The effects of the COVID-19 pandemic on community respiratory virus activity

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused substantial global morbidity and deaths, leading governments to turn to non-pharmaceutical interventions to slow down the spread of infection and lessen the burden on health care systems. These policies have evolved over the course of the COVID-19 pandemic, including after the availability of COVID-19 vaccines, with regional and country-level differences in their ongoing use. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. Reductions in respiratory virus infections, including by influenza virus and respiratory syncytial virus, were most notable at the onset of the COVID-19 pandemic and continued in varying degrees through subsequent waves of SARS-CoV-2 infections. The decreases in community infection burden have resulted in reduced hospitalizations and deaths associated with non-SARS-CoV-2 respiratory infections. Respiratory virus evolution relies on the maintaining of a diverse genetic pool, but evidence of genetic bottlenecking brought on by case reduction during the COVID-19 pandemic has resulted in reduced genetic diversity of some respiratory viruses, including influenza virus. By describing the differences in these changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in community co-circulation of respiratory viruses.

Fig. 1. Prevalence of community respiratory viruses and SARS-CoV-2 from the Seattle Flu Study 2019–2022.

a | Prevalence of influenza A virus A and influenza B virus (2019–2022). b | Prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Included are respiratory specimens from 2018 epidemiological week 47 to 2022 epidemiological week 30; a total of 154,740 specimens were tested: 957 in 2018, 25,019 in 2019, 64,869 in 2020, 48,458 in 2021 and 15,437 in 2022. Respiratory specimens were tested with use of a custom-arrayed reverse transcription–PCR platform (Thermo Fisher). Adapted with permission from ref., Seattle Flu alliance.

Fig. 2. Surveillance of influenza viruses by the World Health Organization Global Influenza Surveillance and Response System 2019–2022.

The prevalence of influenza A(H3N2) virus, influenza A(H1N1)pdm09 virus, influenza B/Yamagata virus and influenza B/Victoria virus is shown. The date range of the data extends from 2019 epidemiological week 17 to 2022 epidemiological week 16. The last confirmed report of influenza B/Yamagata virus was in March 2020 (ref.). Adapted with permission from ref., WHO.