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.

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.

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.

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.