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Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

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 substa...

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Autores principales: Cotten, Matthew, Lam, Tommy T., Watson, Simon J., Palser, Anne L., Petrova, Velislava, Grant, Paul, Pybus, Oliver G., Rambaut, Andrew, Guan, Yi, Pillay, Deenan, Kellam, Paul, Nastouli, Eleni
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Centers for Disease Control and Prevention 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647518/
https://www.ncbi.nlm.nih.gov/pubmed/23693015
http://dx.doi.org/10.3201/eid1905.130057
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author Cotten, Matthew
Lam, Tommy T.
Watson, Simon J.
Palser, Anne L.
Petrova, Velislava
Grant, Paul
Pybus, Oliver G.
Rambaut, Andrew
Guan, Yi
Pillay, Deenan
Kellam, Paul
Nastouli, Eleni
author_facet Cotten, Matthew
Lam, Tommy T.
Watson, Simon J.
Palser, Anne L.
Petrova, Velislava
Grant, Paul
Pybus, Oliver G.
Rambaut, Andrew
Guan, Yi
Pillay, Deenan
Kellam, Paul
Nastouli, Eleni
author_sort Cotten, Matthew
collection PubMed
description 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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spelling pubmed-36475182013-05-14 Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus Cotten, Matthew Lam, Tommy T. Watson, Simon J. Palser, Anne L. Petrova, Velislava Grant, Paul Pybus, Oliver G. Rambaut, Andrew Guan, Yi Pillay, Deenan Kellam, Paul Nastouli, Eleni Emerg Infect Dis Research 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. Centers for Disease Control and Prevention 2013-05 /pmc/articles/PMC3647518/ /pubmed/23693015 http://dx.doi.org/10.3201/eid1905.130057 Text en https://creativecommons.org/licenses/by/4.0/This is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.
spellingShingle Research
Cotten, Matthew
Lam, Tommy T.
Watson, Simon J.
Palser, Anne L.
Petrova, Velislava
Grant, Paul
Pybus, Oliver G.
Rambaut, Andrew
Guan, Yi
Pillay, Deenan
Kellam, Paul
Nastouli, Eleni
Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title_full Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title_fullStr Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title_full_unstemmed Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title_short Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus
title_sort full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647518/
https://www.ncbi.nlm.nih.gov/pubmed/23693015
http://dx.doi.org/10.3201/eid1905.130057
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