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‰ of confirmed cases during Delta vs. 11.57‰ during the Omicron BA.5 wave), suggesting that lineage diversity and persistence may be underestimated. Pre-VOC circulation included ≥12 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 ≥three 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.

Influenza viruses undergo continuous genetic and antigenic evolution, making sustained surveillance essential for monitoring changes in virus circulation and vaccine relevance. We analyzed influenza epidemiology and viral evolution in Kazakhstan across eight consecutive epidemic seasons (2017/18–2024/25) using data from the national influenza sentinel surveillance system, together with antigenic characterization, Sanger sequencing, whole-genome sequencing, and phylogenetic analysis. Influenza activity was almost undetectable during the 2020/21 season, followed by the re-emergence of A(H3N2)-dominated circulation in 2021/22. In 2022/23, influenza B predominated initially, followed by A(H1N1)pdm09, whereas A(H3N2) predominated in 2023/24. A total of 199 A(H1N1)pdm09, 157 A(H3N2), 105 B/Victoria, and 16 B/Yamagata viruses were genetically characterized. A(H1N1)pdm09 viruses showed successive replacement of 6B-derived lineages, with descendants of 6B.1A.5a.2a predominating in the post-pandemic period. A(H3N2) viruses showed substantial genetic diversification, progressing from 3C.2a descendants to 3C.2a1b-related viruses and subsequently to 2a.3a.1/J.2 viruses. Among B/Victoria viruses, V1A was successively replaced by V1A.3 and V1A.3a.2, with V1A.3a.2 accounting for 100% of genetically characterized viruses in 2023/24 and 2024/25. Antigenic analysis showed 16- to 32-fold lower HI titers for A(H1N1)pdm09 6B.1A.5a.2 viruses when tested against antisera to earlier vaccine/reference strains, whereas no detectable antigenic differences were observed between 6B.1A.5a.2a and its recent descendants. These findings demonstrate substantial post-pandemic changes in influenza epidemic timing, subtype dominance, and genetic composition in Kazakhstan, while circulating viruses remained within globally recognized evolutionary lineages. Integrated epidemiological, genetic, and antigenic surveillance is important for detecting emerging variants, assessing vaccine relevance, and supporting timely influenza prevention and control measures.

Despite mass immunization against COVID-19, due to the high rate of spread, as well as the tendency to rapidly change and recombine, the SARS-CoV-2 virus caused several outbreaks (waves) of the disease around the world. Thus, at the end of 2020, WHO announced the emergence of new variants of SARS-CoV-2, which were associated with a new wave of COVID-19 cases. And at the beginning of 2021, sequences of the B.1.1.7 variant, first identified in the United Kingdom (UK) at the end of 2020 and later called the Alpha variant, were registered in several countries. In this regard, Kazakhstan, like other countries, has been conducting molecular genetic studies of SARS-CoV-2 viruses since 2021. To detect the B.1.1.7 variant in Kazakhstan, we used a preliminary screening of viral single nucleotide polymorphism (VirSNP), in particular the N501Y mutation characteristic of the B.1.1.7, B.1.351 and P.1 lineages. Of the 703 positive samples collected from February to May 2021, 321 (45.7%) had the N501Y mutation. The highest number of cases were detected in the populous cities of Almaty and Astana. To identify molecular genetic differences of the Alpha variant in Kazakhstan, we performed whole-genome sequencing using Illumina next-generation sequencing. As a result of sequencing, in addition to the N501Y mutation, we also detected the characteristic B.1.1.7 mutations A570D, P681H and T716I. Additionally, whole-genome sequences from Kazakhstan deposited in GISAID by other researchers were used to determine the genetic diversity of the Alpha variant. Of the 174 SARS-CoV-2 virus sequences obtained, 170 were confirmed to belong to the Alpha variant. Несмотря на массовую иммунизацию от COVID-19, из-за высокой скорости распространения, а также склонности к быстрым изменениям и рекомбинациям, вирус SARS-CoV-2 вызывал несколько вспышек (волн) заболеваемости во всем мире. Так, в конце 2020 года ВОЗ объявила о появлении новых вариантов SARS-CoV-2, с которыми была связана новая волна заболеваемости COVID-19. В начале 2021 года в нескольких странах регистрировались последовательности варианта B.1.1.7, впервые выявленном в Соединенном Королевстве (Великобритания) в конце 2020 года и позже названный вариантом Альфа. В связи с этим Казахстан, как и другие страны, с 2021 году проводит молекулярно-генетические исследования вирусов SARS-CoV-2. Для обнаружения варианта B.1.1.7 в Казахстане использовали предварительный скрининг вирусного однонуклеотидного полиморфизма (VirSNP), в частности мутации N501Y, характерной для линий B.1.1.7, B.1.351 и P.1. Всего из 703 положительных образцов, отобранных с февраля по май 2021 года, 321 (45,7%) имели мутацию N501Y. Наибольшее количество случаев было выявлено для многонаселенных городов Алматы и Астана. Для выявления молекулярно-генетических различий варианта Альфа на территории Казахстана, мы провели полногеномное секвенирование с использованием секвенирования нового поколения Illumina. В результате секвенирования помимо мутации N501Y были также обнаружены характерные B.1.1.7 мутации A570D, P681H и T716I. Дополнительно для определения генетического разнообразия варианта Альфа использовали полногеномные последовательности из Казахстана, депонированные в GISAID другими исследователями. Из 174 полученных последовательностей вируса SARS-CoV-2, для 170 подтверждена принадлежность к варианту Альфа.