{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T07:56:18Z","timestamp":1772697378237,"version":"3.50.1"},"reference-count":27,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"State Research and Development Program","award":["#5-21"],"award-info":[{"award-number":["#5-21"]}]},{"name":"State Research Center of Virology and Biotechnology \u201cVECTOR\u201d","award":["#5-21"],"award-info":[{"award-number":["#5-21"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Studies of HIV-1 molecular epidemiology describe significant differences in HIV infection spread across geographical areas. We examined 80 HIV-1 samples from the Jewish Autonomous Region of Russia in 2024. HIV-1 genome sequences for 12 samples revealed a novel HIV-1 called CRF173_63A6. HIV-1 CRF173_63A6 was found to have arisen through recombination between a specific Russian A6 subtype and the recombinant virus CRF63_02A6, which is responsible for the PWID-associated HIV outbreak in the Siberian region of Russia. Phylogenetic analysis of pol sequences previously deposited in Genbank showed that the CRF173_63A6 samples we described are grouped into a common phylogenetic cluster that includes 54 HIV-1 samples isolated in the JAR and other areas of the Russian Far East, indicating a wide distribution of this virus genovariant. This study once again proves the significant contribution of the key PWID group not only to the development of local Russian HIV epidemics, but also to the change in the characteristics of the circulating virus population.<\/jats:p>","DOI":"10.3390\/pathogens14090836","type":"journal-article","created":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T07:41:45Z","timestamp":1755848505000},"page":"836","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Characterization of a New HIV-1 Second-Generation Circulating Recombinant Form CRF173_63A6 in the Jewish Autonomous Region of Russia"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0465-1260","authenticated-orcid":false,"given":"Vasiliy E.","family":"Ekushov","sequence":"first","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1765-1909","authenticated-orcid":false,"given":"Maksim R.","family":"Halikov","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexei V.","family":"Totmenin","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3218-0371","authenticated-orcid":false,"given":"Mariya E.","family":"Antonets","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatyana V.","family":"Tregubchak","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrey I.","family":"Murzin","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina N.","family":"Pavlova","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Organization \u201cCenter for the Prevention and Control of AIDS\u201d of the Jewish Autonomous Region, 679000 Birobidzhan, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anastasia M.","family":"Troianova","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Organization \u201cCenter for the Prevention and Control of AIDS\u201d of the Jewish Autonomous Region, 679000 Birobidzhan, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatyana P.","family":"Adusheva","sequence":"additional","affiliation":[{"name":"Regional State Budgetary Healthcare Organization \u201cCenter for the Prevention and Control of AIDS\u201d of the Jewish Autonomous Region, 679000 Birobidzhan, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8099-1267","authenticated-orcid":false,"given":"Svetlana N.","family":"Beniova","sequence":"additional","affiliation":[{"name":"Regional Clinical Hospital No 2, 690011 Vladivostok, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra S.","family":"Ermolitskaya","sequence":"additional","affiliation":[{"name":"Regional Clinical Hospital No 2, 690011 Vladivostok, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4635-4678","authenticated-orcid":false,"given":"Irina S.","family":"Gorelova","sequence":"additional","affiliation":[{"name":"Regional Clinical Hospital No 2, 690011 Vladivostok, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2577-0434","authenticated-orcid":false,"given":"Alexander P.","family":"Agafonov","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalya M.","family":"Gashnikova","sequence":"additional","affiliation":[{"name":"State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Abidi, S.H., Aibekova, L., Davlidova, S., Amangeldiyeva, A., Foley, B., and Ali, S. (2021). Origin and evolution of HIV-1 subtype A6. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0260604"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Lebedev, A., Lebedeva, N., Moskaleychik, F., Pronin, A., Kazennova, E., and Bobkova, M. (2019). Human immunodeficiency virus-1 diversity in the Moscow region, Russia: Phylodynamics of the most common subtypes. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00320"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"van de Klundert, M.A.A., Antonova, A., Di Teodoro, G., Diez, R.C., Chkhartishvili, N., Heger, E., Kuznetsova, A., Lebedev, A., Narayanan, A., and Ozhmegova, E. (2022). Molecular epidemiology of HIV-1 in Eastern Europe and Russia. Viruses, 14.","DOI":"10.3390\/v14102099"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Sivay, M.V., Maksimenko, L.V., Osipova, I.P., Nefedova, A.A., Gashnikova, M.P., Zyryanova, D.P., Ekushov, V.E., Totmenin, A.V., Nalimova, T.M., and Ivlev, V.V. (2022). Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.946787"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"veac044","DOI":"10.1093\/ve\/veac044","article-title":"Molecular epidemiology of HIV-1 in Oryol oblast, Russia","volume":"8","author":"Safina","year":"2022","journal-title":"Virus Evol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1089\/aid.2020.0225","article-title":"Genetic Diversity and Drug Resistance Mutations in Reverse Transcriptase and Protease Genes of HIV-1 Isolates from Southwestern Siberia","volume":"37","author":"Rudometova","year":"2021","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"79","DOI":"10.18821\/0507-4088-2019-64-2-79-89","article-title":"Molecular genetic characteristics of HIV-1 variants isolated in the subjects of the Russian far east","volume":"64","author":"Kotova","year":"2019","journal-title":"Vopr. Virusol. (Probl. Virol. Russ. J.)"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Kirichenko, A., Kireev, D., Lapovok, I., Shlykova, A., Lopatukhin, A., Pokrovskaya, A., Bobkova, M., Antonova, A., Kuznetsova, A., and Ozhmegova, E. (2023). HIV-1 drug resistance among treatment-na\u00efve patients in Russia: Analysis of the national database, 2006\u20132022. Viruses, 15.","DOI":"10.3390\/v15040991"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.jinf.2023.11.005","article-title":"Identification of a novel HIV-1 circulating recombinant form CRF157_A6C in Primorsky Territory, Russia","volume":"88","author":"Halikov","year":"2024","journal-title":"J. Infect."},{"key":"ref_10","first-page":"48","article-title":"The importance of detection of the patterns of HIV-1 genome variability in the system of epidemiological surveillance for HIV-infection (on the example of some territories of the Eastern Federal district)","volume":"37","author":"Kotova","year":"2019","journal-title":"Far East. J. Infect. Pathol."},{"key":"ref_11","first-page":"79","article-title":"Circulating recombinant forms of HIV-1 constituent entities of the Far Eastern Federal district","volume":"40","author":"Kotova","year":"2021","journal-title":"Far East. J. Infect. Pathol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular evolutionary genetics analysis version 11","volume":"38","author":"Koichiro","year":"2021","journal-title":"Mol. Biol. Evol."},{"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":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Kazutaka","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1089\/aid.1995.11.1413","article-title":"A Computer Program Designed to Screen Rapidly for HIV Type 1 Intersubtype Recombinant Sequences","volume":"11","author":"Siepel","year":"1995","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"W647","DOI":"10.1093\/nar\/gkp371","article-title":"jpHMM: Improving the reliability of recombination prediction in HIV-1","volume":"37","author":"Schultz","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"veaa087","DOI":"10.1093\/ve\/veaa087","article-title":"RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets","volume":"7","author":"Martin","year":"2020","journal-title":"Virus Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: Real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.drugpo.2003.09.001","article-title":"HIV transmission and HIV prevention associated with injecting drug use in the Russian Federation","volume":"15","author":"Rhodes","year":"2004","journal-title":"Int. J. Drug Policy"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"F25","DOI":"10.1097\/00002030-200209060-00002","article-title":"Explosive spread and high prevalence of HIV infection among injecting drug users in Togliatti City, Russia","volume":"16","author":"Rhodes","year":"2022","journal-title":"Aids"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/S0140-6736(03)12831-0","article-title":"HIV in central and eastern Europe","volume":"361","author":"Hamers","year":"2003","journal-title":"Lancet"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s12954-017-0162-1","article-title":"\u201cUntil people start dying in droves, no actions will be taken\u201d: Perception and experience of HIV-preventive measures among people who inject drugs in northwestern Russia","volume":"14","author":"Meylakhs","year":"2017","journal-title":"Harm Reduct. J."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"88","DOI":"10.22625\/2072-6732-2020-12-2-88-96","article-title":"Detection of HIV-1 resistant to antiretroviral drugs among tomsk oblast population with newly diagnosed HIV-infection","volume":"12","author":"Zyryanova","year":"2020","journal-title":"J. Infectol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/j.jinf.2022.10.001","article-title":"Novel HIV-1 A6\/B recombinant forms (CRF133_A6B and URF_A6\/B) circulating in Krasnoyarsk region, Russia","volume":"85","author":"Maksimenko","year":"2022","journal-title":"J. Infect."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"106308","DOI":"10.1016\/j.jinf.2024.106308","article-title":"Expanding HIV-1 diversity in Russia: Novel circulating recombinant form between subtypes A6 and B (CRF147_A6B)","volume":"89","author":"Maksimenko","year":"2024","journal-title":"J. Infect."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/9\/836\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:33:29Z","timestamp":1760034809000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/9\/836"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,22]]},"references-count":27,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["pathogens14090836"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14090836","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,22]]}}}