Luka, Martha M., Kamau, Everlyn, Adema, Irene, Munywoki, Patrick K., Otieno, Grieven P., Gicheru, Elijah, Gichuki, Alex, Kibinge, Nelson, Agoti, Charles N. and Nokes, D. James (2020) Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya. Open Forum Infectious Diseases, 7 (10). ofaa385. doi:10.1093/ofid/ofaa385 ISSN 2328-8957.

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Abstract

Background
Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been previously described.

Objective
To characterise HRV molecular epidemiology in primary school in a rural location of Kenya.

Methods
Between May 2017 to April 2018, over three school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time RT-PCR. HRV positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification.

Results
A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%), p-value &0.001. HRV-A was the most common species (134/253, 53.0%), followed by HRV-C (73/253, 28.9%) and HRV-B (46/253, 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in one school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all three school terms.

Conclusion
HRV was frequently detected among school-going children with mild ARI symptoms, and particularly in the younger age groups (&5-year-olds). Multiple HRV introductions were observed characterised by the considerable genotype diversity.

Item Type:	Journal Article
Subjects:	R Medicine > RA Public aspects of medicine
Divisions:	Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Rhinoviruses -- Epidemiology -- Kenya
Journal or Publication Title:	Open Forum Infectious Diseases
Publisher:	Oxford University Press
ISSN:	2328-8957
Official Date:	October 2020
Dates:	Date Event October 2020 Published 27 August 2020 Available 20 August 2020 Accepted
Volume:	7
Number:	10
Article Number:	ofaa385
DOI:	10.1093/ofid/ofaa385
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Copyright Holders:	© The Author(s) 2020
Date of first compliant deposit:	3 September 2020
Date of first compliant Open Access:	3 September 2020
RIOXX Funder/Project Grant:	Project/Grant ID RIOXX Funder Name Funder ID Wellcome Senior Investigator Award Wellcome Trust http://dx.doi.org/10.13039/100010269 DELTAS Africa Initiative [DEL-15-003] African Academy of Sciences http://dx.doi.org/10.13039/501100011858 UNSPECIFIED New Partnership for Africa's Development http://dx.doi.org/10.13039/501100009250 [107769/Z/10/Z] Wellcome Trust http://dx.doi.org/10.13039/100010269 UNSPECIFIED Government of the United Kingdom http://dx.doi.org/10.13039/100013986

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