Journal
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
Volume 19, Issue 16, Pages -Publisher
MDPI
DOI: 10.3390/ijerph191610418
Keywords
severe acute respiratory infections; waves of COVID-19 pandemic; respiratory viruses; children; QIAstat-Dx (R) Respiratory SARS-CoV-2 Panel
Funding
- Bill and Melinda Gate Foundation [BMGFOPP1180423_2017]
- National Research Foundation (NRF), South Africa [120814]
- Poliomyelitis Research Foundation (PRF), South Africa [19/16]
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This study reports on the respiratory pathogens in children <= 5 years admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Human rhinovirus/enterovirus, RSV, and SARS-CoV-2 were the most commonly detected pathogens, with a high co-infection rate. During the third wave, there were fewer RSV-positive samples, possibly due to measures against COVID-19 transmission.
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 QlAstat-Dx (R) 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.
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