{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:03:35Z","timestamp":1787241815571,"version":"build-2736575974"},"reference-count":22,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T00:00:00Z","timestamp":1745971200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Administration of Disease Control and Prevention of China","award":["2024018"],"award-info":[{"award-number":["2024018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The recent emergence of new HIV-1 recombinant strains presents a new challenge to the control of HIV-1\/AIDS and the development of an effective vaccine. We employed a near full-length genomic sequence analysis of a newly identified CRF85_BC recombinant strain in Ningxia, China, to determine its recombination pattern. Blood samples were collected from HIV-infected or AIDS patients in Ningxia in 2023. CRF85_BC subtype strains were detected from three samples using an in-house method, and one sample\u2019s near full-length genome sequence was also obtained. MEGA11, jpHMM, and Simplot software were used to identify subtypes and analyze recombination patterns. Neighbor-joining phylogenetic tree analysis showed that HIV-1 pol region sequences of three samples were CRF85_BC subtypes. One near full-length genome sequence of the recombinant strain was obtained, and jpHMM preliminarily judged that the recombinant strain was inserted with two subtype B fragments and two CRF01_AE fragments based on subtype C as the backbone. Further analysis using Simplot software revealed that the recombinant strain was the second-generation recombinant strain of CRF85_BC and CRF01_AE, and the recombination mode was based on the full-length genome of CRF85_BC, and CRF01_AE gene fragments that were inserted at positions 7365\u20138279 and 8431\u20139492, respectively. The results of the fragment phylogenetic tree verified its accuracy. One CRF01_AE and CRF85_BC second-generation recombinant strain was found in HIV-1 infected people in Ningxia, indicating that new HIV-1 recombinant strains continuously emerge and circulate in this region. Genomic surveillance of these recombinants should inform targeted interventions, such as prioritized contact tracing, to mitigate the formation of transmission clusters.<\/jats:p>","DOI":"10.3390\/v17050655","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T11:35:13Z","timestamp":1746185713000},"page":"655","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Sequencing of One Unique Recombinant CRF85_BC\/CRF01_AE Genome and Two Partial Genomes from Ningxia, China"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-2223-8631","authenticated-orcid":false,"given":"Yufeng","family":"Li","sequence":"first","affiliation":[{"name":"School of Public Health, Ningxia Medical University, Yinchuan 750004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianxin","family":"Pei","sequence":"additional","affiliation":[{"name":"Ningxia Center for Disease Control and Prevention, Yinchuan 750011, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohong","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Public Health, Ningxia Medical University, Yinchuan 750004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yichang","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Public Health, Ningxia Medical University, Yinchuan 750004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofa","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Public Health, Ningxia Medical University, Yinchuan 750004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongzhi","family":"Yang","sequence":"additional","affiliation":[{"name":"Ningxia Center for Disease Control and Prevention, Yinchuan 750011, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3420-1268","authenticated-orcid":false,"given":"Zhonglan","family":"Wu","sequence":"additional","affiliation":[{"name":"Ningxia Center for Disease Control and Prevention, Yinchuan 750011, China"},{"name":"College of Life Sciences, Ningxia University, Yinchuan 750021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,30]]},"reference":[{"key":"ref_1","unstructured":"(2025, March 03). HIV Sequence Database Main Page, Available online: https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Bolhassani, A. (2025). Editorial: The Global Phenotypic Diversity of HIV-1: Implications for Pathogenesis, Vaccine, and Cure. Front. Immunol., 16.","DOI":"10.3389\/fimmu.2025.1572732"},{"key":"ref_3","first-page":"1257","article-title":"National and Regional Molecular Epidemiology of HIV-1\u2014China, 2004\u20132023","volume":"6","author":"Wang","year":"2024","journal-title":"China CDC Wkly."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Pei, J., Wu, Z., Si, B., Ma, C., Liu, Y., Ma, X., Kuai, W., Zhang, Y., and Li, Y. (2024). HIV-1 Drug Resistance and Genetic Transmission Networks among Patients with Sexually Transmitted HIV in Ningxia, China. Front. Public Health, 12.","DOI":"10.3389\/fpubh.2024.1485516"},{"key":"ref_5","first-page":"1384","article-title":"Characterization of HIV-1 drug resistance and molecular transmission network in Ningxia, 2023","volume":"40","author":"Liu","year":"2024","journal-title":"Virol. Sin."},{"key":"ref_6","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":"Lv","year":"2019","journal-title":"Guangxi Med. J."},{"key":"ref_7","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":"Zazzi","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"ref_8","unstructured":"(2025, March 03). Global HIV & AIDS Statistics\u2014Fact Sheet. Available online: https:\/\/www.unaids.org\/en\/resources\/fact-sheet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1089\/aid.2016.0029","article-title":"Nationwide Trends in Molecular Epidemiology of HIV-1 in China","volume":"32","author":"Li","year":"2016","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"664","DOI":"10.46234\/ccdcw2023.129","article-title":"Changes in HIV-1 Subtypes\/Sub-Subtypes, and Transmitted Drug Resistance Among ART-Na\u00efve HIV-Infected Individuals\u2014China, 2004\u20132022","volume":"5","author":"Liu","year":"2023","journal-title":"China CDC Wkly."},{"key":"ref_11","first-page":"1160","article-title":"Analysis of Genetic Subtypes and Drug Resistance of HIV-1 Infected Patients in Yinchuan City, 2020","volume":"38","author":"Wu","year":"2022","journal-title":"Virol. Sin."},{"key":"ref_12","first-page":"783","article-title":"Characterization of HIV-1 genotype subtypes and drug resistance in heterosexually transmitted populations in Ningxia, 2021","volume":"39","author":"Si","year":"2023","journal-title":"Virol. Sin."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1016\/S0140-6736(94)92304-3","article-title":"HIV-1 Subtype E in Yunnan, China","volume":"344","author":"Cheng","year":"1994","journal-title":"Lancet"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1089\/088922299311754","article-title":"HIV Type 1 Subtypes in Guangxi Province, China, 1996","volume":"15","author":"Chen","year":"1999","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Li, Z., Liao, L., Feng, Y., Zhang, J., Yan, J., He, C., Xu, W., Ruan, Y., Xing, H., and Shao, Y. (2015). Trends of HIV Subtypes and Phylogenetic Dynamics among Young Men Who Have Sex with Men in China, 2009\u20132014. Sci. Rep., 5.","DOI":"10.1038\/srep16708"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1071\/SH04024","article-title":"HIV-1 Co-Infection, Superinfection and Recombination","volume":"1","author":"Steain","year":"2004","journal-title":"Sex Health"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1089\/aid.2016.0053","article-title":"Identification of a Novel HIV-1 Circulating Recombinant Form (CRF85_BC) in Sichuan, China","volume":"32","author":"Su","year":"2016","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_18","first-page":"2499","article-title":"Analysis of HIV Sentinel Surveillance Results of Male Mobile Population in Dongcheng District, Beijing, 2016\u20132020","volume":"38","author":"Liu","year":"2022","journal-title":"Occup. Health"},{"key":"ref_19","first-page":"184","article-title":"Analysis of the results of HIV sentinel surveillance of the mobile population at construction sites in Changping District, Beijing, China, 2018\u20132021","volume":"17","author":"Wang","year":"2023","journal-title":"Cap. J. Public Health"},{"key":"ref_20","first-page":"142","article-title":"Advances in the drug resistance genotype detection of HIV-1","volume":"2","author":"Chen","year":"2017","journal-title":"J. Mol. Diagn. Ther."},{"key":"ref_21","first-page":"436","article-title":"Replication kinetic properties of HIV-1 CRF_BC novel drug resistance associated mutations","volume":"49","author":"Jiao","year":"2015","journal-title":"Chin. J. Prev. Med."},{"key":"ref_22","first-page":"746","article-title":"Study on the molecular transmission network of HIV-1 drug-resistant strains in the pre-treatment population in Hebei Province, China","volume":"36","author":"Liu","year":"2020","journal-title":"Chin. J. 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