Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

Matthew Cotten; Tommy T Lam; Simon J Watson; Anne L Palser; Velislava Petrova; Paul Grant; Oliver G Pybus; Andrew Rambaut; Yi Guan; Deenan Pillay; Paul Kellam; Eleni Nastouli

doi:10.3201/eid1905.130057

Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

Matthew Cotten, Tommy T Lam, Simon J Watson, Anne L Palser, Velislava Petrova, Paul Grant, Oliver G Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.

Original language	English
Pages (from-to)	736-742B
Journal	Emerging Infectious Diseases
Volume	19
Issue number	5
DOIs	https://doi.org/10.3201/eid1905.130057
Publication status	Published - May 2013

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PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach
Rambaut, A. (Principal Investigator)
EU government bodies
1/11/11 → 30/04/17
Project: Research

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)
Rambaut, A. (Member)
Sept 2009 → Aug 2015
Activity: Membership types › Membership of external research organisation

Cite this

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title = "Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus",

abstract = "A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.",

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year = "2013",

month = may,

doi = "10.3201/eid1905.130057",

language = "English",

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AU - Cotten, Matthew

AU - Lam, Tommy T

AU - Watson, Simon J

AU - Palser, Anne L

AU - Petrova, Velislava

AU - Grant, Paul

AU - Pybus, Oliver G

AU - Rambaut, Andrew

AU - Guan, Yi

AU - Pillay, Deenan

AU - Kellam, Paul

AU - Nastouli, Eleni

PY - 2013/5

Y1 - 2013/5

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AB - A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient's sputum sample. Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family. Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.

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DO - 10.3201/eid1905.130057

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JF - Emerging Infectious Diseases

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Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus

Abstract

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Projects

PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach

Activities

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)

Cite this