PubMed Journals: Viruses

  Source:		PMID: 21994708

    		Viruses. 2010 Aug;2(8):1804-20. doi:
     		10.3390/v2081803. Epub 2010 Aug 24.

			Coronavirus genomics and bioinformatics

			Woo PC(1), Huang Y, Lau SK, Yuen KY.

			Author Information
			(1) State Key Laboratory of Emerging Infectious
			Diseases, The University of Hong Kong,
			Hong Kong; China; E-Mail: kyyuen@hkucc.hku.hk.

			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.

			DOI: 10.3390/v2081803 PMCID: PMC3185738
			PMID: 21994708

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