Epidemiological Analysis Of Canine Astrovirus And Canine Coronavirus In Multiple Provinces Of China From 2018 To 2019

Diarrhea can lead to the loss of water and electrolytes.Severe diarrhea may cause severe dehydration,electrolyte disturbance,and even death of animals.Therefore,we must diagnose the cause of diarrhea as soon as possible while carrying out symptomatic treatment.Canine coronavirus(CCoV)and Canine astrovirus(CaAstV)are members of canine diarrhea-related virus,but the current research on these two viruses is relatively lacking.CaAstV has a high prevalence rate in dogs with diarrhea.Considering that the isolation of CaAstV in vitro is relatively difficult,the current research on CaAstV mainly focuses on epidemiology.Moreover,recombination between animal AstV and HAstV has been reported,suggesting a potential risk for the emergence of novel human AstV.Coronavirus has strong antigenic variability,and its frequent mutation and recombination may lead to the emergence of new coronavirus variants.Therefore,we conducted an epidemiological investigation and according to all the available CCoV and CaAstV sequences to provides insights into viral epidemiology,evolution and genetic diversity of currently strains circulating in China.The aim of this study is to provide useful information for the future prevention of CCoV and CaAstV.1.Epidemiology,Genetic Diversity,and Evolution of Canine AstrovirusIn the epidemiology research of CaAstV,we sequenced 12 nearly full-length CaAstV genomes and found 14(13.2%)and 7(3.35%)CaAstV positive samples from pet dogs with and without diarrhea,respectively.Phylogenetic analysis of ORF2 gene revealed 4 major lineages.In particular,lineage 4 might have evolved from a recombinant virus from lineage2 and lineage 3.The strains sequenced here clustered with lineages 2,3,and 4 in contrast with other Chinese strains identified previously that clustered with lineages 2 and 4.Amino acid sequence alignment within lineage revealed intra-lineage amino acid diversity and that the type of epidemic strains within lineages changes over time.Three amino acids substitutions located in predicted B cell epitopes,which might be involved escape of host immunity.Moreover,frequent interclade ORF2 gene recombinants were identified.The identification of individual recombination events and a recombinant lineage indicated that recombination plays a crucial role in CaAstV genetic evolution and diversity by generating divergent viruses.Moreover,phylogenetic analysis of ORF1 b,the most conserved gene of astrovirus,revealed a close relationship between CaAstV and California sea lion astroviruses.Overall,we report detailed information on the genetic evolution and diversity of CaAstV,which indicates that CaAstV may pose challenges for diagnostics and future control strategies.2.Epidemiology and Genetic Evolution of Canine Coronavirus Circulating in Five Provinces of China,During 2018-2019We 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(Ca KV),Torque teno canis virus(TTCa V)were ubiquitous existed.Mixed infection of different CCoV subtypes exists extensively.Considering the limited sequences data in recent years,we sequenced 7nearly 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 provided a useful clue as to the epidemiology 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.