Journal Article

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

Ghosh, Souvik, Kulberg, Jessica L., Becker, Anne A. M. J., Malik, Yashpal S.

2025

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Alphacoronavirus / Alphacoronavirus - classification / Alphacoronavirus - genetics / Alphacoronavirus - isolation & purification / Amino acids / Aminopeptidase / Analysis / Animals / Biomedical and Life Sciences / Biomedicine / Canine coronavirus-2 lineage / Coronavirus genetic diversity / Coronavirus infections / Coronavirus spike protein / Coronaviruses / Coronaviruses: emerging and re-emerging pathogens in humans and animals / Disease transmission / Distribution / DNA-directed RNA polymerase / Dogs / Evolution / Feces / Feces - virology / Genetic aspects / Genetic diversity / Genetic Variation / Genomes / Gut microbiota / Herpestidae - virology / Host range / Identification and classification / Mongoose / Pathogens / Phylogeny / Polymerase chain reaction / Proteins / Rabies / Recombination events / Risk factors / RNA / RNA, Viral - genetics / RNA-directed RNA polymerase / S gene / Spike Glycoprotein, Coronavirus - genetics / Virology / Viruses / Zoonoses