Limitations of using feline coronavirus spike protein gene mutations to diagnose feline infectious peritonitis

Barker, Emily N.; Stranieri, Angelica; Helps, Chris R.; Porter, Emily L.; Davidson, Andrew D.; Day, Michael J.; Knowles, Toby; Kipar, Anja; Tasker, Séverine

S gene mutation analysis was performed on 222 of the 235 FCoV RT-qPCR-positive samples, of which 16 (7.1%) failed target gene sequencing. Four of the 16 samples that failed target gene sequencing were collected from two cats (#45 and #127) for which analysis of other tissue samples indicated the presence of mutated virus. These four samples had very low relative FCoV copy numbers (relative FCoV copy number ≤ 19; see Table 3 ). Twelve of the 16 samples that failed sequencing were from five cats (#82, #92, #145, #146, and #147), all tissues had relative FCoV copy numbers (≥ 41; see Table 3 ) that were expected to be successful at sequencing; additional PCRs of these samples revealed the presence of serotype 2 FCoV. Only one of these cats (#92) had evidence of a nonmutated, serotype 1 FCoV in another tissue sample. All of the cats found to have serotype 2 FCoVs were either resident in Greece (#145, #146, and #147), were imported to the UK from Greece (#82), or were suspected of having been in contact with a cat imported to the UK from Greece that was euthanased with suspected FIP (#92). The origin of the remainder of the cats contained within the Bristol FIP Biobank, where known, was the UK. Four tissue samples from three cats (#92, #97 and #103) had non-mutated FCoVs present in mesenteric lymph node (n = 2), liver (n = 1) and/or spleen (n = 1): one cat (#97) had mutated FCoV in another tissue sample; one cat (#103) had both mutated and non-mutated FCoVs detected in other tissues; and one cat (#92) had serotype 2 FCoV in another tissue sample. Ten tissue samples from three cats (#43, #70 and #103) had sequence data consistent with the presence of both non-mutated and mutated (nucleotide 23531A>T/C) FCoVs, these comprised mesenteric lymph node (n = 1), liver (n = 3), omentum (n = 2), spleen (n = 2), lung (n = 1) and kidney (n = 1): one cat (#103) had non-mutated FCoV sequence in another tissue sample; and one cat (#43) had mutated FCoVs detected in other tissues. Two tissue samples from one cat (#79) had sequence data consistent with the presence of either non-mutated and double-mutated (nucleotides 23531A>T and 23537T>G in the same sample) FCoVs or both types of mutated FCoVs; these comprised omentum and spleen (n = 2), which also had mutated FCoV detected in another tissue. These mixed FCoVs were not further characterised (i.e. as double or single mutants). Only mutated FCoVs were detected in 190 samples: 186 with the M1058L mutation (nucleotide 23531A>T n = 151; nucleotide 23531A>C n = 31; mixed, nucleotides 23531A>T and 23531A>C n = 4); and four with the S1060A mutation. In five of the cats (8.8%; #37, #43, #70, #100, and #101) different mutations were detected in different tissues.