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).