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Pan-genome analysis of coronaviruses derived from major of canine and feline

Coronaviruses (CoVs) are a well-known cause of severe enteric,
respiratory, and systemic disease in a wide range of animals and in
humans. To understand the route of disease origin and viral transmission
in companion animals, a comparative pan-genomic analysis of coronavirus
sequences originating from major felines and canines were conducted. The
average nucleotide identity (ANI) is a rapid procedure for assessing the
very close antigenic relationship between feline CoV (FCoVs) and canine
CoV (CCoVs) and ANI-based phylogenetic tree that clustered CoVs
according to their respective host species. While pan-genomic analysis
demarcated strains clearly. The distribution of the clinical isolates
all across the categories in the hierarchical phylogenetic model enabled
the visualization of their original ecological niche rather than their
isolation source, as infections are extremely rare events and
evolutionary dead-ends. In polymorphism analysis, we found seven
accessory gene clusters common to the FCoV/CCoV category clade,
including pantropic strains, that perform functions supporting their
pathogenicity. In addition, the gene presence/absence among FCoVs and
CCoVs would provide very valuable information on species-specific
control measures against CoV disease, such as the selection of good
markers for differentiating new species from common and/or pantropic
isolates. Also, the virulent FCoV strains were grouped with human CoV
strains NL63 and 229E confirming hypotheses stating that cats are highly
susceptible to HCoVs, while dogs have low susceptibility to the virus.
In conclusion, the combined analysis allows for better phylogenetic
resolution and the implication of virus origins, recombination, and
virus–host interaction, as well as biomarkers.