ref013","first-page":"1182","article-title":"Chinese guidelines for diagnosis and treatment of HIV\/AIDS (2021 edition)","volume":"27","author":"AIDS and Hepatitis C Professional Group SoID CMA, Chinese Center for Disease Control and Prevention","year":"2021","journal-title":"Chinese Journal of AIDS & STD"},{"issue":"11","key":"pone.0342301.ref014","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1086\/503914","article-title":"Web resources for HIV type 1 genotypic-resistance test interpretation","volume":"42","author":"TF Liu","year":"2006","journal-title":"Clin Infect Dis"},{"issue":"22","key":"pone.0342301.ref015","doi-asserted-by":"crossref","first-page":"2744","DOI":"10.1097\/CM9.0000000000002881","article-title":"Drug resistance mutations among people living with HIV with treatment failure in Henan Province, China","volume":"136","author":"J Liu","year":"2023","journal-title":"Chin Med J (Engl)"},{"issue":"6","key":"pone.0342301.ref016","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1089\/aid.2021.0079","article-title":"High Rate of HIV-1 drug resistance in antiretroviral therapy-failure patients in Liaoning Province, China","volume":"38","author":"Q Wei","year":"2022","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"1","key":"pone.0342301.ref017","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s12985-020-01311-3","article-title":"Prevalence of acquired drug resistance mutations in antiretroviral- experiencing subjects from 2012 to 2017 in Hunan Province of central South China","volume":"17","author":"X Zou","year":"2020","journal-title":"Virol J"},{"issue":"8","key":"pone.0342301.ref018","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0320623","article-title":"Prevalence of HIV drug resistance, its correlates and common mutations among people living with HIV failing on ART in northern Uganda: A cross-sectional study","volume":"20","author":"F Kayinda","year":"2025","journal-title":"PLOS One"},{"issue":"1","key":"pone.0342301.ref019","doi-asserted-by":"crossref","first-page":"2278254","DOI":"10.1080\/21505594.2023.2278254","article-title":"Prevalence and analysis of acquired and transmitted integrase strand transfer inhibitor-associated HIV-1 drug resistance in Chongqing, China","volume":"14","author":"H Zhang","year":"2023","journal-title":"Virulence"},{"issue":"4","key":"pone.0342301.ref020","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/cid\/ciad219","article-title":"Plasma human immunodeficiency virus 1 RNA and CD4+ T-Cell Counts Are Determinants of Virological nonsuppression outcomes with initial integrase inhibitor-based regimens: a prospective RESPOND cohort study","volume":"77","author":"H \u00c1lvarez","year":"2023","journal-title":"Clin Infect Dis"},{"key":"pone.0342301.ref021","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.2147\/PPA.S527229","article-title":"Unlocking the keys to swift HIV treatment: a qualitative exploration of rapid antiretroviral therapy initiation among people living with HIV in China","volume":"19","author":"T Chen","year":"2025","journal-title":"Patient Prefer Adherence"},{"issue":"2","key":"pone.0342301.ref022","first-page":"78","article-title":"Impact of pre-antiretroviral therapy CD4 counts on drug resistance and treatment failure: A systematic review","volume":"22","author":"M Diallo","year":"2020","journal-title":"AIDS Rev"},{"issue":"10","key":"pone.0342301.ref023","doi-asserted-by":"crossref","first-page":"2575","DOI":"10.1093\/jac\/dkae260","article-title":"Exploring disparities in HIV-1 pretreatment and acquired drug resistance in China from 2003 to 2022","volume":"79","author":"Z Wang","year":"2024","journal-title":"J Antimicrob Chemother"},{"key":"pone.0342301.ref024","doi-asserted-by":"crossref","first-page":"1391215","DOI":"10.3389\/fcimb.2024.1391215","article-title":"Men with a history of commercial heterosexual contact play essential roles in the transmission of HIV-1 CRF55_01B from men who have sex with men to the general population in Guangxi, China","volume":"14","author":"T Luo","year":"2024","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"pone.0342301.ref025","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1007\/s11904-019-00478-x","article-title":"Optimizing treatment for adults with HIV\/AIDS in China: successes over two decades and remaining challenges","volume":"17","author":"W Cao","year":"2020","journal-title":"Curr HIV\/AIDS Rep"},{"issue":"7","key":"pone.0342301.ref026","doi-asserted-by":"crossref","DOI":"10.1093\/cid\/ciaa1161","article-title":"Pretreatment and acquired antiretroviral drug resistance among persons living with HIV in Four African Countries","volume":"73","author":"TA Crowell","year":"2021","journal-title":"Clin Infect Dis"},{"issue":"5","key":"pone.0342301.ref027","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1093\/jac\/dkz561","article-title":"Prevalence of viral load suppression, predictors of virological failure and patterns of HIV drug resistance after 12 and 48 months on first-line antiretroviral therapy: a national cross-sectional survey in Uganda","volume":"75","author":"D Ssemwanga","year":"2020","journal-title":"J Antimicrob Chemother"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0342301","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T18:30:22Z","timestamp":1771957822000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0342301"}},"subtitle":[],"editor":[{"given":"Benjamin","family":"Chimukangara","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,24]]},"references-count":27,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0342301","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,24]]}}}