Abstract
The yak (Bosgrunniens) is a unique domestic bovine species that plays an indispensable role for herdsmen in the Qinghai–Tibet Plateau. Here, 336 diarrhoeic samples were collected from yaks on 29 farms in the Qinghai–Tibet Plateau from 2015 to 2017. Approximately 69.05 % (232/336) of the diarrhoeic samples were assessed as bovine coronavirus (BCoV)-positive by RT-PCR assay, and most of the detected strains showed a unique evolution based on 40 spike (S), nucleocapsid (N) and haemagglutinin-esterase (HE) gene fragments. Notably, the 12 complete S genes detected shared 1 identical amino acid mutation (E121V) in the S1 subunit compared with the other 150 complete S genes in the GenBank database. Furthermore, a BCoV strain (designated YAK/HY24/CH/2017) was isolated from one diarrhoeic sample (virus titre : 108.17TCID50 ml−1), and a phylogenetic analysis based on complete genome sequences revealed that strain YAK/HY24/CH/2017 has the closest genetic relationship with the BCoV prototype strain Mebus. Interestingly, 2 significant characteristics were observed in the genome of strain YAK/HY24/CH/2017 : (1) the strain had 26 unique amino acid variations in the S gene compared with the other 150 BCoV S genes in the GenBank database and (2) a recombination event was identified between the esterase and lectin domains of the HE gene. In conclusion, this study revealed the high prevalence of BCoV in yaks in the Qinghai–Tibet Plateau. To the best of our knowledge, this is the first description of the molecular prevalence of BCoV in yaks and of a BCoV genome with an HE gene recombination.
Highlights
Bovine coronavirus (BCoV) is a causative agent of diarrhoea in neonatal calves, winter dysentery in adult cattle and respiratory tract illness in cattle of all ages, leading to serious economic losses [1]
A phylogenetic analysis of the 40 partial S gene sequences showed that all 40 yak CoV strains detected in this study were most closely related to strain AKS-01, which was isolated from a Chinese dairy cow (GenBank accession number KU886219.1), and they were located in an independent sub-branch (Fig. 2a)
A phylogenetic tree of the complete HE gene amino acid sequences showed that strain YAK/HY24/CH/2017 is clustered into an independent branch with strain AKS-01, which was determined in China (GenBank accession number KU886219.1) (Fig. 5)
Summary
Bovine coronavirus (BCoV) is a causative agent of diarrhoea in neonatal calves, winter dysentery in adult cattle and respiratory tract illness in cattle of all ages, leading to serious economic losses [1]. Dual pneumoenteric tropism is a common feature of BCoV [12]; a recent study suggested that human nasal mucosa can temporarily carry BCoV RNA after exposure to virus-shedding calves [13]. These results indicate that the public health impact of BCoVs needs to be further investigated. Host species-specific mutations involving deletion in the variable region of the S1 subunit (from amino acid 543 to amino acid 547) were detected in giraffe CoV [14], but the genomic features of CoV detected in other wild ruminants could not be discriminated from BCoV [2, 10]. The BCoV virion contains five structural proteins: the spike (S) protein, the haemagglutinin-esterase (HE) protein, the nucleocapsid (N) protein, the Received 4 February 2019; Accepted 9 March 2019; Published 1 April 2019 Author affiliations: 1College of Life Science and Technology, Southwest University for Nationalities, Chengdu, PR China; 2Key Laboratory of Qinghai-
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