Changes in the Etiology of Acute Respiratory Infections among Children in Novosibirsk, Russia, between 2019 and 2022: The Impact of the SARS-CoV-2 Virus

Abstract

A wide range of human respiratory viruses are known that may cause acute respiratory infections (ARIs), such as influenza A and B viruses (HIFV), respiratory syncytial virus (HRSV), coronavirus (HCoV), parainfluenza virus (HPIV), metapneumovirus (HMPV), rhinovirus (HRV), adenovirus (HAdV), bocavirus (HBoV), and others. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COronaVIrus Disease (COVID) that lead to pandemic in 2019 and significantly impacted on the circulation of ARIs. The aim of this study was to analyze the changes in the epidemic patterns of common respiratory viruses among children and adolescents hospitalized with ARIs in hospitals in Novosibirsk, Russia, from November 2019 to April 2022. During 2019 and 2022, nasal and throat swabs were taken from a total of 3190 hospitalized patients 0-17 years old for testing for HIFV, HRSV, HCoV, HPIV, HMPV, HRV, HAdV, HBoV, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time PCR. The SARS-CoV-2 virus dramatically influenced the etiology of acute respiratory infections among children and adolescents between 2019 and 2022. We observed dramatic changes in the prevalence of major respiratory viruses over three epidemic research seasons: HIFV, HRSV, and HPIV mainly circulated in 2019-2020; HMPV, HRV, and HCoV dominated in 2020-2021; and HRSV, SARS-CoV-2, HIFV, and HRV were the most numerous agents in 2021-2022. Interesting to note was the absence of HIFV and a significant reduction in HRSV during the 2020-2021 period, while HMPV was absent and there was a significant reduction of HCoV during the following epidemic period in 2021-2022. Viral co-infection was significantly more frequently detected in the 2020-2021 period compared with the other two epidemic seasons. Certain respiratory viruses, HCoV, HPIV, HBoV, HRV, and HAdV, were registered most often in co-infections. This cohort study has revealed that during the pre-pandemic and pandemic periods, there were dramatic fluctuations in common respiratory viruses registered among hospitalized patients 0-17 years old. The most dominant virus in each research period differed: HIFV in 2019-2020, HMPV in 2020-2021, and HRSV in 2021-2022. Virus-virus interaction was found to be possible between SARS-CoV-2 and HRV, HRSV, HAdV, HMPV, and HPIV. An increase in the incidence of COVID-19 was noted only during the third epidemic season (January to March 2022).

Keywords: HAdV; HBoV; HCoV; HIFV; HMPV; HPIV; HRSV; HRV; SARS-CoV-2.

Figure 1

Age and gender distribution data from a total of 3190 children and adolescents hospitalized with acute respiratory infections in 2019–2022. (A) PCR-confirmed samples from children aged 0–17 years (B) Age and gender distribution data by the three successive research periods: the first being 2019–2020), which was the pre-pandemic season; the second was 2020–2021, and the third was 2021–2022. *** and **: Differences between groups were statistically significant (Chi-square test, p < 0.01 and p < 0.05, respectively).

Figure 2

Viral load among various child age groups between 2019 and 2022. All data are presented as a percentage of the positive cases relative to the total number of PCR-confirmed samples received from patients during the research period from 2019–2022. Abbreviations: HIFV—influenza A and B viruses; HRSV—respiratory syncytial virus; HRV—rhinovirus; HPIV—parainfluenza virus types 1–4; HCoV—alphacoronaviruses (NL63/229E) and betacoronaviruses (OC43/HKU1); HMPV—metapneumovirus; HBoV—bocavirus; HAdV—adenovirus; and SARS-CoV-2—severe acute respiratory syndrome coronavirus 2. *** and **—Differences between groups were statistically significant (Chi-square test, p < 0.01 and p < 0.05, respectively).

Figure 3

Most common acute respiratory virus fluctuations during 2019–2022. “Total PCR+” refers to the data that are presented as a percentage of the positive cases of PCR-confirmed samples from patients during the three research periods (2019–2022); HIFV—influenza A and B viruses; HRSV—respiratory syncytial virus; SARS-CoV-2—severe acute respiratory syndrome coronavirus 2, HMPV—metapneumovirus; and HRV—rhinovirus.

Figure 4

Incidence of co-infections among hospitalized patients aged 0–17 years during 2019–2022. (A) Age and gender distribution data of co-infected children and adolescents. (B) This figure displays the observed co-infection for each pairing. The co-infection data are plotted as a heat map to aid the visualization of any seasonal trends for each virus during 2019–2022, across all sites. All data are presented as the numerical data of the analyzed medical records of patients who were positive for co-infections during the three research periods. Abbreviations for (B–D): HIFV—influenza A and B viruses; HRSV—respiratory syncytial virus; HRV—rhinovirus; HPIV—parainfluenza virus types 1–4; HCoV—alphacoronaviruses (NL63/229E) and betacoronaviruses (OC43/HKU1); HMPV—metapneumovirus; HBoV—bocavirus; HAdV—adenovirus; and SARS-CoV-2—severe acute respiratory syndrome coronavirus 2. (D) Mono-inf—mono-infection; Co-inf—co-infections. Numbers represent relative frequencies (%). *** and **—Differences between groups were statistically significant (Chi-square test, p < 0.01 and p < 0.05, accordingly).