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.
【저자키워드】 children, respiratory viruses, QIAstat-Dx® Respiratory SARS-CoV-2 Panel, severe acute respiratory infections, waves of COVID-19 pandemic., 【초록키워드】 COVID-19, Treatment, coronavirus disease, respiratory infections, SARS-CoV-2, infection control, Severe infection, coronavirus, Mortality, Immunity, Influenza, susceptibility, COVID-19 pandemic, Diagnosis, Influenza virus, severe acute respiratory syndrome Coronavirus, respiratory viruses, South Africa, pathogen, COVID-19 infection, respiratory syncytial virus, Co-infection, Waves, Respiratory pathogens, Acute respiratory infection, Pathogens, Viral detection, Swab, circulation, respiratory, acute respiratory infections, change, detection rate, Ct values, COVID-19 transmission, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, respiratory pathogen, measure, severe infections, SARI, negativity, aetiology, collected, virus, respiratory virus, exacerbated, contribute, absence, complicate, Panel, waned, 【제목키워드】 COVID-19, respiratory, profile, state, Free,