The genomic and epidemiological investigations of enteric viruses of domestic caprine (
Capra hircus
) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species
Authors: Boros Ákos , Pankovics Péter , László Zoltán , Urbán Péter , Herczeg Róbert , Gáspár Gábor , Tóth Fruzsina , Reuter Gábor 
Published: October 2023

In this study, the enteric virome of diarrheic caprine was investigated using next-generation sequencing, reverse transcription PCR methods, and bioinformatics analyses. The complete or nearly complete genomes of seven novel viruses including (i) a caprine astrovirus (OQ758025) of family
Astroviridae
, four picornaviruses in genera (ii)
Boosepivirus
(OQ758026), (iii)
Enterovirus
(OQ758028), (iv)
Kobuvirus
(OQ758029), and (v) an unassigned picornavirus provisionally called as capripivirus (from the term
capri
ne
pi
corna
virus
) of the family
Picornaviridae
(OQ758027), as well as (vi) a tusavirus of family
Parvoviridae
(OL692339.2) and an (vii) unassigned CRESS DNA virus (OQ758030) have been identified. Structural analyses of the internal ribosomal entry sites revealed the presence of unique motifs and suggest the modular exchange of certain elements between co-infecting viruses. Epidemiological investigations and genotyping PCR reactions of identified RNA virus groups were also conducted using multiple “
in-house
” developed SYBRgreen-based screening quantitative PCR (qPCR) assays and generic capsid primers on additional fecal samples from ruminant livestock species (
n
= 62 caprine,
n
= 32 ovine, and
n
= 94 cattle) of three different age groups from
n
= 12 geographically distant sampling sites in Hungary. The results of qPCR screening assays as well as K-means cluster and phylogenetic analyses of the determined sequences suggest that diverse members of the above RNA virus groups were found in all age groups, but mostly in <1-year-old ruminants. Members of the analyzed virus groups were found frequently (37.2%) in multiple (even in quintuple) co-infections, while strains related closely to the identified index viruses were detectable only in certain caprine and ovine samples indicating a wide range of viral diversity.

IMPORTANCE

Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family
Parvoviridae
) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family
Astroviridae
), enteroviruses, or novel caripiviruses (named after the term
capri
ne
pi
corna
virus
) of family
Picornaviridae
found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.