We report here the first canine polyomavirus genome, identified by metagenomics in respiratory secretions of two dogs with severe pneumonia, which tested negative for all canine respiratory pathogens except Mycoplasma cynos The isolate, Canis familiaris polyomavirus 1 (DogPyV-1), is a beta polyomavirus whose closest known LT antigen relatives are primate polyomaviruses.

A viral metagenomic analysis of feces from an unexplained outbreak of feline diarrhea revealed the presence of Lyon-IARC polyomavirus (LIPyV) DNA. LIPyV, whose genome was originally sequenced from swabs of human skin, was fecally shed by three out of five diarrheic cats.

In December 2016, influenza A (H7N2) was first detected among cats in the New York City shelter system with subsequent widespread transmission. The sequence of the first clinical isolate, A/feline/New York/16-040082-1/2016(H7N2), and its genetic similarity to the live bird market lineage of H7N2 low-pathogenicity avian influenza are described.