Skip to content Skip to navigation
University of Warwick
  • Study
  • |
  • Research
  • |
  • Business
  • |
  • Alumni
  • |
  • News
  • |
  • About

University of Warwick
Publications service & WRAP

Highlight your research

  • WRAP
    • Home
    • Search WRAP
    • Browse by Warwick Author
    • Browse WRAP by Year
    • Browse WRAP by Subject
    • Browse WRAP by Department
    • Browse WRAP by Funder
    • Browse Theses by Department
  • Publications Service
    • Home
    • Search Publications Service
    • Browse by Warwick Author
    • Browse Publications service by Year
    • Browse Publications service by Subject
    • Browse Publications service by Department
    • Browse Publications service by Funder
  • Help & Advice
University of Warwick

The Library

  • Login
  • Admin

Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-2016

Tools
- Tools
+ Tools

Abidha, C., Nyiro, J., Kamau, E., Abdullahi, O., Nokes, D. James and Agoti, C. N. (2020) Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-2016. Virus Evolution, 6 (1). veaa031. doi:10.1093/ve/veaa031 ISSN 2057-1577.

[img]
Preview
PDF
WRAP-Transmission-evolutionary-dynamics-Covid-Kenya-Nokes-2020.pdf - Published Version - Requires a PDF viewer.
Available under License Creative Commons Attribution 4.0.

Download (614Kb) | Preview
[img] PDF
WRAP-Transmission-evolutionary-dynamics-Covid-Kenya-Nokes-2020.pdf - Accepted Version
Embargoed item. Restricted access to Repository staff only - Requires a PDF viewer.

Download (1073Kb)
Official URL: https://doi.org/10.1093/ve/veaa031

Request Changes to record.

Abstract

Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.

Item Type: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
R Medicine > RC Internal medicine
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): COVID-19 (Disease), Epidemiology, Respiratory infections
Journal or Publication Title: Virus Evolution
Publisher: Oxford University Press
ISSN: 2057-1577
Official Date: January 2020
Dates:
DateEvent
January 2020Published
2 June 2020Available
15 April 2020Accepted
Volume: 6
Number: 1
Article Number: veaa031
DOI: 10.1093/ve/veaa031
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 22 April 2020
Date of first compliant Open Access: 5 June 2020
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
DEL-15-003African Academy of Scienceshttp://dx.doi.org/10.13039/501100011858
UNSPECIFIEDNew Partnership for Africa's Developmenthttp://dx.doi.org/10.13039/501100009250
107769/Z/10/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
UNSPECIFIEDGovernment of the United Kingdomhttp://dx.doi.org/10.13039/100013986

Request changes or add full text files to a record

Repository staff actions (login required)

View Item View Item

Downloads

Downloads per month over past year

View more statistics

twitter

Email us: wrap@warwick.ac.uk
Contact Details
About Us