First report on detection and molecular characterization of alphacoronaviruses in the small Indian mongoose (Urva auropunctata).

BACKGROUND: Members of the species Alphacoronavirus suis/Alphacoronavirus-1 (αCoV-1) are important viral pathogens of canids/felids that exhibit complex evolutionary patterns and have been associated with interspecies transmission events including zoonoses. Mongooses (family Herpestidae, order Carnivora) are scavengers that pose a risk as potential carrier of viral pathogens. To date, there are no reports on the genetic make-up/diversity of CoVs circulating in mongoose populations.

METHODS: Fecal samples obtained from 53 small Indian mongooses (Urva auropunctata) on the Caribbean island of St. Kitts were screened for CoVs using a pan-CoV RT-semi-nested PCR assay and canine αCoV-specific RT-PCR assays. The partial RNA-dependent RNA polymerase (RdRp) and membrane protein (M) coding sequences (CDS) and the nearly full-length spike (S) protein CDS were determined from the mongoose CoVs and analyzed in the present study.

RESULTS: We report here high detection rates of αCoVs (30.18%, 16/53 samples) in small Indian mongooses on St. Kitts, indicating that αCoVs might be widely circulating in the island mongoose population. Analysis of the CoV RdRp-, M- and S- CDS revealed significant genetic diversity among the mongoose CoVs, and between mongoose CoVs and other αCoVs, including evidence for at least 2 recombination events (involving S gene), one of which involved the putative receptor binding domain (RBD). Phylogenetically, the mongoose CoVs formed distinct cluster/s within the canine CoV-2 (CCoV-2) lineage and appeared to be more related to CCoV-2b than other αCoVs. Despite differences in the S CDS including those in the RBD, the mongoose CoVs preserved certain features that are characteristic of CCoV-2 (lack of furin cleavage motif at S1/S2 site and presence of cleavage motif at S2' site) and retained the crucial amino acid residues essential for αCoV binding to the host aminopeptidase N receptor.

CONCLUSIONS: The present study is the first to report high detection rates and genetic makeup/diversity of CoVs in mongooses, expanding our knowledge on the host range and complex evolutionary patterns of αCoVs. Considering our findings, the proximity of mongoose to other canids/felids and humans, and cross-species transmission potential of CoVs, large-scale studies on prevalence and genetic diversity of CoVs that might be circulating in different mongoose species/populations, and in-depth investigation of mongoose CoV RBD-host receptor interactions are of utmost importance.