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

Ayodeji E Ogunbayo; Milton T Mogotsi; Hlengiwe Sondlane; Kelebogile R Nkwadipo; Saheed Sabiu; Martin M Nyaga

doi:10.3390/ijerph191610418

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.

Authors

Ayodeji E Ogunbayo¹, Milton T Mogotsi¹, Hlengiwe Sondlane¹, Kelebogile R Nkwadipo¹, Saheed Sabiu², Martin M Nyaga¹

Affiliations

¹ Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa.
² Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.

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.