The close similarity of FECV to FIPV, and the low incidence of FIP, despite the high proportion of FCoV seropositive cats, led to the hypothesis that FECV carriers are sources of FIPV, which is proposed to be generated by small mutations in FECV [
5,
19]. After this hypothesis was first postulated in the literature, several studies have been conducted to test its validity.
Initially, this mutational theory was questioned, when the 3′ ends of the genomes (the corresponding ORF7a/7b) of an FIPV strain, which had been adapted to tissue culture (strain WSU 79-1146), and an FECV strain (strain WSU 79-1683) were genetically compared. FECV was shown to contain a 238-nucleotide deletion in ORF7b [
20], in contrast to what might be expected if FIPV were indeed a mutant of FECV. According to Vennema et al. [
20], it is possible that both FECV and avirulent FIPV strains are derived from FIP inducing strains but have been attenuated by the loss of virulence factors. The authors further propose that recombination of two attenuated viruses during a rare mixed infection event could result in the resurgence of a virulent FIPV strain.
Evidence in support of the mutation theory came from comparative analysis of 1.2

kb genomic fragments obtained from nine additional FECV and FIPV isolates [
21]. All of these isolates were found to have intact ORF7bs, indicating that the deletion observed in FECV 79-1683 is associated with adaptation to cell culture. These results are in agreement with previous studies that showed that four strains of FCoV (79-1683, TN406-HP, UCD2, and ts-DF2) with deletions in ORF7b were avirulent [
22,
28]. Thus, it is likely that, for these viruses, ORF7b deletions contribute to the loss of virulence. Therefore, ORF7b seems to provide a distinct selective advantage during natural infection [
21].
Because ORF7b deletions had been identified in previous studies, researchers began to assess the involvement of other regions of the genome in FCoV pathogenicity. Subsequent studies have shown that both deletions and nonsense mutations within ORF3c and, less often, specific mutations in OFR7b are present in FIPVs but not in FECVs [
9]. Sequencing of attenuated derivatives of virulent FIPV strains shows good correlation between deletions in ORF7b and attenuation of virulence [
21]. This latter observation indicates that the 7b protein encoded by ORF7b is important for virulence. Thus, the virulence-associated ORF7b may be somewhat suppressed in FECVs not adapted to tissue culture, and the presence of an intact ORF3c in these FECVs may be involved in this suppression. Moreover, two cats from the same household were found to contain distinct ORF3c deletions, demonstrating that these two FIPVs were independently derived from FECV and not transmitted horizontally [
9].
Kennedy et al. [
23] analyzed ORF7a and ORF7b in cheetah FCoVs over a period of 4 years. In most isolates, a deletion mutation was observed in ORF7a that results in an open reading frame change, possibly leading to expression of an aberrant ORF7a product, or loss of ORF7a expression. In addition, although specific mutations were also found in ORF7b, these mutations would not result in important changes within the resulting protein, suggesting that this protein may be essential for viral replication or infection [
23].
Subsequent analysis of ORF7a and ORF7b revealed two distinct virus variants circulating in a population of 15 Persian cats: one with ORF7a intact and the other with two major deletions (nucleotides 20–120 and nucleotides 164–226) in ORF7a [
24]. ORF7b was intact and similar among all isolates, but specific mutations resulted in changes in ORF7b protein amino acids. Some cats in this study were doubly infected with both viral variants. Because the cats were exposed to both variants, the authors concluded that there must be a causal relationship between the occurrence of these mutations and the increased incidence of FIP in this population [
24]. According to these authors, in addition to the viral variant, disease variation must be related to host factors, such as the ability of the host to generate an effective immune response.
Alternatively, many authors have proposed that mutations in other genomic regions might be responsible for the variation in virulence observed in FCoV strains [
8,
25]. Specifically, analysis of the 5′ hypervariable region of the S gene revealed consecutive accumulation of nucleotide substitutions nonsynonymous in this region, suggesting sequential emergence of viral variants, each time replacing the pre-existing virus population as a result of immune selection during chronic infection [
25].
Because deletions in ORF7b were previously identified in laboratory strains with variable numbers of passages, these were considered to be associated with loss of virulence [
20,
21,
29]. In contrast to these previous findings, sequence comparisons of FCoV ORF7bs isolated from some cats with FIP revealed small, in-frame deletions in the 3′ region of ORF7b, implying that the presence of this deletion is not correlated with FIP pathogenicity [
30].
Studies have also shown that ORF3c presents great genetic variability in cats with FIP [
2,
26]. The expression of functional ORF3c protein is crucial for FECV replication in the gut, but dispensable for systemic FIPV replication [
26]. It was observed that ORF3c is intact in all strains of FECVs, but it is mutated in most FIPV strains. However, as some FIPVs seem to have intact ORF3c, it is likely that 3c mutations are not the only cause of FIP [
2,
26].
To investigate the genetic differences that may result in the increased pathogenicity of FIPV with respect to FECV, Dye and Siddell [
13] compared the complete sequences of viral RNA samples extracted from the liver and jejunum of a cat with classical FIP and observed 100% identity between them, calling into question the internal mutation theory. However, studies in support of this theory contend that, because deleterious ORF3c mutations tend to be found in the tissues of sick animals, while intact ORF3c is found mainly in feces [
2], fecal samples of FIPV may be present as a result of extensive intestinal lesions, which could explain the presence of the FIPV in the jejunum in the experiments carried out by Dye and Siddell [
13].
Sequence comparisons also show that FECVs and FIPVs taken from cats in the same geographical area are closely related, whereas there are significant genetic variations between FECVs and FIPVs from different geographic areas [
2,
9]. According to these authors, the high genetic similarity between FIPV and FECV isolates from cats of the same geographic region strongly suggest a common ancestor. Furthermore, the occurrence of deleterious mutations in FIPVs, but not in FECVs, is believed to confirm the hypothesis that FIPVs emerged from FECVs.
The theory that FIPVs originated from mutations in FECVs was reinforced by studies of experimental infection. Cats experimentally infected with an FECV RM strain [
7] remained asymptomatic during the first 2 months postinfection, but 8 to 10 weeks postinfection, 2 cats developed FIP. Viruses isolated from these two cats (FIPV-UCD9 and FIPV-UCD10) were found to have high sequence identity with each other and with FECV-RM and induced FIP when inoculated intraperitoneally in specific pathogen-free (SPF) cats [
7]. This study showed that FIPVs can rapidly arise by mutations in FECVs and that these mutations frequently occur, although another study showed that cats persistently infected by FECV rarely develop FIP [
31].
According to Kipar et al. [
32], an increase in viral replication capacity may be a key feature in the development of FIP. Failure to control FCoV replication could lead to an increase in viral load, thus increasing the chances that a pathogenic mutation will be generated [
25]. Furthermore, immunosuppression caused by infection with feline leukemia virus (FELV) or feline immunodeficiency virus (FIV) can reinforce the creation and selection of mutant FIPVs by increasing the rate of FECV replication in the gut and inhibiting the ability of the host to fight mutated viruses once they are formed. Thus, both viral and host factors determine the outcome of FCoV infection [
4,
7].