4.2 The virome of healthy cats
Excluding anelloviruses, read counts for feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 were high in the healthy control cats (Table 1). The finding of high feline coronavirus read counts in this cohort is not surprising since feline coronavirus is endemic in shelters where the housing of multiple cats in close proximity favours virus transmission and one or more chronically infected “super-shedders” maintain cycles of infection and re-infection, since immunity is short-lived (Addie et al., 2000; Cave et al., 2004). After feline coronavirus, Mamastrovirus 2 was the most abundant virus detected in shelter-housed cats in this study, corroborating the findings of others that infection rates of astroviruses are high among clinically healthy shelter cats (Zhang et al., 2014).
We observed FPV contigs in core-vaccinated healthy control cats. All FPV vaccine contigs that contained the VP2 region of the genome displayed the amino acid leucine at position 562. This leucine amino acid is present in the FPV attenuated vaccine virus in the Feligen (Virbac, France) vaccine and in other vaccine strains Felocell (Zoetis, USA) and Purevax (Boehringer Ingelheim, Germany). Notably the 562-leucine amino acid was missing from all field strains in the 23 FPV cats in this study. The FPV read counts in the cases were markedly higher than FPV vaccine virus read counts in the healthy controls, consistent with active infection. On average FPV vaccine read counts in healthy controls were 3-6 log lower than the average read count for FPV-cases. Furthermore, our read abundance data suggests that FPV vaccine virus can be shed in faeces up to four weeks after vaccination. Previous studies have demonstrated vaccine virus shedding up to 28 days after vaccination with a live modified FPV vaccine (Bergmann et al., 2019; Jacobson et al., 2022). FPV vaccine virus was detected in one control cat (#CPS35) several months after vaccination with reads detected in the metagenomic library but not in the metatranscriptomic library (Supplementary Data S3). It is also possible that the read count for this healthy control cat is a result of index-hopping during sequencing and not active shedding since a preliminary faecal PCR test was negative for FPV DNA.
Here, feline chaphamaparvovirus sequences were only detected in healthy control cats from both shelters sampled. Similar to other studies, co-infections with other enteric viruses were common (Di Profio et al., 2021; Li et al., 2020). While feline chaphamaparvovirus has been detected in faecal or oropharyngeal samples from healthy cats elsewhere (Abayli et al., 2021; Di Profio et al., 2021), there is some evidence to suggest that feline chaphamaparvovirus may have pathogenic potential as a co-pathogen rather than as a single agent. One study detected feline chaphamaparvovirus in 14/38 (36.8%) sick cats with acute gastroenteritis and 1/51 (2%) controls and all but one of the positive sick cats were co-infected with FPV, feline kobuvirus and/or feline norovirus (Di Profio et al., 2021).