NCM 2022: Intra-and inter-cattery epidemiology of feline coronavirus in Belgium between 2018 and 2021

As an enzootic pathogen in all cat populations, feline enteric coronavirus can persist up to years within the intestinal epithelium, facilitating intra-host evolution. The latter poses a threat since a shift in viral tropism to monocytes and macrophages is thought to result in feline infectious peritonitis (FIP), a lethal systemic infection. This work focused on establishing a feces-to-whole-genome-sequence workflow to evaluate the epidemiology of Belgian feline coronavirus (FCoV) strains. Fecal samples (n=513) were collected across Belgium between 2018 and 2021. A targeted FCoV amplicon-tiling protocol was used to generate FCoV genomes using long-read sequencing. Genomes (n=157) were used to study Belgian FCoV diversity, but also evolutionary rates and traces within the 30-kbp genome. The current data represents the biggest FCoV WGS dataset from a single country. Our targeted FCoV WGS protocol will shed light on unanswered questions on FCoV-to-FIPV conversion and will facilitate new sequencing-driven diagnostic tools and cures.