{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T05:24:28Z","timestamp":1764653068704,"version":"3.46.0"},"reference-count":37,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,11,30]],"date-time":"2025-11-30T00:00:00Z","timestamp":1764460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100017638","name":"Ministry of Health of the Russian Federation","doi-asserted-by":"crossref","award":["125022102789-9"],"award-info":[{"award-number":["125022102789-9"]}],"id":[{"id":"10.13039\/501100017638","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>This study aimed to assess the genetic diversity of HIV-1 in the Far Eastern Federal District (Russia) to implement effective anti-epidemic measures, including the development of an anti-HIV vaccine and the selection of optimal antigens. The first stage of the study included an analysis of HIV-1 nucleotide sequences obtained in Khabarovsk city from 2022 to 2024. The second stage of the study included an additional download of nucleotide sequences from the Los Alamos HIV Sequence Database for phylogenetic cluster analysis. Additionally, an analysis of drug resistance mutations was conducted. The results showed the following distribution of HIV-1 genetic variants: A6\u201472.15%, CRF63\u201410.13%, URFs\u20147.59%, C\u20145.06%, B\u20143.8%, and CRF157\u20141.27%. The phylogenetic cluster analysis revealed a statistically significant difference in the number of clusters depending on the genetic variant. Among drug resistance mutations (DRMs), those associated with nucleoside reverse transcriptase inhibitors (NRTIs) were the most frequently observed, accounting for 55.7% (95% CI: 44.75%\u201466.65%). The most commonly detected NRTI DRMs were A62V (43.04%) and M184V (13.92%). The results of this study highlight several important indicators for public health, particularly in the development of vaccines aimed at combating HIV infection.<\/jats:p>","DOI":"10.3390\/v17121568","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T13:03:02Z","timestamp":1764594182000},"page":"1568","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Assessment of Regional Genetic Diversity of HIV-1"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9180-9846","authenticated-orcid":false,"given":"Anastasiia","family":"Antonova","sequence":"first","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna V.","family":"Kuznetsova","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Institution \u201cCenter for the Prevention and Control of AIDS and Infectious Diseases\u201d, The Ministry of Health of the Khabarovsk Krai, 680031 Khabarovsk, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5299-3081","authenticated-orcid":false,"given":"Anna I.","family":"Kuznetsova","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksei","family":"Mazus","sequence":"additional","affiliation":[{"name":"Moscow City Center for AIDS Prevention and Control, 105275 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina","family":"Loifman","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Institution \u201cCenter for the Prevention and Control of AIDS and Infectious Diseases\u201d, The Ministry of Health of the Khabarovsk Krai, 680031 Khabarovsk, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liudmila","family":"Grigoreva","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Institution \u201cCenter for the Prevention and Control of AIDS and Infectious Diseases\u201d, The Ministry of Health of the Khabarovsk Krai, 680031 Khabarovsk, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9422-7238","authenticated-orcid":false,"given":"Denis","family":"Kleimenov","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2269-1469","authenticated-orcid":false,"given":"Evgeniia","family":"Bykonia","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry","family":"Shcheblyakov","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0639-8390","authenticated-orcid":false,"given":"Irina","family":"Favorskaya","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1107-9351","authenticated-orcid":false,"given":"Andrei","family":"Pochtovyi","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"},{"name":"Department of Medical Genetics and Postgenomic Technologies, Sechenov First Moscow State Medical University, 119991 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Tsyganova","sequence":"additional","affiliation":[{"name":"Moscow City Center for AIDS Prevention and Control, 105275 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inna","family":"Kulikova","sequence":"additional","affiliation":[{"name":"Department of Emergency Medical Assistance Organisation and Health Risk Management, Ministry of Health of the Russian Federation, 127994 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei","family":"Plutnitskii","sequence":"additional","affiliation":[{"name":"Federal Medical Biophysical Center Named After A.I. Burnazyan, 123098 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Gushchin","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"},{"name":"Department of Medical Genetics and Postgenomic Technologies, Sechenov First Moscow State Medical University, 119991 Moscow, Russia"},{"name":"Department of Virology, Lomonosov Moscow State University, 119234 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandr","family":"Gintsburg","sequence":"additional","affiliation":[{"name":"Federal State Budget Institution \u201cNational Research Center for Epidemiology and Microbiology Named After the Honorary Academician N.F. Gamaleya\u201d, The Ministry of Health of the Russian Federation, 123098 Moscow, Russia"},{"name":"Department of Infectiology and Virology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,30]]},"reference":[{"key":"ref_1","unstructured":"UNAIDS (2025, August 04). Documents. Fact Sheets 2025. Global HIV Statistic. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/cardiovascular-diseases-(cvds)."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"100912","DOI":"10.1016\/S2666-5247(24)00151-4","article-title":"Global and regional genetic diversity of HIV-1 in 2010-21: Systematic review and analysis of prevalence","volume":"5","author":"Nair","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1097\/00126334-200306010-00020","article-title":"High genetic diversity of HIV-1 strains in Chad, West Central Africa","volume":"33","author":"Vidal","year":"2003","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/bmb\/58.1.19","article-title":"Evolutionary and immunological implications of contemporary HIV-1 variation","volume":"58","author":"Korber","year":"2001","journal-title":"Br. Med. Bull."},{"key":"ref_5","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\u20132015: A systematic review, global survey, and trend analysis","volume":"19","author":"Hemelaar","year":"2019","journal-title":"Lancet Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1002\/jmv.20599","article-title":"Global epidemiology of HIV","volume":"78","author":"McCutchan","year":"2006","journal-title":"J. Med. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Khan, A.M., Hu, Y., Miotto, O., Thevasagayam, N.M., Sukumaran, R., Abd Raman, H.S., Brusic, V., Tan, T.W., and Thomas August, J. (2017). Analysis of viral diversity for vaccine target discovery. BMC Med. Genom., 10.","DOI":"10.1186\/s12920-017-0301-2"},{"key":"ref_8","first-page":"204","article-title":"Current Status of HIV-1 Diversity and Drug Resistance Monitoring in the Former USSR","volume":"15","author":"Bobkova","year":"2013","journal-title":"AIDS Rev."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Antonova, A., Kazennova, E., Lebedev, A., Ozhmegova, E., Kuznetsova, A., Tumanov, A., and Bobkova, M. (2023). Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses, 15.","DOI":"10.3390\/v15122312"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5935","DOI":"10.1128\/jvi.70.9.5935-5943.1996","article-title":"Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand","volume":"70","author":"Carr","year":"1996","journal-title":"J. Virol."},{"key":"ref_11","unstructured":"State Anti-Drug Committee (2025, August 04). Report on the Drug Situation in the Russian Federation in 2021. (In Russian)."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Mazus, A., Antonova, A., Adgamov, R., Ogarkova, D., Kuznetsova, A., Pochtovyi, A., Tsyganova, E., Zlobin, V., Gushchin, V., and Plutnitskii, A. (2024). Current Trends in HIV Infection in the Republic of Crimea. Viruses, 16.","DOI":"10.3390\/v16111716"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","article-title":"AliView: A Fast and Lightweight Alignment Viewer and Editor for Large Datasets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e144","DOI":"10.1093\/nar\/gku739","article-title":"COMET: Adaptive Context-Based Modeling for Ultrafast HIV-1 Subtype Identification","volume":"42","author":"Struck","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"S51","DOI":"10.1086\/505356","article-title":"Rationale and Uses of a Public HIV Drug-Resistance Database","volume":"194","author":"Shafer","year":"2006","journal-title":"J. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated Subtyping of HIV-1 Genetic Sequences for Clinical and Surveillance Purposes: Performance Evaluation of the New REGA Version 3 and Seven Other Tools","volume":"19","author":"Faria","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"W193","DOI":"10.1093\/nar\/gks414","article-title":"jpHMM: Recombination Analysis in Viruses with Circular Genomes Such as the Hepatitis B Virus","volume":"40","author":"Schultz","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (ITOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Ragonnet-Cronin, M., Hodcroft, E., Hu\u00e9, S., Fearnhill, E., Delpech, V., Brown, A.J., and Lycett, S. (2013). UK HIV Drug Resistance Database. Automated analysis of phylogenetic clusters. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-317"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1097\/QAD.0000000000001470","article-title":"Defining HIV-1 transmission clusters based on sequence data","volume":"3","author":"Hassan","year":"2017","journal-title":"AIDS"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"15","DOI":"10.21292\/2075-1230-2021-99-5-15-24","article-title":"HIV Situation in Russia at the Beginning of Implementation of State Strategy Aimed to Combat the Spread of HIV Infection","volume":"99","author":"Nechaeva","year":"2021","journal-title":"Tuberc. Lung Dis."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Ogarkova, D., Antonova, A., Kuznetsova, A., Adgamov, R., Pochtovyi, A., Kleimenov, D., Tsyganova, E., Gushchin, V., Gintsburg, A., and Mazus, A. (2023). Current Trends of HIV Infection in the Russian Federation. Viruses, 15.","DOI":"10.3390\/v15112156"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1089\/aid.2013.0196","article-title":"HIV-1 genetic diversity in Russia: CRF63_02A1, a new HIV type 1 genetic variant spreading in Siberia","volume":"30","author":"Baryshev","year":"2014","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_24","first-page":"14","article-title":"Rapid spread of the HIV-1 circular recombinant CRF02-AG in Russia and neighboring countries","volume":"60","author":"Moskaleychik","year":"2015","journal-title":"Vopr. Virusol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1097\/00002030-199814000-00023","article-title":"HIV-1 genetic subtype A\/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad","volume":"12","author":"Liitsola","year":"1998","journal-title":"AIDS"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1089\/08892220252781301","article-title":"Identification of a new circulating recombinant form of HIV type 1, CRF11-cpx, involving subtypes A, G, J, and CRF01-AE, in Central Africa","volume":"18","author":"Montavon","year":"2002","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Partsuneva, A., Gancheva, A., Dimitrova, R., Grigorova, L., Kostadinova, A., Nikolova, M., Emilova, R., Yancheva, N., Grozdeva, R., and Alexiev, I. (2025). Distinct Molecular Epidemiology, Transmission Patterns, and Resistance Mutations of HIV-1 Subtypes A1, A6, and A7 in Bulgaria. Microorganisms, 13.","DOI":"10.3390\/microorganisms13051108"},{"key":"ref_28","unstructured":"Stanford University (2025, August 04). HIV Drug Resistance Database. Major Nucleoside RT Inhibitor (NRTI) Resistance Mutations. Available online: https:\/\/hivdb.stanford.edu\/dr-summary\/resistance-notes\/NRTI\/."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2231","DOI":"10.1128\/AAC.37.10.2231","article-title":"High-level resistance to (-) enantiomeric 2\u2032-deoxy-3\u2032-thiacytidine in vitro is due to one amino acid substitution in the catalytic site of human immunodeficiency virus type 1 reverse transcriptase","volume":"37","author":"Boucher","year":"1993","journal-title":"Antimicrob Agents Chemother."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"5653","DOI":"10.1073\/pnas.90.12.5653","article-title":"Rapid in vitro selection of human immunodeficiency virus type 1 resistant to 3\u2032-thiacytidine inhibitors due to a mutation in the YMDD region of reverse transcriptase","volume":"90","author":"Tisdale","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Karaseva, E.V., and Sesorova, I.S. (2025, August 04). Development of a Vaccine Against HIV Infection Caused by the Human Immunodeficiency Virus: Domestic and Foreign Practice. Modern Problems of Science and Education. 2025, No. 2. (In Russian).","DOI":"10.17513\/spno.34007"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2355","DOI":"10.1038\/s41467-019-10262-5","article-title":"Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence","volume":"10","author":"Sliepen","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1089\/aid.2008.0219","article-title":"Appreciating HIV type 1 diversity: Subtype differences in Env","volume":"25","author":"Lynch","year":"2009","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e0260604","DOI":"10.1371\/journal.pone.0260604","article-title":"Origin and evolution of HIV-1 subtype A6","volume":"16","author":"Abidi","year":"2021","journal-title":"PLoS ONE"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1089\/aid.2011.0380","article-title":"Genetic characterization of HIV type 1 Tat exon 1 from a southern Indian clinical cohort: Identification of unique epidemiological signature residues","volume":"28","author":"Neogi","year":"2012","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_36","unstructured":"HIV Sequence Database (2025, August 04). CATNAP: Compile, Analyze and Talle Nab Panels, Available online: https:\/\/www.hiv.lanl.gov\/components\/sequence\/HIV\/neutralization\/main.comp."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1128\/JVI.02853-13","article-title":"Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies","volume":"88","author":"deCamp","year":"2014","journal-title":"J. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/12\/1568\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T05:19:53Z","timestamp":1764652793000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/12\/1568"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,30]]},"references-count":37,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["v17121568"],"URL":"https:\/\/doi.org\/10.3390\/v17121568","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,11,30]]}}}