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Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya

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Kiyuka, Patience K, Agoti, Charles N, Munywoki, Patrick K, Njeru, Regina, Bett, Anne, Otieno, James R, Otieno, Grieven P, Kamau, Everlyn, Clark, Taane G, van der Hoek, Lia, Kellam, Paul, Nokes, D. James and Cotten, Matthew (2018) Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya. The Journal of Infectious Diseases, 217 (11). pp. 1728-1739. doi:10.1093/infdis/jiy098 ISSN 0022-1899.

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Official URL: http://dx.doi.org/10.1093/infdis/jiy098

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Abstract

Background:

Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime.

Methods:

Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing.

Results:

HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching.

Conclusions:

In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.

Item Type: Journal Article
Subjects: R Medicine > RC Internal medicine
R Medicine > RJ Pediatrics > RJ101 Child Health. Child health services
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Coronavirus infections -- Kenya, Respiratory infections -- Kenya, Pneumonia in children -- Kenya, Medicine, Rural -- Kenya
Journal or Publication Title: The Journal of Infectious Diseases
Publisher: Oxford University Press
ISSN: 0022-1899
Official Date: 5 May 2018
Dates:
DateEvent
5 May 2018Published
21 March 2018Available
27 February 2018Accepted
Volume: 217
Number: 11
Page Range: pp. 1728-1739
DOI: 10.1093/infdis/jiy098
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 17 July 2018
Date of first compliant Open Access: 17 July 2018
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
KECD-2013–54Commonwealth Scholarship Commissionhttp://dx.doi.org/10.13039/501100000867
MR/K000551/1 [MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MR/M01360X/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MR/N010469/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MC_PC_15103[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265

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