Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans

ABSTRACT A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome cont...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sander van Boheemen, Miranda de Graaf, Chris Lauber, Theo M. Bestebroer, V. Stalin Raj, Ali Moh Zaki, Albert D. M. E. Osterhaus, Bart L. Haagmans, Alexander E. Gorbalenya, Eric J. Snijder, Ron A. M. Fouchier
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2012
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/343f6080f80c49178f07466abfa9639e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:343f6080f80c49178f07466abfa9639e
record_format	dspace
spelling	oai:doaj.org-article:343f6080f80c49178f07466abfa9639e2021-11-15T15:39:11ZGenomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans10.1128/mBio.00473-122150-7511https://doaj.org/article/343f6080f80c49178f07466abfa9639e2012-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00473-12https://doaj.org/toc/2150-7511ABSTRACT A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to Tylonycteris bat coronavirus HKU4 (BtCoV-HKU4) and Pipistrellus bat coronavirus HKU5 (BtCoV-HKU5), which prototype two species in lineage C of the genus Betacoronavirus. In accordance with the guidelines of the International Committee on Taxonomy of Viruses, and in view of the 75% and 77% amino acid sequence identity in 7 conserved replicase domains with BtCoV-HKU4 and BtCoV-HKU5, respectively, we propose that HCoV-EMC/2012 prototypes a novel species in the genus Betacoronavirus. HCoV-EMC/2012 may be most closely related to a coronavirus detected in Pipistrellus pipistrellus in The Netherlands, but because only a short sequence from the most conserved part of the RNA-dependent RNA polymerase-encoding region of the genome was reported for this bat virus, its genetic distance from HCoV-EMC remains uncertain. HCoV-EMC/2012 is the sixth coronavirus known to infect humans and the first human virus within betacoronavirus lineage C. IMPORTANCE Coronaviruses are capable of infecting humans and many animal species. Most infections caused by human coronaviruses are relatively mild. However, the outbreak of severe acute respiratory syndrome (SARS) caused by SARS-CoV in 2002 to 2003 and the fatal infection of a human by HCoV-EMC/2012 in 2012 show that coronaviruses are able to cause severe, sometimes fatal disease in humans. We have determined the complete genome of HCoV-EMC/2012 using an unbiased virus discovery approach involving next-generation sequencing techniques, which enabled subsequent state-of-the-art bioinformatics, phylogenetics, and taxonomic analyses. By establishing its complete genome sequence, HCoV-EMC/2012 was characterized as a new genotype which is closely related to bat coronaviruses that are distant from SARS-CoV. We expect that this information will be vital to rapid advancement of both clinical and vital research on this emerging pathogen.Sander van BoheemenMiranda de GraafChris LauberTheo M. BestebroerV. Stalin RajAli Moh ZakiAlbert D. M. E. OsterhausBart L. HaagmansAlexander E. GorbalenyaEric J. SnijderRon A. M. FouchierAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 3, Iss 6 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Sander van Boheemen Miranda de Graaf Chris Lauber Theo M. Bestebroer V. Stalin Raj Ali Moh Zaki Albert D. M. E. Osterhaus Bart L. Haagmans Alexander E. Gorbalenya Eric J. Snijder Ron A. M. Fouchier Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
description	ABSTRACT A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to Tylonycteris bat coronavirus HKU4 (BtCoV-HKU4) and Pipistrellus bat coronavirus HKU5 (BtCoV-HKU5), which prototype two species in lineage C of the genus Betacoronavirus. In accordance with the guidelines of the International Committee on Taxonomy of Viruses, and in view of the 75% and 77% amino acid sequence identity in 7 conserved replicase domains with BtCoV-HKU4 and BtCoV-HKU5, respectively, we propose that HCoV-EMC/2012 prototypes a novel species in the genus Betacoronavirus. HCoV-EMC/2012 may be most closely related to a coronavirus detected in Pipistrellus pipistrellus in The Netherlands, but because only a short sequence from the most conserved part of the RNA-dependent RNA polymerase-encoding region of the genome was reported for this bat virus, its genetic distance from HCoV-EMC remains uncertain. HCoV-EMC/2012 is the sixth coronavirus known to infect humans and the first human virus within betacoronavirus lineage C. IMPORTANCE Coronaviruses are capable of infecting humans and many animal species. Most infections caused by human coronaviruses are relatively mild. However, the outbreak of severe acute respiratory syndrome (SARS) caused by SARS-CoV in 2002 to 2003 and the fatal infection of a human by HCoV-EMC/2012 in 2012 show that coronaviruses are able to cause severe, sometimes fatal disease in humans. We have determined the complete genome of HCoV-EMC/2012 using an unbiased virus discovery approach involving next-generation sequencing techniques, which enabled subsequent state-of-the-art bioinformatics, phylogenetics, and taxonomic analyses. By establishing its complete genome sequence, HCoV-EMC/2012 was characterized as a new genotype which is closely related to bat coronaviruses that are distant from SARS-CoV. We expect that this information will be vital to rapid advancement of both clinical and vital research on this emerging pathogen.
format	article
author	Sander van Boheemen Miranda de Graaf Chris Lauber Theo M. Bestebroer V. Stalin Raj Ali Moh Zaki Albert D. M. E. Osterhaus Bart L. Haagmans Alexander E. Gorbalenya Eric J. Snijder Ron A. M. Fouchier
author_facet	Sander van Boheemen Miranda de Graaf Chris Lauber Theo M. Bestebroer V. Stalin Raj Ali Moh Zaki Albert D. M. E. Osterhaus Bart L. Haagmans Alexander E. Gorbalenya Eric J. Snijder Ron A. M. Fouchier
author_sort	Sander van Boheemen
title	Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
title_short	Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
title_full	Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
title_fullStr	Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
title_full_unstemmed	Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
title_sort	genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans
publisher	American Society for Microbiology
publishDate	2012
url	https://doaj.org/article/343f6080f80c49178f07466abfa9639e
work_keys_str_mv	AT sandervanboheemen genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT mirandadegraaf genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT chrislauber genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT theombestebroer genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT vstalinraj genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT alimohzaki genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT albertdmeosterhaus genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT bartlhaagmans genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT alexanderegorbalenya genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT ericjsnijder genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans AT ronamfouchier genomiccharacterizationofanewlydiscoveredcoronavirusassociatedwithacuterespiratorydistresssyndromeinhumans
_version_	1718427757125304320

Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans

Ejemplares similares