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

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 20...

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Main Authors: Xin Chen, Dillon Charles Adam, Abrar Ahmad Chughtai, Sacha Stelzer-Braid, Matthew Scotch, Chandini Raina MacIntyre
Format: Article
Language:English
Published: MDPI AG 2020-05-01
Series:Viruses
Subjects:
Online Access:https://www.mdpi.com/1999-4915/12/5/540
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spelling doaj-52cae0e494e742478a129740182a559d2020-11-25T03:23:39ZengMDPI AGViruses1999-49152020-05-011254054010.3390/v12050540The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi ArabiaXin Chen0Dillon Charles Adam1Abrar Ahmad Chughtai2Sacha Stelzer-Braid3Matthew Scotch4Chandini Raina MacIntyre5Biosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, AustraliaBiosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, AustraliaSchool of Public Health and Community Medicine, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, AustraliaSchool of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, AustraliaBiodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USABiosecurity Research Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney NSW 2052, AustraliaThis 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<sup>−4</sup> 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.https://www.mdpi.com/1999-4915/12/5/540MERS-CoVphylogeneticsphylogeographyepidemiologyhospital outbreaksnosocomial
collection DOAJ
language English
format Article
sources DOAJ
author Xin Chen
Dillon Charles Adam
Abrar Ahmad Chughtai
Sacha Stelzer-Braid
Matthew Scotch
Chandini Raina MacIntyre
spellingShingle Xin Chen
Dillon Charles Adam
Abrar Ahmad Chughtai
Sacha Stelzer-Braid
Matthew Scotch
Chandini Raina MacIntyre
The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
Viruses
MERS-CoV
phylogenetics
phylogeography
epidemiology
hospital outbreaks
nosocomial
author_facet Xin Chen
Dillon Charles Adam
Abrar Ahmad Chughtai
Sacha Stelzer-Braid
Matthew Scotch
Chandini Raina MacIntyre
author_sort Xin Chen
title The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
title_short The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
title_full The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
title_fullStr The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
title_full_unstemmed The Phylogeography of MERS-CoV in Hospital Outbreak-Associated Cases Compared to Sporadic Cases in Saudi Arabia
title_sort phylogeography of mers-cov in hospital outbreak-associated cases compared to sporadic cases in saudi arabia
publisher MDPI AG
series Viruses
issn 1999-4915
publishDate 2020-05-01
description 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<sup>−4</sup> 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.
topic MERS-CoV
phylogenetics
phylogeography
epidemiology
hospital outbreaks
nosocomial
url https://www.mdpi.com/1999-4915/12/5/540
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