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Viruses 2010, 2(8), 1804-1820; doi:10.3390/v2081803
Review

Coronavirus Genomics and Bioinformatics Analysis

1,2,3,4,†,* , 4,†
, 1,2,3,4,*  and 1,2,3,4
Received: 1 July 2010; Accepted: 12 August 2010 / Published: 24 August 2010
(This article belongs to the Special Issue Viral Genomics and Bioinformatics)
Download PDF [300 KB, uploaded 24 August 2010]
Abstract: 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.
Keywords: coronavirus; genome; bioinformatics coronavirus; genome; bioinformatics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Woo, P.C.Y.; Huang, Y.; Lau, S.K.P.; Yuen, K.-Y. Coronavirus Genomics and Bioinformatics Analysis. Viruses 2010, 2, 1804-1820.

AMA Style

Woo PCY, Huang Y, Lau SKP, Yuen K-Y. Coronavirus Genomics and Bioinformatics Analysis. Viruses. 2010; 2(8):1804-1820.

Chicago/Turabian Style

Woo, Patrick C. Y.; Huang, Yi; Lau, Susanna K. P.; Yuen, Kwok-Yung. 2010. "Coronavirus Genomics and Bioinformatics Analysis." Viruses 2, no. 8: 1804-1820.


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