Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus

ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of t...

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Autores principales:	Matthew Cotten, Simon J. Watson, Alimuddin I. Zumla, Hatem Q. Makhdoom, Anne L. Palser, Swee Hoe Ong, Abdullah A. Al Rabeeah, Rafat F. Alhakeem, Abdullah Assiri, Jaffar A. Al-Tawfiq, Ali Albarrak, Mazin Barry, Atef Shibl, Fahad A. Alrabiah, Sami Hajjar, Hanan H. Balkhy, Hesham Flemban, Andrew Rambaut, Paul Kellam, Ziad A. Memish
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/56fc0730f1bf408fa17fe783becde606
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spelling	oai:doaj.org-article:56fc0730f1bf408fa17fe783becde6062021-11-15T15:45:10ZSpread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus10.1128/mBio.01062-132150-7511https://doaj.org/article/56fc0730f1bf408fa17fe783becde6062014-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01062-13https://doaj.org/toc/2150-7511ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R0) for the virus that is less than 1. IMPORTANCE MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus.Matthew CottenSimon J. WatsonAlimuddin I. ZumlaHatem Q. MakhdoomAnne L. PalserSwee Hoe OngAbdullah A. Al RabeeahRafat F. AlhakeemAbdullah AssiriJaffar A. Al-TawfiqAli AlbarrakMazin BarryAtef ShiblFahad A. AlrabiahSami HajjarHanan H. BalkhyHesham FlembanAndrew RambautPaul KellamZiad A. MemishAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 1 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Matthew Cotten Simon J. Watson Alimuddin I. Zumla Hatem Q. Makhdoom Anne L. Palser Swee Hoe Ong Abdullah A. Al Rabeeah Rafat F. Alhakeem Abdullah Assiri Jaffar A. Al-Tawfiq Ali Albarrak Mazin Barry Atef Shibl Fahad A. Alrabiah Sami Hajjar Hanan H. Balkhy Hesham Flemban Andrew Rambaut Paul Kellam Ziad A. Memish Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
description	ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R0) for the virus that is less than 1. IMPORTANCE MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus.
format	article
author	Matthew Cotten Simon J. Watson Alimuddin I. Zumla Hatem Q. Makhdoom Anne L. Palser Swee Hoe Ong Abdullah A. Al Rabeeah Rafat F. Alhakeem Abdullah Assiri Jaffar A. Al-Tawfiq Ali Albarrak Mazin Barry Atef Shibl Fahad A. Alrabiah Sami Hajjar Hanan H. Balkhy Hesham Flemban Andrew Rambaut Paul Kellam Ziad A. Memish
author_facet	Matthew Cotten Simon J. Watson Alimuddin I. Zumla Hatem Q. Makhdoom Anne L. Palser Swee Hoe Ong Abdullah A. Al Rabeeah Rafat F. Alhakeem Abdullah Assiri Jaffar A. Al-Tawfiq Ali Albarrak Mazin Barry Atef Shibl Fahad A. Alrabiah Sami Hajjar Hanan H. Balkhy Hesham Flemban Andrew Rambaut Paul Kellam Ziad A. Memish
author_sort	Matthew Cotten
title	Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
title_short	Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
title_full	Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
title_fullStr	Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
title_full_unstemmed	Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
title_sort	spread, circulation, and evolution of the middle east respiratory syndrome coronavirus
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/56fc0730f1bf408fa17fe783becde606
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Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus

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