The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia.

Chen, X; Adam, DC; Chughtai, AA; Stelzer-Braid, S; Scotch, M; MacIntyre, CR

The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia.

Chen, X Adam, DC Chughtai, AA Stelzer-Braid, S

Scotch, M MacIntyre, CR

Permalink

Publisher:: MDPI
Publication Type:: Journal Article
Citation:: Viruses, 2020, 12, (5)
Issue Date:: 2020-05-14

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download full textAdobe PDF (2.38 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Chen, X
dc.contributor.author	Adam, DC
dc.contributor.author	Chughtai, AA
dc.contributor.author	Stelzer-Braid, S https://orcid.org/0000-0001-6037-9305
dc.contributor.author	Scotch, M
dc.contributor.author	MacIntyre, CR
dc.date.accessioned	2020-11-27T03:30:21Z
dc.date.available	2020-05-12
dc.date.available	2020-11-27T03:30:21Z
dc.date.issued	2020-05-14
dc.identifier.citation	Viruses, 2020, 12, (5)
dc.identifier.issn	1999-4915
dc.identifier.issn	1999-4915
dc.identifier.uri	http://hdl.handle.net/10453/144408
dc.description.abstract	This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10-4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.
dc.format	Electronic
dc.language	eng
dc.publisher	MDPI
dc.relation.ispartof	Viruses
dc.relation.isbasedon	10.3390/v12050540
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0605 Microbiology
dc.subject.mesh	Animals
dc.subject.mesh	Chiroptera
dc.subject.mesh	Humans
dc.subject.mesh	Community-Acquired Infections
dc.subject.mesh	Cross Infection
dc.subject.mesh	Coronavirus Infections
dc.subject.mesh	Disease Outbreaks
dc.subject.mesh	Disease Reservoirs
dc.subject.mesh	Mutation
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Saudi Arabia
dc.subject.mesh	Phylogeography
dc.subject.mesh	Mutation Rate
dc.subject.mesh	Middle East Respiratory Syndrome Coronavirus
dc.subject.mesh	Camelus
dc.subject.mesh	Animals
dc.subject.mesh	Chiroptera
dc.subject.mesh	Humans
dc.subject.mesh	Community-Acquired Infections
dc.subject.mesh	Cross Infection
dc.subject.mesh	Coronavirus Infections
dc.subject.mesh	Disease Outbreaks
dc.subject.mesh	Disease Reservoirs
dc.subject.mesh	Mutation
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Saudi Arabia
dc.subject.mesh	Phylogeography
dc.subject.mesh	Mutation Rate
dc.subject.mesh	Middle East Respiratory Syndrome Coronavirus
dc.subject.mesh	Camelus
dc.subject.mesh	Animals
dc.subject.mesh	Camelus
dc.subject.mesh	Chiroptera
dc.subject.mesh	Community-Acquired Infections
dc.subject.mesh	Coronavirus Infections
dc.subject.mesh	Cross Infection
dc.subject.mesh	Disease Outbreaks
dc.subject.mesh	Disease Reservoirs
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Humans
dc.subject.mesh	Middle East Respiratory Syndrome Coronavirus
dc.subject.mesh	Mutation
dc.subject.mesh	Mutation Rate
dc.subject.mesh	Phylogeography
dc.subject.mesh	Saudi Arabia
dc.title	The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia.
dc.type	Journal Article
utslib.citation.volume	12
utslib.location.activity	Switzerland
utslib.for	0605 Microbiology
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney
utslib.copyright.status	open_access	*
pubs.consider-herdc	false
dc.date.updated	2020-11-27T03:30:10Z
pubs.issue	5
pubs.publication-status	Published
pubs.volume	12
utslib.citation.issue	5

Abstract:

This study compared the phylogeography of MERS-CoV between hospital outbreak-associated cases and sporadic cases in Saudi Arabia. We collected complete genome sequences from human samples in Saudi Arabia and data on the multiple risk factors of human MERS-CoV in Saudi Arabia reported from 2012 to 2018. By matching each sequence to human cases, we identified isolates as hospital outbreak-associated cases or sporadic cases. We used Bayesian phylogenetic methods including temporal, discrete trait analysis and phylogeography to uncover transmission routes of MERS-CoV isolates between hospital outbreaks and sporadic cases. Of the 120 sequences collected between 19 June 2012 and 23 January 2017, there were 64 isolates from hospital outbreak-associated cases and 56 from sporadic cases. Overall, MERS-CoV is fast evolving at 7.43 × 10-4 substitutions per site per year. Isolates from hospital outbreaks showed unusually fast evolutionary speed in a shorter time-frame than sporadic cases. Multiple introductions of different MERS-CoV strains occurred in three separate hospital outbreaks. MERS-CoV appears to be mutating in humans. The impact of mutations on viruses transmissibility in humans is unknown.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/144408