Impact of COVID-19 pandemic on the etiology and severity of respiratory viral infections in children

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Abstract

Objective. To analyze the age-related characteristics of the contribution of influenza viruses, RSV, SARS-CoV-2, other pathogens to the development of severe acute respiratory infections (SARI) in children with an assessment of the disease severity depending on its etiology and epidemic period.

Materials and methods. SARI monitoring was carried out over six consecutive epidemic seasons, starting from 2018–2019 in 9 infectious hospitals of three cities of Russia with an assessment of the disease severity depending on its etiology.

Results. Among all hospitalized children, the proportion of children hospitalized with laboratory-confirmed influenza from 2018 to 2020 ranged from 25.7% to 44.7%, and for RSV infection from 25.7% to 26.8%. However, during the peak of the pandemic, these rates dropped significantly to 0.3% and 1.7%, respectively. In the subsequent three seasons (2021–2024), laboratory-confirmed influenza among hospitalized children was registered in 4.5–20.2% of cases, while RSV infection was identified in 13.4–24.1% of cases, accompanied by a shift in viral subgroups. RSV infections were most severe during the 2022–2023 season, presenting in some cases with hyperthermia, hypoxia, dyspnea, and altered consciousness. Among hospitalized children, the proportion with COVID-19 was relatively low in 2020–2021 (0.8–2.4%) but increased significantly to 10.6%–13.6% following the emergence of the Omicron variant in 2022, before decreasing again in subsequent years. The main genetic lineages of SARS-CoV-2 circulating in the Russian Federation are presented.

Conclusion. Influenza and RSV viruses were predominant among viral pathogens identified in hospitalized children aged ≤ 2 years. COVID-19 cases among children were relatively rare and generally less severe compared to RSV and rhinovirus infections.

About the authors

Anna А. Sominina

Smorodintsev Research Institute of Influenza, Ministry of Health

Author for correspondence.
Email: anna.sominina@influenza.spb.ru
ORCID iD: 0000-0001-9671-0629

Doctor of Medical Sciences, Professor, Head of the Laboratory of the of Risk Factors Assessment in Influenza and ARVI

Russian Federation, 197022, St. Petersburg

Darya M. Danilenko

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: daria.baibus@gmail.com
ORCID iD: 0000-0001-6174-0836

Candidate of Biological Sciences, Deputy Director for Scientific Work, Head of the Department of Etiology and Epidemiology

Russian Federation, 197022, St. Petersburg

Andrey B. Komissarov

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: a.b.komissarov@gmail.com
ORCID iD: 0000-0003-1733-1255

Head of the lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Artem V. Fadeev

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: artem.fadeev@influenza.spb.ru
ORCID iD: 0000-0003-3558-3261

senior researcher, lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Ksenia S. Komissarova

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: kseniya.sintsova@influenza.spb.ru
ORCID iD: 0000-0002-1465-5548

researcher, lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Maria M. Pisareva

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: maria.pisareva@influenza.spb.ru
ORCID iD: 0000-0002-1499-9957

Candidate of Biological Sciences, leading researcher, lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Tamila D. Musayeva

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: tamila.musaeva@influenza.spb.ru
ORCID iD: 0000-0002-3050-1936

junior researcher, lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Veronika A. Eder

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: veronika.eder@influenza.spb.ru
ORCID iD: 0000-0002-9970-3325

PhD, senior researcher, lab. of molecular virology

Russian Federation, 197022, St. Petersburg

Tatiana P. Levanyuk

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: tatyana.levanyuk@influenza.spb.ru
ORCID iD: 0009-0003-6888-6848

leading programmer, Laboratory of Risk Factors Assessment in Influenza and ARVI

Russian Federation, 197022, St. Petersburg

Kirill A. Stolyarov

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: kirill@influenza.spb.ru
ORCID iD: 0000-0002-1765-2799

leading programmer, lab. of epidemiology of influenza and ARVI

Russian Federation, 197022, St. Petersburg

Vera Z. Krivitskaya

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: vera.kriv@influenza.spb.ru
ORCID iD: 0000-0002-9146-0816

Doctor of Biological Sciences, leading researcher, Laboratory of Risk Factors Assessment for Influenza and ARVI

Russian Federation, 197022, St. Petersburg

Ekaterina R. Petrova

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: ekaterina.petrova@influenza.spb.ru
ORCID iD: 0000-0003-2258-4679

researcher, Laboratory of Risk Factors Assessment for Influenza and ARVI

Russian Federation, 197022, St. Petersburg

Olga I. Afanasyeva

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: olga-afanaseva57@mail.ru
ORCID iD: 0000-0002-1229-171X

Doctor of Medical Sciences, Head of the Department of RVI in children

Russian Federation, 197022, St. Petersburg

Veronika S. Timonina

SPB GUBZ St. Olga Children’s City Hospital

Email: karina88888888@list.ru
ORCID iD: 0000-0002-2887-0126

Doctor

Russian Federation, 194156, St. Petersburg

Elena V. Obraztsova

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: alorz@mail.ru
ORCID iD: 0000-0001-8762-6724

Candidate of Medical Sciences, senior researcher of the Department of RVI in children

Russian Federation, 197022, St. Petersburg

Ekaterina G. Golovacheva

Smorodintsev Research Institute of Influenza, Ministry of Health

Email: ekaterina.golovacheva@influenza.spb.ru
ORCID iD: 0000-0002-1934-7288

Doctor of Medical Sciences, senior researcher of the Department of RVI in children

Russian Federation, 197022, St. Petersburg

Elena A. Dondurey

Smorodintsev Research Institute of Influenza, Ministry of Health; SPB GUBZ St. Olga Children’s City Hospital

Email: dondureyelena@yandex.ru
ORCID iD: 0000-0003-2382-9172

Candidate of Medical Sciences, senior researcher of the Department of RVI in Children

Russian Federation, 197022, St. Petersburg; 194156, St. Petersburg

Evgenya V. Lelenkova

Federal Scientific Research Institute of Viral Infections “Virom”, Rospotrebnadzor

Email: lelenkova_ev@eniivi.ru
ORCID iD: 0000-0003-2004-0977

epidemiologist

Russian Federation, 620030, Ekaterinburg

Olga G. Kurskaya

Federal Research Center for Fundamental and Translational Medicine, Research Institute of Virology

Email: kurskaya09_@mail.ru
ORCID iD: 0000-0002-1931-2026

Candidate of Medical Sciences, senior researcher, lab. of virology

Russian Federation, 630117, Novosibirsk

Alexander M. Shestopalov

Federal Research Center for Fundamental and Translational Medicine, Research Institute of Virology

Email: shestopalov2@ngs.ru
ORCID iD: 0000-0002-1880-8708

Doctor of Biological Sciences, Professor, Director

Russian Federation, 630117, Novosibirsk

Dmitry A. Lioznov

Smorodintsev Research Institute of Influenza, Ministry of Health; First St. Petersburg State Medical University named after Academician I. P. Pavlov

Email: dlioznov@yandex.ru
ORCID iD: 0000-0003-3643-7354

Doctor of Medical Sciences, Professor, Director

Russian Federation, 197022, St. Petersburg; 197022, St. Petersburg

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2. Fig. 1. The main genetic lineages of SARS-CoV-2 (according to Pangolin classification) that circulated in the Russian Federation in 2020–2024 among children aged 0–17 years. The Y-axis shows the percentage of this line from the total number of SARS-CoV-2 sequences sequenced in this quarter; the X-axis shows the year and quarter of the study. n ≤ 5 – a combination of different lineages of the Omicron variant, each with a frequency not exceeding 5% in the overall structure of identified variants.

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3. Fig. 2. Age-related differences in the etiology of SARI in children admitted in hospital departments for ARI (HD) and in intensive care units (ICU) over a 6-year observation period. On the Y-axis – the frequency of detection of a given pathogen as a percentage of the total number of examined children of the specified age group. On X-axis – seasons.

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Copyright (c) 2025 Sominina A.А., Danilenko D.M., Komissarov A.B., Fadeev A.V., Komissarova K.S., Pisareva M.M., Musayeva T.D., Eder V.A., Levanyuk T.P., Stolyarov K.A., Krivitskaya V.Z., Petrova E.R., Afanasyeva O.I., Timonina V.S., Obraztsova E.V., Golovacheva E.G., Dondurey E.A., Lelenkova E.V., Kurskaya O.G., Shestopalov A.M., Lioznov D.A.

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