{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T23:19:16Z","timestamp":1769555956275,"version":"3.49.0"},"reference-count":29,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["AP23485202"],"award-info":[{"award-number":["AP23485202"]}]},{"name":"US CDC","award":["5NU2GGH002389-05-00"],"award-info":[{"award-number":["5NU2GGH002389-05-00"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had major social and economic consequences worldwide. Whole genome sequencing (WGS) is essential for genomic monitoring, enabling tracking of viral evolution, detection of emerging variants, and identification of introductions and transmission chains to inform timely public health responses. Here, we compile and harmonize SARS-CoV-2 genomic data generated by multiple laboratories across Kazakhstan together with publicly available sequences to provide a national overview of genomic dynamics across successive epidemic waves from 2020 to 2022. We analyzed 4462 genomes deposited in GISAID (including 340 generated in this study), of which 3299 passed Nextclade quality filters, and summarized lineage turnover across major phases (pre-VOC, Alpha, Delta, Omicron BA.1\/BA.2, Omicron BA.4\/BA.5, and a later recombinant-dominant period). Sequencing intensity varied markedly over time (0.60\u2030 of confirmed cases during Delta vs. 11.57\u2030 during the Omicron BA.5 wave), suggesting that lineage diversity and persistence may be underestimated. Pre-VOC circulation included \u226512 Pango lineages with evidence of multiple introductions and sustained local transmission, including a Kazakhstan-restricted B.4.1 lineage that emerged in Nur-Sultan\/Astana and disappeared after April 2020. The Tengizchevroil oilfield outbreak comprised B.1.1 viruses with phylogenetic support for \u2265three independent introductions. Alpha and Omicron waves were characterized by repeated introductions and heterogeneous origins, whereas Delta was dominated by AY.122 with an additional distinct AY.122 cluster; a notable BF.7 local transmission event was observed during BA.5. We also highlight locally enriched non-lineage-defining mutations. Overall, recurrent importations and variable local amplification shaped SARS-CoV-2 dynamics in Kazakhstan, while interpretation is constrained by strongly time-skewed sequencing.<\/jats:p>","DOI":"10.3390\/v18010138","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T13:59:54Z","timestamp":1769003994000},"page":"138","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Diversity of SARS-CoV-2 in Kazakhstan from 2020 to 2022"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2323-5043","authenticated-orcid":false,"given":"Altynay","family":"Gabiden","sequence":"first","affiliation":[{"name":"National Center of Public Health Care, The Ministry of Health of the Republic of Kazakhstan, Almaty 050008, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1733-1255","authenticated-orcid":false,"given":"Andrey","family":"Komissarov","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197022 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9608-4138","authenticated-orcid":false,"given":"Aknur","family":"Mutaliyeva","sequence":"additional","affiliation":[{"name":"National Center of Public Health Care, The Ministry of Health of the Republic of Kazakhstan, Almaty 050008, Kazakhstan"},{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5117-5490","authenticated-orcid":false,"given":"Aidar","family":"Usserbayev","sequence":"additional","affiliation":[{"name":"National Center of Public Health Care, The Ministry of Health of the Republic of Kazakhstan, Almaty 050008, Kazakhstan"},{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0829-3330","authenticated-orcid":false,"given":"Kobey","family":"Karamendin","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5961-1856","authenticated-orcid":false,"given":"Alexander","family":"Perederiy","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197022 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3558-3261","authenticated-orcid":false,"given":"Artem","family":"Fadeev","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197022 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1391-4253","authenticated-orcid":false,"given":"Ainagul","family":"Kuatbaeva","sequence":"additional","affiliation":[{"name":"National Center of Public Health Care, The Ministry of Health of the Republic of Kazakhstan, Almaty 050008, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0965-0942","authenticated-orcid":false,"given":"Dariya","family":"Jussupova","sequence":"additional","affiliation":[{"name":"Faculty of Natural Sciences and Geography, Abai Kazakh National Pedagogical University, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1106-3468","authenticated-orcid":false,"given":"Askar","family":"Abdaliyev","sequence":"additional","affiliation":[{"name":"National Center of Expertise of the Committee of Sanitary and Epidemiological Control, The Ministry of Health of the Republic of Kazakhstan, Astana 010000, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0905-8121","authenticated-orcid":false,"given":"Manar","family":"Smagul","sequence":"additional","affiliation":[{"name":"National Center of Public Health Care, The Ministry of Health of the Republic of Kazakhstan, Almaty 050008, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6279-3419","authenticated-orcid":false,"given":"Yelizaveta","family":"Khan","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6148-8204","authenticated-orcid":false,"given":"Marat","family":"Kumar","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7564-2097","authenticated-orcid":false,"given":"Temirlan","family":"Sabyrzhan","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2940-962X","authenticated-orcid":false,"given":"Aigerim","family":"Abdimadiyeva","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8374-6128","authenticated-orcid":false,"given":"Aidyn","family":"Kydyrmanov","sequence":"additional","affiliation":[{"name":"Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1080\/22221751.2020.1719902","article-title":"Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan","volume":"9","author":"Chan","year":"2020","journal-title":"Emerg\n\t\t\t            . 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