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 and
Martin M. Nyaga (nyagamm@ufs.ac.za)
Additional contact information
Ayodeji E. Ogunbayo: 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
Milton T. Mogotsi: 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
Hlengiwe Sondlane: 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
Kelebogile R. Nkwadipo: 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
Saheed Sabiu: Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
Martin M. Nyaga: 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
IJERPH, 2022, vol. 19, issue 16, 1-13
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: severe acute respiratory infections; waves of COVID-19 pandemic; respiratory viruses; children; QIAstat-Dx ® Respiratory SARS-CoV-2 Panel (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2022
References: Add references at CitEc
Citations:
Downloads: (external link)
https://www.mdpi.com/1660-4601/19/16/10418/pdf (application/pdf)
https://www.mdpi.com/1660-4601/19/16/10418/ (text/html)
Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.
Export reference: BibTeX
RIS (EndNote, ProCite, RefMan)
HTML/Text
Persistent link: https://EconPapers.repec.org/RePEc:gam:jijerp:v:19:y:2022:i:16:p:10418-:d:893989
Access Statistics for this article
IJERPH is currently edited by Ms. Jenna Liu
More articles in IJERPH from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager (indexing@mdpi.com).