Abstract
Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.
Highlights
Bovine coronavirus (BCoV) causes neonatal calf diarrhea, winter dysentery in adult cattle, and respiratory tract disorders in cattle of all age groups [1,2,3,4,5]
ORF1 sequences from 41 BCoV isolates and the IWT-14 isolate were 21281 and 21269 nucleotides in length, different from the length of those (21284 nt) of the 25 remaining
We determined the whole genome sequences of 67 BCoV isolates collected from 46 farms throughout Japan, using a generation sequencer based on methods we previously developed to analyze other coronaviruses, porcine epidemic diarrhea virus, and porcine deltacoronavirus [44,45]
Summary
Bovine coronavirus (BCoV) causes neonatal calf diarrhea, winter dysentery in adult cattle, and respiratory tract disorders in cattle of all age groups [1,2,3,4,5]. There are two different types (enteric and respiratory) of BCoVs based on disease symptoms. Some previous reports have suggested that several candidate amino acids may contribute to the differences between the two disease types, it still remains unclear [8,9,10]. The genome is a single-stranded, positive-sense RNA of approximately 31 kb. It includes 10 open reading frames (ORFs) flanked by 5’and 3’untranslated regions. ORF1a and ORF1b encode polyproteins, which are further cleaved to multiple nonstructural proteins. The remaining ORFs encode unknown or less-characterized proteins
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