Candidate Gene Markers Associated with Fecal Shedding of the Feline Enteric Coronavirus (FECV)

Abstract

The Feline coronavirus (FCoV) can cause a fatal disease, the Feline Infectious Peritonitis. Persistent shedders represent the most important source of infection. The role of the host in FCoV fecal shedding is unknown. The objective of this study was to develop gene markers and to test their associations with FCoV shedding patterns. Fecal samples were taken from 57 cats of 12 breeds on the day 0 and after 2, 4 and 12 months. Variation from persistent and/or high-intensity shedding to no shedding was observed. Thirteen immunity-related genes were selected as functional and positional/functional candidates. Positional candidates were selected in a candidate region detected by a GWAS analysis. Tens to hundreds of single nucleotide polymorphisms (SNPs) per gene were identified using next generation sequencing. Associations with different phenotypes were assessed by chi-square and Fisher’s exact tests. SNPs of one functional and one positional candidate (NCR1 and SLX4IP, respectively) and haplotypes of four genes (SNX5, NCR2, SLX4IP, NCR1) were associated with FCoV shedding at pcorected < 0.01. Highly significant associations were observed for extreme phenotypes (persistent/high-intensity shedders and non-shedders) suggesting that there are two major phenotypes associated with different genotypes, highly susceptible cats permanently shedding high amounts of viral particles and resistant non-shedders.

The Population Diversity of Candidate Genes for Resistance/Susceptibility to Coronavirus Infection in Domestic Cats: An Inter-Breed Comparison

“…Comparisons including all candidate genes and comparisons made for genes associated with fecal shedding at p uncorrected < 0.01 and at p > 0.05 in our previous study [ 19 ] revealed specific clustering patterns of genes associated at p corrected < 0.01.…”

“…Population parameters of nine haplotypes ( NCR1-D , NCR2-M/A , NCR2-S , SLX4IP-A , SNX5-A , SNX5-B , SNX5-C , SNX5-D , SNX5-E ) associated with FCoV shedding in our previous study [ 19 ] are summarized in Supplementary Material SM4 . Data for all haplotypes analyzed are in Supplementary Table ST3 .…”

“…Our panel of markers covered functional and/or positional candidates potentially associated with both clinical disease (FIP) and fecal shedding. Ten of these markers were fully characterized in this report [ 19 ]. Three IR gene markers were developed as functional candidates based on the roles of perforin (PRF1), granzyme B (GZMB) and granzyme A (GZMA) in the cytotoxicity of natural killer cells and T lymphocytes.…”

“…On the other hand, the association of genes with FCoV shedding at different levels of significance [ 19 ] allowed us to analyze different types of markers separately and to include haplotypes. For SNP markers of two genes associated with FCoV shedding at p corrected < 0.01, three clearly distinct clusters differing in the presence and frequencies of alleles associated with FCoV shedding were defined by PCoA and confirmed by STRUCTURE ( Figure 2 A,C; Table 3 ; Supplementary Material SM3 ).…”

“…A study of molecular markers on a limited number of cats did not find statistical associations between FCoV fecal shedding status and the feline Major Histocompatibility Complex (MHC) FLA class II DRB genes [ 18 ]. Recently, we have found associations between SNPs of one functional and one positional candidate gene ( NCR1 and SLX4IP , respectively) and haplotypes of four genes ( SNX5, NCR2, SLX4IP, NCR1 ) with FCoV shedding in a multiple-breed study [ 19 ].…”