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.
(1) State Key Laboratory of Emerging Infectious
Diseases, The University of Hong Kong,
Hong Kong; China; E-Mail: email@example.com.
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