Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa

Int J Environ Res Public Health. 2022 Aug 21;19(16):10418. doi: 10.3390/ijerph191610418.

Abstract

Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.

Keywords: QIAstat-Dx® Respiratory SARS-CoV-2 Panel; children; respiratory viruses; severe acute respiratory infections; waves of COVID-19 pandemic.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / epidemiology
  • Child
  • Coinfection* / epidemiology
  • Humans
  • Pandemics
  • Respiratory Tract Infections* / microbiology
  • SARS-CoV-2
  • South Africa / epidemiology
  • Virus Diseases*
  • Viruses*

Grants and funding

This research was funded by the Bill and Melinda Gate Foundation, grant number BMGF-OPP1180423_2017, the National Research Foundation (NRF), South Africa, grant number 120814, and the Poliomyelitis Research Foundation (PRF), South Africa, grant number 19/16.