Coronavirus Genomics and Bioinformatics Analysis

The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA...

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Main Authors:	Woo, Patrick C. Y., Huang, Yi, Lau, Susanna K. P., Yuen, Kwok-Yung
Format:	Online
Language:	English
Published:	Molecular Diversity Preservation International (MDPI) 2010
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185738/

id	pubmed-3185738
recordtype	oai_dc
spelling	pubmed-31857382011-10-12 Coronavirus Genomics and Bioinformatics Analysis Woo, Patrick C. Y. Huang, Yi Lau, Susanna K. P. Yuen, Kwok-Yung Review The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999–2002, with estimated substitution rate of 4×10−4 to 2×10−2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses. Molecular Diversity Preservation International (MDPI) 2010-08-24 /pmc/articles/PMC3185738/ /pubmed/21994708 http://dx.doi.org/10.3390/v2081803 Text en © 2010 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Woo, Patrick C. Y. Huang, Yi Lau, Susanna K. P. Yuen, Kwok-Yung
spellingShingle	Woo, Patrick C. Y. Huang, Yi Lau, Susanna K. P. Yuen, Kwok-Yung Coronavirus Genomics and Bioinformatics Analysis
author_facet	Woo, Patrick C. Y. Huang, Yi Lau, Susanna K. P. Yuen, Kwok-Yung
author_sort	Woo, Patrick C. Y.
title	Coronavirus Genomics and Bioinformatics Analysis
title_short	Coronavirus Genomics and Bioinformatics Analysis
title_full	Coronavirus Genomics and Bioinformatics Analysis
title_fullStr	Coronavirus Genomics and Bioinformatics Analysis
title_full_unstemmed	Coronavirus Genomics and Bioinformatics Analysis
title_sort	coronavirus genomics and bioinformatics analysis
description	The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999–2002, with estimated substitution rate of 4×10−4 to 2×10−2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.
publisher	Molecular Diversity Preservation International (MDPI)
publishDate	2010
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185738/
_version_	1611479116666634240

Coronavirus Genomics and Bioinformatics Analysis

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