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

Kiyuka, P. K. et al. (2018) Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya. Journal of Infectious Diseases, 217(11), pp. 1728-1739. (doi: 10.1093/infdis/jiy098) (PMID:29741740) (PMCID:PMC6037089)

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: Articles
• Additional Information: This work was supported by the Wellcome Trust, UK (grant number 102975) and the Commonwealth Distance Learning Scholarship Scheme to P. K. K. (grant number KECD-2013–54). T. G. C. is funded by the Medical Research Council, UK (grant numbers MR/K000551/1 and MR/M01360X/1, MR/N010469/1, MC_PC_15103). P. K. and M. C. were supported by Wellcome Trust core grant funding to P. K.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: Kiyuka, P. K., Agoti, C. N., Munywoki, P. K., Njeru, R., Bett, A., Otieno, J. R., Otieno, G. P., Kamau, E., Clark, T. G., van der Hoek, L., Kellam, P., Nokes, J., and Cotten, M.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Journal of Infectious Diseases
• Publisher: Oxford University Press
• ISSN: 0022-1899
• ISSN (Online): 1537-6613
• Published Online: 21 March 2018
• Copyright Holders: Copyright © 2018 The Authors
• First Published: First published in Journal of Infectious Diseases 217(11):1728–1739
• Publisher Policy: Reproduced under a Creative Commons License