The FIPV P3 position showed small variation compared with FECV after the introduction of a polar uncharged residue (T) in 1 sample.
Overall, in terms of FIP-positive animals, we found that 10 of 11 cats harbored viruses with mutations in the furin motif R-R-S/A-R-R-S found in FECV of asymptomatic cats.
In cat 234, the virus underwent a transition from FECV to FIPV, and had a functionally relevant mutation in the S1/S2 motif (P2 R-L).
Sequence data from samples D04-397-1 and D04-397-2 provide evidence that both FECV and FIPV populations can be identified within an affected animal.
This was done by counting, for every nucleotide position, the number of FIPV genomes for which the identify at that position differed from that in all FECV genomes.
Nucleotide identity differed the most at position 23531: it was highly conserved (100% A) in all FECV genomes, and it was C or T in 9 of the 11 FIPV genomes.
Altogether, 183 FECV and 118 FIPV RNAs isolated from different cats were sequenced in this specific region.
Overall, we have detected characteristic differences with FECV for 113 (95.
Fca-4590 was asymptomatic but infected with FECV in May 2004.
For example, the FECV strains in asymptomatic cats from the Weller household were associated together in a major FECV subclade; strains in cats from the Frederick Animal Shelter were classified in a different subclade, nested within the FECV-asymptomatic clade (Figure 4).
Given the clear genetic differentiation between viruses from FIP cases and FECV asymptomatic cats in multiple gene segments, we infer that cats become reinfected with new strains of FCoV from external sources, rather than by in vivo mutations.
A tyrosine at position 108, which is found in all FIPV biotypes and shared among SARS-CoV, has a neutral polarity (in contrast to a histidine there, found in most FECV biotypes, which have a positive polarity) and may play a role in the stability of the virus within the membrane.