key: cord-1016986-nhf3rbwf authors: He, Hai-Jian; Zhang, Wenyan; Liang, Jiawei; Lu, Meng; Wang, Ruyi; Li, Gairu; He, Jia-Wei; Chen, Jun; Xing, Gang; Chen, Ye title: Etiology and genetic evolution of canine coronavirus circulating in five provinces of China, during 2018–2019 date: 2020-04-18 journal: Microb Pathog DOI: 10.1016/j.micpath.2020.104209 sha: 22cf6aaf9f7f07851592c1b9a1015275b21d5980 doc_id: 1016986 cord_uid: nhf3rbwf Abstract As the outbreaks of COVID-19 in worldwide, coronavirus has once again caught the attention of people. Canine coronavirus is widespread among dog population, and sometimes causes even fatal cases. Here, to characterize the prevalence and evolution of current circulating canine coronavirus (CCoV) strains in China, we collected 213 fecal samples from diarrheic pet dogs between 2018 and 2019. Of the 213 samples, we found 51 (23.94%) were positive for CCoV. Co-infection with canine parvovirus (CPV), canine astrovirus (CaAstV), canine kobuvirus (CaKV), Torque teno canis virus (TTCaV) were ubiquitous existed. Mixed infection of different CCoV subtypes exists extensively. Considering the limited sequences data in recent years, we sequenced 7 nearly complete genomes and 10 complete spike gene. Phylogenetic analysis of spike gene revealed a new subtype CCoV-II Variant and CCoV-IIa was the most prevalent subtype currently circulating. Moreover, we identified strain B906_ZJ_2019 shared 93.24% nucleotide identifies with previous strain A76, and both of them clustered with CCoV-II Variant, which were not well clustered with the known subtypes. Recombination analysis of B906_ZJ_2019 indicated that strain B906_ZJ_2019 may a recombinant variant between CCoV–I and CCoV-II, which is consistent with strain A76. Furthermore, amino acid variations widely existed among current CCoV-IIa strains circulating in China and the classic CCoV-IIa strains, in spite of the unknown functions. In a word, we report a useful information as to the etiology and evolution of canine coronavirus in China based on the available sequences, which is urgent for the devise of future effective disease prevention and control strategies. In a word, we report a useful information as to the etiology and evolution of canine 40 coronavirus in China based on the available sequences, which is urgent for the devise 41 of future effective disease prevention and control strategies. Coronaviruses, as single-stranded RNA viruses, have been widely detected in a 46 variety of mammals and several birds [1, 2] . Its genome has ranged from 26 to 32 kb in 47 Kit (CW Biotech, Jiangsu, China) protein among CCoV-IIa strains sequenced here and the classical CCoV-IIa strains. 165 We found amino acid changes in around 45 residues, most of these are located in S1 CCoV-II groups ( Figure 3B ). In contrast, the sequence of S2 domain of 189 B906_ZJ_2019 clustered closely with these strains identified in this study which 190 belong to CCoV-IIa ( Figure 3C ). K-H L Ja pa n D Q 0 1 0 9 2 1 F C o V 7 9 -1 1 4 6 K P 1 4 3 5 0 7 F C o V 2 7 C 2 0 1 3 D 1 3 0 9 6 C C o V IN S A V C -1 K C 1 7 5 3 3 9 1 7 1 G e rm a n y 1 9 7 1 ree scale: 0.1 New enteric viruses In the dog Fatal Coronavirus Infection in Puppies following Canine Parvovirus 2b Infection Journal of Veterinary Diagnostic Investigation Official Publication of the American 321 Association of Veterinary Laboratory Diagnosticians Inc 11 Disease in an Animal Shelter Associated with Dual Infections by Canine Adenovirus 324 Type 1 and Canine Coronavirus Molecular characterisation of the virulent canine coronavirus CB/05 327 strain Molecular characterization of a canine coronavirus 330 UWSMN-1) in Australia Genetic Diversity, and Evolutionary Dynamics of Novel 427 Interspecies Transmission, Genetic Diversity, and Evolutionary 431 Dynamics of Pseudorabies Virus Human infection with influenza H9N2 Transmission of 437 H7N7 avian influenza A virus to human beings during a large outbreak in commercial 438 poultry farms in the Netherlands Evidence for Camel-to-Human Transmission of MERS Coronavirus COVID-19: Epidemiology, Evolution, and Cross-Disciplinary 450 Perspectives 1999 1999 1999