Abstract
BackgroundBovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host’s immune system and evolution.MethodsWe performed a comprehensive analysis of codon usage and composition of BCoV.ResultsThe global codon usage among BCoV strains is similar. Significant differences of codon preferences in BCoV genes in relation to codon usage of Bos taurus host genes were found. Most of the highly frequent codons are U-ending. G + C compositional constraint and dinucleotide composition also plays a role in the overall pattern of BCoV codon usage.ConclusionsThe results of these studies revealed that mutational bias is a leading force shaping codon usage in this virus. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern.
Highlights
Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae
Codon usage preferences in BCoV in relation to the codon usage of Bos taurus were established by means of the use of the codon adaptation index (CAI) [23]
In order to show whether the BCoV genes are well adapted to the codon usage of the reference set, as measured by CAI, we constructed a dataset composed of 22 Bos taurus genes selected at random and obtained from ARSA at DNA Database of Japan
Summary
Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. Coronaviruses belong to the family Coronaviridae and are the largest enveloped single-strand RNA viruses, ranging from 26 to 31 kilobases in genome size [1, 2]. These viruses infect a wide range of avian and mammalian species, and are responsible for enteric or respiratory infections [3]. There is a rising concern about the emergence of two human coronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle-East respiratory syndrome coronavirus (MERS-CoV), who emerged in 2002 and 2012, respectively [4, 5]. Bovine coronavirus (BCoV) belongs to the Betacoronavirus genus clade A [7, 8]
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