Coronavirus Genomics and Bioinformatics Analysis

By Patrick C. Y. Woo, Yi Huang, Susanna K. P. Lau, Kwok-Yung Yuen. Viruses, 2010

773 citations recorded by the source corpus.

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.

Subfields: Animal Science and Zoology, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/8f124016fda610e3e9147dd046fb306f219a8c85

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Animal Science and Zoology

1. Rolf Hilgenfeld
2. T. S. Fung
3. D. Liu

In Infectious Diseases

1. Marion Koopmans
2. Rolf Hilgenfeld
3. Christian Drosten
4. T. S. Fung
5. D. Liu
6. Junmei Wang

Citations in the corpus

• Accessory proteins of SARS-CoV and other coronaviruses (2014, background): “…of viral envelope glycoproteins that mediate reversible attachment to O-acetylated sialic acids by acting both as receptor-binding (‘‘lectins’’) and as receptor-destroying enzymes (RDEs) with esterase activity (Woo et al., 2010; Zhang et al., 1992; Vlasak et al., 1988; Schultze et al., 1991).”
• Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model (2020, background): “The family includes four genera, such as Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus [4].”
• COVID-19 and multisystem inflammatory syndrome in children and adolescents (2020, neutral): “69 Six species of human coronaviruses are known, with one species subdivided into two different strains.”
• Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study (2013, background): “35 In addition, the Omani camels were once racing camels now held for breeding and might be kept in circumstances that favour virus transmission.”