SARS-COV-2 VARIANT EVOLUTION: GLOBAL PATTERNS, NEW SUBVARIANTS, AND REGIONAL CONTEXT (UKRAINE & HIV)
DOI:
https://doi.org/10.11603/1681-2727.2026.1.16166Keywords:
SARS-CoV-2, variants of concern, Omicron, JN.1, BA.2.86, recombination, immune escape, genomic surveillance, Ukraine, HIV, immunocompromised hosts, antiretroviral therapyAbstract
Since late 2019, SARS-CoV-2 has diversified into numerous lineages, driving recurrent global waves of COVID-19. This narrative review synthesizes evidence on the evolutionary dynamics of SARS-CoV-2 with emphasis on Omicron subvariants, including JN.1 and its descendants, and emerging 2025 lineages (Nimbus and Stratus).
We summarize major mechanisms shaping viral diversification – mutation/antigenic drift, recombination, and prolonged infection in immunocompromised hosts (including people living with HIV) – that can promote stepwise accumulation of immune-escape mutations.
The review covers literature and genomic surveillance reports from 2019–2025 (WHO resources, GISAID, outbreak.info, PubMed/Scopus) and focuses on mutation profiles of key variants, global prevalence trends, and Ukraine-specific context.
A dedicated section addresses why Ukraine – despite a relatively high HIV burden in Eastern Europe – has not been recognized as a major source of globally dominant variants of concern. Contributing factors discussed include limited sequencing coverage, reduced travel/export potential, expansion of ART, and stochastic and structural determinants required for widespread dissemination of newly arising lineages.We conclude that ongoing immune escape remains likely, underscoring the need for robust genomic surveillance, timely vaccine/therapeutic updates, and integration of COVID-19 monitoring with HIV services.
References
World Health Organization. (2023–2025). Tracking SARS-CoV-2 variants. World Health Organization. https://www.who.int
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403–1407. https://doi.org/10.1038/s41564-020-0770-5 DOI: https://doi.org/10.1038/s41564-020-0770-5
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Peacock, S. J., & Robertson, D. L. (2021). SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19(7), 409–424. https://doi.org/10.1038/s41579-021-00573-0 DOI: https://doi.org/10.1038/s41579-021-00573-0
Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., … de Oliveira, T. (2022). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, 603(7902), 679–686. https://doi.org/10.1038/s41586-022-04411-y DOI: https://doi.org/10.1038/s41586-022-04411-y
Cele, S., Jackson, L., Khoury, D. S., Khan, K., Moyo-Gwete, T., Tegally, H., … Sigal, A. (2022). Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, 602(7898), 654–656. https://doi.org/10.1038/s41586-021-04387-1 DOI: https://doi.org/10.1038/s41586-021-04387-1
Planas, D., Saunders, N., Maes, P., Guivel-Benhassine, F., Planchais, C., Buchrieser, J., … Schwartz, O. (2022). Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature, 602(7898), 671–675. https://doi.org/10.1038/s41586-021-04389-z DOI: https://doi.org/10.1038/s41586-021-04389-z
Cao, Y., Yisimayi, A., Jian, F., Song, W., Xiao, T., Wang, L., … Xie, X. S. (2022). BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature, 608(7923), 593–602. https://doi.org/10.1038/s41586-022-04980-y DOI: https://doi.org/10.1038/s41586-022-04980-y
Santos da Silva, E., Servais, J. Y., Kohnen, M., Arendt, V., Gilson, G., Staub, T., Seguin-Devaux, C., & Perez-Bercoff, D. (2023). Vaccine- and breakthrough infection-elicited pre-Omicron immunity more effectively neutralizes Omicron BA.1, BA.2, BA.4 and BA.5 than pre-Omicron infection alone. Current Issues in Molecular Biology, 45(2), 1741–1761. https://doi.org/10.3390/cimb45020112 DOI: https://doi.org/10.3390/cimb45020112
Tamura, T., Ito, J., Uriu, K., Zahradnik, J., Kida, I., Anraku, Y., … Sato, K. (2023). Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nature Communications, 14, Article 2800. https://doi.org/10.1038/s41467-023-38435-3 DOI: https://doi.org/10.1038/s41467-023-38435-3
Tamura, T., Mizuma, K., Nasser, H., Deguchi, S., Padilla-Blanco, M., Oda, Y., … Sato, K. (2024). Virological characteristics of the SARS-CoV-2 BA.2.86 variant. Cell Host & Microbe, 32(2), 170–180.e12. https://doi.org/10.1016/j.chom.2024.01.001 DOI: https://doi.org/10.1016/j.chom.2024.01.001
Khare, S., Gurry, C., Freitas, L., Schultz, M. B., Bach, G., Diallo, A., Akite, N., Ho, J., Lee, R. T., Yeo, W., GISAID Curation Team, & Maurer-Stroh, S. (2021). GISAID’s role in pandemic response. China CDC Weekly, 3(49), 1049–1051. https://doi.org/10.46234/ccdcw2021.255 DOI: https://doi.org/10.46234/ccdcw2021.255
European Centre for Disease Prevention and Control. (2025). SARS-CoV-2 variants situation updates. European Centre for Disease Prevention and Control. https://www.ecdc.europa.eu/en/covid-19/variants-concern
Tarcsai, K. R., Corolciuc, O., Tordai, A., & Ongrádi, J. (2022). SARS-CoV-2 infection in HIV-infected patients: Potential role in the high mutational load of the Omicron variant emerging in South Africa. GeroScience, 44(5), 2337–2345. https://doi.org/10.1007/s11357-022-00603-6 DOI: https://doi.org/10.1007/s11357-022-00603-6
Kandeel, M., Mohamed, M. E. M., El-Lateef, H. M. A., Verugopala, K. N., & El-Beltagi, H. S. (2022). Omicron variant genome evolution and phylogenetics. Journal of Medical Virology, 94, 1627–1632. https://doi.org/10.1002/jmv.27515 DOI: https://doi.org/10.1002/jmv.27515
Magiorkinis, G. (2023). On the evolution of SARS-CoV-2 and the emergence of variants of concern. Trends in Microbiology, 31(1), 5–8. https://doi.org/10.1016/j.tim.2022.10.008 DOI: https://doi.org/10.1016/j.tim.2022.10.008
European Centre for Disease Prevention and Control. (2022). Assessment of the further spread and potential impact of the SARS-CoV-2 Omicron variant of concern in the EU/EEA (19th update, 27 January 2022). European Centre for Disease Prevention and Control. DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.43.2210271
Thye, A. Y., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K.-G., & Lee, L.-H. (2021). Emerging SARS-CoV-2 variants of concern (VOCs): An impending global crisis. Biomedicines, 9(10), Article 1303. https://doi.org/10.3390/biomedicines9101303 DOI: https://doi.org/10.3390/biomedicines9101303
World Health Organization. (n.d.). WHO COVID-19 variants dashboard. World Health Organization. https://data.who.int/dashboards/covid19/variants
Dimaano, A., Carreon, K. D., Camaya, G. S., Rondolo, I., & Tolentino, J. E. (2024). Genomic analysis of the SARS-CoV-2 variants circulated in the Philippines, 2020–2024. Dialogues in Health, 5, Article 100193. https://doi.org/10.1016/j.dialog.2024.100193 DOI: https://doi.org/10.1016/j.dialog.2024.100193
Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E., Tsueng, G., … Hughes, L. D. (2023). Outbreak.info genomic reports: Scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nature Methods, 20(4), 512–522. https://doi.org/10.1038/s41592-023-01769-3 DOI: https://doi.org/10.1038/s41592-023-01769-3
Joint United Nations Programme on HIV/AIDS. (2024). Global AIDS update: Eastern Europe and Central Asia (EECA) profile. UNAIDS.
Choi, B., Choudhary, M. C., Regan, J., Sparks, J. A., Padera, R. F., Qiu, X., Solomon, I. H., Kuo, H.-H., Boucau, J., Bowman, K., Adhikari, U. D., Winkler, M. L., Mueller, A. A., Hsu, T. Y., Desjardins, M., Baden, L. R., Chan, B. T., Walker, B. D., Lichterfeld, M., … Li, J. Z. (2020). Persistence and evolution of SARS-CoV-2 in an immunocompromised host. New England Journal of Medicine, 383(23), 2291–2293. https://doi.org/10.1056/NEJMc2031364 DOI: https://doi.org/10.1056/NEJMc2031364
Clark, S. A., Clark, L. E., Pan, J., Coscia, A., McKay, L. G. A., Shankar, S., Johnson, R. I., Brusic, V., Choudhary, M. C., Regan, J., Li, J. Z., Griffiths, A., & Abraham, J. (2021). SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms. Cell, 184(10), 2605–2617.e18. https://doi.org/10.1016/j.cell.2021.03.027 DOI: https://doi.org/10.1016/j.cell.2021.03.027
Iaruchyk, A., Farlow, J., Skrypnyk, A., Matchyshyn, S., Kovalchuk, A., Demchyshyna, I., Rosada, M., Aregay, A. K., & Habicht, J. (2025). Genomic epidemiology of SARS-CoV-2 in Ukraine from May 2022 to March 2024 reveals Omicron variant dynamics. Viruses, 17(7), Article 1000. https://doi.org/10.3390/v17071000 DOI: https://doi.org/10.3390/v17071000
Centers for Disease Control and Prevention. (n.d.). Variant proportions and genomic surveillance. CDC. https://www.cdc.gov/covid/php/variants/variants-and-genomic-surveillance.html
Neduzhko, O., Kiriazova, T., Zeziulin, O., Legkostup, L., Riabokon, S., DeHovitz, J. A., & Dumchev, K. (2024). The effects of the COVID-19 pandemic on HIV service provision in Ukraine. Journal of the International Association of Providers of AIDS Care, 23, 23259582241277649. https://doi.org/10.1177/23259582241277649 DOI: https://doi.org/10.1177/23259582241277649
Parczewski, M., & Gökengin, D. (2024). The HIV epidemic in Eastern Europe and Central Asia in difficult times: A story of resilience and change. Journal of the International AIDS Society, 27(Suppl 3), e26325. https://doi.org/10.1002/jia2.26325 DOI: https://doi.org/10.1002/jia2.26325
Weigang, S., Fuchs, J., Zimmer, G., Schnepf, D., Kern, L., Beer, J., Luxenburger, H., Ankerhold, J., Falcone, V., Kemming, J., Hofmann, M., Thimme, R., Neumann-Haefelin, C., Ulferts, S., Grosse, R., Hornuss, D., Tanriver, Y., Rieg, S., Wagner, D., … Kochs, G. (2021). Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants. Nature Communications, 12, Article 6405. https://doi.org/10.1038/s41467-021-26602-3 DOI: https://doi.org/10.1038/s41467-021-26602-3
Rocklöv, J., & Sjödin, H. (2020). High population densities catalyze the spread of COVID-19. Journal of Travel Medicine, 27(3), taaa038. https://doi.org/10.1093/jtm/taaa038 DOI: https://doi.org/10.1093/jtm/taaa038
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Accepted 2026-04-18
Published 2026-04-20
