Influenza viruses are significant causes of acute respiratory infections, often leading to severe health issues and mortality. These viruses undergo continuous mutations and genetic reassortments, resulting in annual epidemics and potential pandemics. The A(H3N2) strains exhibit high genetic and antigenic variability, that influence vaccine efficacy. This study aimed to assess the prevalence of influenza viruses, including A(H3N2) strains, in Kazakhstan during 2020–2025. The study used nasopharyngeal swab and serum samples obtained from patients. The presence of influenza virus antigens in nasopharyngeal swabs was analyzed using real-time polymerase chain reaction. The level of specific antibodies in the blood serum was determined using the hemagglutination inhibition reaction and enzyme-linked immunosorbent assay methods. Influenza A/H1N1, A/H3N2 and B viruses were diagnosed using real-time PCR. Antibodies to A/H1N1pdm09, A/H3N2 and B were detected in serological studies. Our studies revealed a trend toward seasonal patterns in influenza A viruses circulation. Therefore, it was established that the A/H3N2 strains dominated in Kazakhstan during the 2021–2022 and 2023–2024 epidemic seasons. The 2023–2024 strains belong to the specific genetic clade J.2 or 3C.2a1b.2a.2a.3a.1. These studies confirmed the role of influenza viruses in the etiology of respiratory infections and emphasized the need to continue monitoring their spread in Kazakhstan.

Relevance. In 2018 over 151 000 cases of whooping cough were reported worldwide. In the Republic of Kazakhstan the incidence of whooping cough has always remained relevant. The incidence is recorded mainly among children under 14 years of age, whose share is 96–100% of the total incidence in certain years. It should also be noted that 82,9–96% of sick people are not vaccinated against whooping cough. Aims. Assessment of the duration of protection after vaccination against pertussis infection in Kazakhstan using antibodies against pertussis toxin (PT) and (IgA and IgG) as a specific marker of pertussis infection or vaccination in children and adolescents in the cities of the Republic of Kazakhstan: Aktobe, Karaganda, Taldykorgan, Shymkent for evaluation appropriate age for booster vaccination. Materials and methods. For the study included medical organizations in the cities of Aktobe, Karaganda, Taldykorgan, Shymkent. Participants aged 10–14 years who were hospitalized in children's hospitals and 15–18 years old who visited polyclinics were invited to participate in the study. Each city has 1 children's hospital (4 in total) and 2 polyclinics (8 in total). A total of 520 people of different age groups participated. Study period: February 2021 – October 2021. Inclusion criteria were such aspects as: age from 10 years to 18 years 11 months 29 days, informed consent obtained from parents or guardian(s) and patient consent, enrollment after visiting the clinic, the presence of documented evidence of immune status. An association between two qualitative variables is considered statistically significant if the p-value calculated using the Chi-squared test is less than 0.05. Results. Among 520 participants aged 10–14 years – 200 (38.5%) and 15–18 years – 320 (61.5%), including boys – 284 (54.6%), girls – 236 (45.4%). The largest number of study participants was aged 15, 16 and 17 years, 10 participants (1.9%) had periods of prolonged coughing in the past 6 months. The first, second and third pertussis vaccines were received by 100% of children. The first and second vaccine for all children was the Adsorbed Diphtheria-Tetanus-Pertussis Vaccine (DPT). The third vaccine for 519 children was also DPT, for one child – AbDPT, due to the transition to a cell-free vaccine from the second half of 2013. The additional vaccine scheduled at 18 months of age was given to 519 participants (99.8%), of which 517 children (99.6%) received DPT and two children (0.4%) DPT. Just over half of the children (276 or 53.1%) also received the whooping cough vaccine at age 6. In biological blood samples of 17 participants (3.3%). antibodies of the IgA class were detected in 245 samples (47.1%) – antibodies of the IgG class. Of the 17 participants with IgA antibodies, 15 also tested positive for IgG. In total antibodies of the IgA and IgG classes were detected in 247 participants which amounted to 47.5%. Conclusions. This study showed the duration of protection after pertussis vaccination in Kazakhstan among different age groups. In total, antibodies of the IgA and IgG classes were detected in 247 participants out of 520 which amounted to 47.5%. IgA antibodies were detected in biological blood samples in 17 participants (3.3%), IgG class antibodies in 245 samples (47.1%). The prevalence of IgA antibodies was statistically significantly higher among older children and among children who had respiratory symptoms in the 6 months prior to the study. The prevalence of IgG antibodies was statistically significantly higher among children vaccinated against whooping cough at the age of 6 years (47.1%) and at the age of 10–14 years (56.2%) than in the age group of 15–18 years (43.8%) and also significantly higher among those, who share a bedroom with other family members compared to children living in separate rooms. Thus an increase in whooping cough and a decrease in protective vaccine immunity among older age groups can be stated which raises concerns about transmission of the infection in the home to vulnerable children and the need to strengthen vaccination strategies.

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.

Background/Objectives: Seasonal influenza threatens global public health through rapid mutations. This study evaluated the prevalence and molecular-genetic characteristics of seasonal influenza viruses circulating in Kazakhstan during the 2023–2026 epidemic seasons. Methods: Nasopharyngeal swabs (n = 1756) and serum samples (n = 718) were screened using RT-qPCR, HI, and ELISA assays. Selected A(H1N1)pdm09 isolates underwent full-length HA and NA gene next-generation sequencing, followed by phylogenetic and phenotypic analyses. Results: Influenza A(H3N2) strains dominated in Kazakhstan during the 2023–2024 and 2025–2026 seasons. Conversely, the 2024–2025 season showed a shifting landscape, characterized by co-circulation of influenza B and A(H1N1)pdm09 strains belonging to genetic clade 6B.1A.5a.2a (subclades C.1.9 and C.1.9.3). Mutational mapping revealed ongoing in situ microevolution adjacent to the receptor-binding site (HA-R222K). Genomic screening of the NA gene identified critical I223R and S247N mutations traditionally linked to resistance. In silico profiling predicted that while the majority maintained baseline sensitivity, the solitary A/Shymkent/NRL-1999/2024 isolate harboring the I223R substitution exhibited a multidrug-resistant genotype to oseltamivir, peramivir, and zanamivir. Conclusions: These findings demonstrate dynamic inter-seasonal etiological shifts and the predicted emergence of an independent resistant lineage (NA-I223R). This underscores the necessity for continuous, expanded genomic surveillance of respiratory pathogens across Kazakhstan.

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.

Seasonal human coronaviruses (HCoVs) remain underrepresented in genomic surveil-lance in Central Asia. We applied species-specific tiled amplicon sequencing on the Oxford Nanopore Technologies platform to residual HCoV-positive respiratory samples collected in Kazakhstan. Of 102 samples received, 17 were tested with tiled panels and seven were sequenced. Six consensus genomes were near-complete (97.27–100.00% unambiguous positions), whereas one additional HCoV-OC43 genome was partial (39.97%) and excluded from phylogenetic analysis. Maximum-likelihood trees were reconstructed from a quality-controlled panel derived from public GenBank accessions, and whole-genome, ORF1ab, and Spike topologies were compared. The HCoV-229E/187 genome was tentatively assigned to genotype 7b. HCoV-NL63/324 and HCoV-NL63/327 were tentatively assigned to genotype C2, and HCoV-NL63/487 was also tentatively assigned to C2, with lower confidence. HCoV-OC43/259 was G-associated in whole-genome and Spike analyses but showed a different, weakly resolved ORF1ab context. HCoV-HKU1/1042 was B-like but unresolved because Spike could not be evaluated. RDP4 screening identified study-associated candidate signals for HCoV-229E/187, HCoV-OC43/259, and HCoV-HKU1/1042, but not for the three Kazakhstan HCoV-NL63 genomes. Automated breakpoint and parental assignments were treated as provisional and did not confirm individual recombination events. These findings expand genome-level evidence for all four endemic HCoV species in Kazakhstan while illustrating the importance of coverage-aware, cross-locus interpretation of genotype assignments.