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Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus

Title: Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus
Authors: Cotten, M
Watson, SJ
Zumla, AI
Makhdoom, HQ
Palser, AL
Ong, SH
Al Rabeeah, AA
Alhakeem, RF
Assiri, A
Al-Tawfiq, JA
Albarrak, A
Barry, M
Shibl, A
Alrabiah, FA
Hajjar, S
Balkhy, HH
Flemban, H
Rambaut, A
Kellam, P
Memish, ZA
Item Type: Journal Article
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.
Issue Date: 18-Feb-2014
Date of Acceptance: 16-Jan-2014
URI: http://hdl.handle.net/10044/1/69464
DOI: https://dx.doi.org/10.1128/mBio.01062-13
ISSN: 2150-7511
Publisher: American Society for Microbiology
Journal / Book Title: mBio
Volume: 5
Issue: 1
Copyright Statement: © 2014 Cotten et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license (https://creativecommons.org/licenses/by/3.0/).
Keywords: Science & Technology
Life Sciences & Biomedicine
Microbiology
HOST-RANGE EXPANSION
SAUDI-ARABIA
CLINICAL-FEATURES
SARS-CORONAVIRUS
DROMEDARY CAMELS
FUSION CORE
MERS-COV
TRANSMISSION
INFECTION
RECEPTOR
Basic Reproduction Number
Cluster Analysis
Coronavirus
Coronavirus Infections
Evolution, Molecular
Genome, Viral
Humans
Molecular Sequence Data
Phylogeny
RNA, Viral
Selection, Genetic
Sequence Analysis, DNA
0605 Microbiology
Publication Status: Published
Article Number: e01062-13
Online Publication Date: 2014-02-18
Appears in Collections:Department of Medicine



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