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

Author

Listed:
  • 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)

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.

Suggested Citation

  • Ayodeji E. Ogunbayo & Milton T. Mogotsi & Hlengiwe Sondlane & Kelebogile R. Nkwadipo & Saheed Sabiu & Martin M. Nyaga, 2022. "Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa," IJERPH, MDPI, vol. 19(16), pages 1-13, August.
    • Handle: RePEc:gam:jijerp:v:19:y:2022:i:16:p:10418-:d:893989
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    References listed on IDEAS

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    1. Zhong-Jie Li & Hai-Yang Zhang & Li-Li Ren & Qing-Bin Lu & Xiang Ren & Cui-Hong Zhang & Yi-Fei Wang & Sheng-Hong Lin & Xiao-Ai Zhang & Jun Li & Shi-Wen Zhao & Zhi-Gang Yi & Xiao Chen & Zuo-Sen Yang & L, 2021. "Etiological and epidemiological features of acute respiratory infections in China," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    2. Anna Chiara Vittucci & Livia Piccioni & Luana Coltella & Claudia Ciarlitto & Livia Antilici & Elena Bozzola & Fabio Midulla & Paolo Palma & Carlo Federico Perno & Alberto Villani, 2021. "The Disappearance of Respiratory Viruses in Children during the COVID-19 Pandemic," IJERPH, MDPI, vol. 18(18), pages 1-8, September.
    3. Li-Ping Wang & Shi-Xia Zhou & Xin Wang & Qing-Bin Lu & Lu-Sha Shi & Xiang Ren & Hai-Yang Zhang & Yi-Fei Wang & Sheng-Hong Lin & Cui-Hong Zhang & Meng-Jie Geng & Xiao-Ai Zhang & Jun Li & Shi-Wen Zhao &, 2021. "Etiological, epidemiological, and clinical features of acute diarrhea in China," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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