Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period

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

doi:10.3390/v14112516

Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period

Viruses. 2022 Nov 14;14(11):2516. doi: 10.3390/v14112516.

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, Bloemfontein 9300, South Africa.
² Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.

Abstract

Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae, Paramoxyviridae, Pneumoviridae, Picobirnaviridae, Totiviridae, and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.

Keywords: children; metagenomics; severe acute respiratory infection; summer; virome; winter.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
COVID-19*
Child
Humans
Pandemics
Pneumonia*
RNA
Respiratory System
Respiratory Tract Infections*
Seasons
South Africa / epidemiology
Virome
Viruses* / genetics

Substances

RNA

Grants and funding

This research was funded by the Bill and Melinda Gates 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.