3.2.1 Protoparvovirus
FPV contigs were detected in 2/8 healthy control cats from shelter 1 and 25/28 cats from shelter 2. The FPV sequence in the two cats from shelter 1 had 100% nucleotide sequence identity to a sequence isolated from sick FPV cats in this study, which is circulating throughout the greater Sydney region and has only been identified in cats from New South Wales (NSW) (Van Brussel et al., 2019). At the time of collection both shelter 1 cats were clinically healthy, consistent with a subclinical infection of FPV. For cats from shelter 2 the nucleotide sequence similarity of FPV contigs compared to the FPV vaccine strain was 99.9-100% for NS1 and 99.8-99.9 for VP2, and 23/25 had been vaccinated within the previous 30 days. Read abundance for the healthy control cats was calculated by mapping to a complete FPV genome isolated from a healthy control cat (Supplementary Data S3). Thus, the FPV detected in shelter 2 cats likely represents the vaccine strain or a variant of the vaccine strain. In addition, one healthy control cat from shelter 2 had an FPV VP2 sequence (1448bp contig) with 100% identity to an FPV sequence isolated from an Australian outbreak of FPL in Mildura, Victoria in 2015 (Van Brussel et al., 2019).