FCoV Viral Sequences of Systemically Infected Healthy Cats Lack Gene Mutations Previously Linked to the Development of FIP

Deciphering Viral Replication Dynamics in Feline Infectious Peritonitis: A Quantitative Approach

Feline infectious peritonitis (FIP) is a complex immune-mediated disease caused by feline coronavirus (FCoV). Despite advancements in understanding its pathogenesis, challenges persist in elucidating viral factors related to virion composition and replication. This study examined FCoV-infected cats with and without FIP for potential associations with or variation in expression ratios for different viral genes. We analyzed tissue samples with FIP lesions from 46 cats with FIP and mesenteric lymph nodes from 10 FCoV-infected cats (7b RT-qPCR positive) without FIP with three RT-qPCR assays, targeting (sub)-genomic RNAs of the RNA-dependent RNA polymerase (RdRp) and envelope (E) genes. In cats with FIP, the RdRp mRNA assay yielded the highest copy numbers, followed by the combined RdRp gRNA and mRNA assay; the E mRNA assay yielded the lowest copy numbers. In cats without FIP, significantly fewer viral RNA copies were detected regardless of the assay. Viral gene expression was not detected in six and was observed only at low levels in one or more assays in four samples. The observed correlation between assays and the intragroup correlation assay indicate consistent transcription of both the structural E protein and RdRp genes within FIP lesions in cats with FIP but not in cats with systemic FCoV infection alone.

Molecular detection using hybridization capture and next-generation sequencing reveals cross-species transmission of feline coronavirus type-1 between a domestic cat and a captive wild felid

Feline coronavirus (FCoV) infection normally causes mild or subclinical signs and is common in domestic cats. However, in some cats, FCoV infection can also lead to the development of feline infectious peritonitis (FIP)-a typically lethal disease. FCoV has two serotypes or genotypes, FCoV-1 and FCoV-2, both of which can cause FIP. The main difference between the genotypes is the viral spike (S) protein that determines tropism and pathogenicity, crucial mechanisms in the development of FIP. Subclinical infection and FIP have both been reported in wild felids, including in threatened species. Due to the high genetic variability of the S gene and the technical challenges to sequencing it, detection and characterization of FCoV in wild felids have mainly centered on other more conserved genes. Therefore, the genotype causing FIP in most wild felids remains unknown. Here, we report a retrospective molecular epidemiological investigation of FCoV in a zoological institution in the U.Ss. In 2008, a domestic cat (Felis catus) and a Pallas' cat (Otocolobus manul) sharing the same room succumbed to FIP. Using in situ hybridization, we detected FCoV RNA in different tissues of both felids. Using hybridization capture and next-generation sequencing, we detected, sequenced, and characterized the whole genome of the FCoV infecting both felids. Our data show for the first time that FCoV-1 can be transmitted between domestic and wild felids and extends the known host range of FCoV-1. Our findings highlight the importance of identifying the genotype causing FIP, to develop effective control measures.

IMPORTANCE

Feline coronavirus (FCoV) is highly prevalent in domestic cats worldwide and has also been reported in wild felids, including endangered species, in which it has caused substantial population declines. Characterizing the genetic diversity of FCoV is crucial due to recent reports of novel pathogenic recombinant variants causing high mortality in feral cats in Cyprus. In this retrospective molecular epidemiology study, we used archived samples collected in a zoological institution in the U.S. in which a domestic and a wild felid succumbed to FCoV. Using hybridization capture (HC) and next-generation sequencing, we show for the first time that FCoV can be naturally transmitted between domestic and wild felids. We demonstrate the efficacy of HC for detecting and sequencing the whole genome of FCoV, which is essential to characterize its different genotypes.

An adenovirus-vectored vaccine based on the N protein of feline coronavirus elicit robust protective immune responses

Feline coronavirus (FCoV) is an unsegmented, single-stranded RNA virus belonging to the Alphacoronavirus genus. It can cause fatal feline infectious peritonitis (FIP) in cats of any ages. Currently, there are no effective prevention and control measures to against FCoV. In this study, we developed a recombinant adenovirus vaccine, AD5-N, based on the nucleocapsid(N) protein of FCoV. The immunogenicity of AD5-N was evaluated through intramuscular immunization in 6-week-old Balb/c mice and 9-12 months old cats. Compared to the control group, AD5-N specifically induced a significant increase in IgG and SIgA levels in the vaccinated mice. Furthermore, AD5-N not only effectively promoted strong cellular immune responses in cats but also induced high levels of specific SIgA, effectively helping cats resist FCoV infection. Our findings suggest that adenovirus vector vaccines based on the N gene have the potential to become candidate vaccines for the prevention and control of FCoV infection.

Feline Infectious Peritonitis: European Advisory Board on Cat Diseases Guidelines

Feline coronavirus (FCoV) is a ubiquitous RNA virus of cats, which is transmitted faeco-orally. In these guidelines, the European Advisory Board on Cat Diseases (ABCD) presents a comprehensive review of feline infectious peritonitis (FIP). FCoV is primarily an enteric virus and most infections do not cause clinical signs, or result in only enteritis, but a small proportion of FCoV-infected cats develop FIP. The pathology in FIP comprises a perivascular phlebitis that can affect any organ. Cats under two years old are most frequently affected by FIP. Most cats present with fever, anorexia, and weight loss; many have effusions, and some have ocular and/or neurological signs. Making a diagnosis is complex and ABCD FIP Diagnostic Approach Tools are available to aid veterinarians. Sampling an effusion, when present, for cytology, biochemistry, and FCoV RNA or FCoV antigen detection is very useful diagnostically. In the absence of an effusion, fine-needle aspirates from affected organs for cytology and FCoV RNA or FCoV antigen detection are helpful. Definitive diagnosis usually requires histopathology with FCoV antigen detection. Antiviral treatments now enable recovery in many cases from this previously fatal disease; nucleoside analogues (e.g., oral GS-441524) are very effective, although they are not available in all countries.

Intra-host variation in the spike S1/S2 region of a feline coronavirus type-1 in a cat with persistent infection

Feline coronavirus type 1 (FCoV-1) is widely known for causing feline infectious peritonitis (FIP), a systemic infection that is often fatal, with the virus known as the FIPV biotype. However, subclinical disease also occurs, in which cats may not show signs and intermittently shed the virus, including in feces, possibly for long periods of time. This virus is known as the FECV biotype. Progression of FECV to FIPV has been linked to several genomic changes, however a specific region of the viral spike protein at the interface of the spike S1 and S2 domains has been especially implicated. In this study, we followed a cat (#576) for six years from 2017, at which time FCoV-1 was detected in feces and conjunctival swabs, until 2022, when the animal was euthanized based on a diagnosis of alimentary small cell lymphoma. Over this time period, the cat was clinically diagnosed with inflammatory bowel disease and chronic rhinitis, and cardiac problems were also suspected. Using hybridization capture targeting the spike (S) gene of FCoV followed by next-generation sequencing, we screened 27 clinical samples. We detected FCoV-1 in 4 samples taken in 2017 (intestine and nasal tissue, feces, and conjunctiva), and 3 samples taken in 2022 (feces, and intestinal and heart tissue), but not in fecal samples taken in 2019 and 2020. Next, we focused on the S1/S2 region within S, which contains the furin cleavage site (FCS), a key regulator of viral transmission and pathogenesis. We show that the FCoV-1 variants obtained from feces in 2017 and 2022 were identical, while the ones from conjunctiva (2017), heart (2022), and intestine (2017 and 2022) were distinct. Sequence comparison of all the variants obtained showed that most of the non-synonymous changes in the S1/S2 region occur within the FCS. In the heart, we found two variants that differed by a single nucleotide, resulting in distinct FCS motifs that differ in one amino acid. It is predicted that one of these FCS motifs will down-regulate spike cleavability. The variant from the conjunctiva (2017) had a 6-nucleotide in-frame insertion that resulted in a longer and more exposed S1/S2 loop, which is predicted to be more accessible to the furin protease. Our studies indicate that FCoV-1 can independently persist in the gastrointestinal tract and heart of a cat over a long period of time without evidence of typical FIP signs, with intermittent viral shedding from the gastrointestinal and respiratory tracts.

The first study on clinicopathological changes in cats with feline infectious peritonitis with and without retrovirus coinfection

Background and Aim

Feline infectious peritonitis (FIP) is an infectious, immune-mediated, and fatal disease in cats caused by a mutant feline coronavirus (FCoV) infection. Feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) are two common retroviruses that play a role in reducing feline immune function with opportunistic retrovirus infection being a predisposing factor for the development of FIP. This study aimed to evaluate the clinicopathological parameters of FIP in cats with and without retrovirus coinfection.

Materials and Methods

In total, 62 cats presenting with pleural and/or peritoneal effusion at the Kasetsart University Veterinary Teaching Hospital, Bangkok, Thailand, were selected for the study. Effusion samples were collected and a reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed on all samples using the 3' untranslated region primer. All FCoV-positive cats were tested for retrovirus infection using a commercial kit (Witness FeLV-FIV [Zoetis]; United States). Clinical signs, hematological, and biochemical parameters of these cats were investigated and grouped.

Results

Of the 62 cats with pleural and/or peritoneal effusion, FCoV was detected in 32, of which 21 were highly suspicious for FIP. The cats suspected of FIP were divided into three subgroups following viral detection. A total of 14 had only FCoV infection (Group A), four had FCoV and FeLV infection (Group B), and three had FCoV, FeLV, and FIV infection (Group C). Of the rest, 11 had definitive diagnoses, which included three being FCoV and FeLV-positive (Group D), and eight were retrovirus-negative (Group E). Mild anemia and lymphopenia were found in cats infected with these three viruses. An albumin-to-globulin ratio lower than 0.5 was found in FIP cats with only FCoV infection.

Conclusion

Typically, cats with clinical effusion and FIP, with and without retrovirus coinfection, had similar hematological findings. Clinical signs, blood parameters, fluid analysis with cytological assessment, and RT-PCR assays could identify better criteria to diagnose FIP with and without retrovirus coinfection.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes

Feline coronaviruses (FCoVs) commonly cause mild enteric infections in felines worldwide (termed feline enteric coronavirus [FECV]), with around 12 per cent developing into deadly feline infectious peritonitis (FIP; feline infectious peritonitis virus [FIPV]). Genomic differences between FECV and FIPV have been reported, yet the putative genotypic basis of the highly pathogenic phenotype remains unclear. Here, we used state-of-the-art molecular evolutionary genetic statistical techniques to identify and compare differences in natural selection pressure between FECV and FIPV sequences, as well as to identify FIPV- and FECV-specific signals of positive selection. We analyzed full-length FCoV protein coding genes thought to contain mutations associated with FIPV (Spike, ORF3abc, and ORF7ab). We identified two sites exhibiting differences in natural selection pressure between FECV and FIPV: one within the S1/S2 furin cleavage site (FCS) and the other within the fusion domain of Spike. We also found fifteen sites subject to positive selection associated with FIPV within Spike, eleven of which have not previously been suggested as possibly relevant to FIP development. These sites fall within Spike protein subdomains that participate in host cell receptor interaction, immune evasion, tropism shifts, host cellular entry, and viral escape. There were fourteen sites (twelve novel sites) within Spike under positive selection associated with the FECV phenotype, almost exclusively within the S1/S2 FCS and adjacent to C domain, along with a signal of relaxed selection in FIPV relative to FECV, suggesting that furin cleavage functionality may not be needed for FIPV. Positive selection inferred in ORF7b was associated with the FECV phenotype and included twenty-four positively selected sites, while ORF7b had signals of relaxed selection in FIPV. We found evidence of positive selection in ORF3c in FCoV-wide analyses, but no specific association with the FIPV or FECV phenotype. We hypothesize that some combination of mutations in FECV may contribute to FIP development, and that it is unlikely to be one singular 'switch' mutational event. This work expands our understanding of the complexities of FIP development and provides insights into how evolutionary forces may alter pathogenesis in coronavirus genomes.

Detection of Feline Coronavirus Variants in Cats without Feline Infectious Peritonitis

(1) Background: This study aimed to detect feline coronavirus (FCoV) and characterize spike (S) gene mutation profiles in cats suffering from diseases other than feline infectious peritonitis (FIP) using commercial real-time reverse transcription polymerase chain reaction (RT-qPCR) and reevaluating results by sequencing. (2) Methods: In 87 cats in which FIP was excluded by histopathology and immunohistochemistry, FCoV 7b gene and S gene mutation RT-qPCR was performed prospectively on incisional biopsies and fine-needle aspirates of different organs, body fluids, and feces. Samples positive for S gene mutations or mixed FCoV underwent sequencing. (3) Results: In 21/87 cats, FCoV RNA was detectable. S gene mutations were detected by commercial RT-qPCR (and a diagnostic algorithm that was used at the time of sample submission) in at least one sample in 14/21 cats (66.7%), with only mutated FCoV in 2/21, only mixed in 1/21, and different results in 11/21 cats; in the remaining 7/21 cats, RNA load was too low to differentiate. However, sequencing of 8 tissue samples and 8 fecal samples of 9 cats did not confirm mutated FCoV in any of the FCoV RNA-positive cats without FIP. (4) Conclusions: Sequencing results did not confirm results of the commercial S gene mutation RT-qPCR.

Fecal Feline Coronavirus RNA Shedding and Spike Gene Mutations in Cats with Feline Infectious Peritonitis Treated with GS-441524

As previously demonstrated by our research group, the oral multicomponent drug Xraphconn® containing GS-441524 was effective at curing otherwise fatal feline infectious peritonitis (FIP) in 18 feline coronavirus (FCoV)-infected cats. The aims of the current study were to investigate, using samples from the same animals as in the previous study, (1) the effect of treatment on fecal viral RNA shedding; (2) the presence of spike gene mutations in different body compartments of these cats; and (3) viral RNA shedding, presence of spike gene mutations, and anti-FCoV antibody titers in samples of 12 companion cats cohabitating with the treated cats. Eleven of the eighteen treated FIP cats (61%) were shedding FCoV RNA in feces within the first three days after treatment initiation, but all of them tested negative by day 6. In one of these cats, fecal shedding reoccurred on day 83. Two cats initially negative in feces were transiently positive 1-4 weeks into the study. The remaining five cats never shed FCoV. Viral RNA loads in feces decreased with time comparable with those in blood and effusion. Specific spike gene mutations linked to systemic FCoV spread were consistently found in blood and effusion from treated FIP cats, but not in feces from treated or companion cats. A new mutation that led to a not yet described amino acid change was identified, indicating that further mutations may be involved in the development of FIP. Eight of the twelve companion cats shed FCoV in feces. All but one of the twelve companion cats had anti-FCoV antibodies. Oral treatment with GS-441524 effectively decreased viral RNA loads in feces, blood, and effusion in cats with FIP. Nonetheless, re-shedding can most likely occur if cats are re-exposed to FCoV by their companion cats.

A duplex SYBR green I-based real-time polymerase chain reaction assay for concurrent detection of feline parvovirus and feline coronavirus

Feline coronavirus (FCoV) contains two serotypes, feline enteric coronavirus (FECV) and Feline infectious peritonitis virus (FIPV). FECV and feline parvovirus (FPV) can cause similar clinical symptoms in cats, such as diarrhea. The objective of this study was to establish a duplex SYBR Green I-based quantitative polymerase chain reaction (qPCR) assay for rapid and simultaneous detection of FPV and FCoV. Two pairs of specific PCR primers were designed to target fragments of the VP2 gene of FPV and of the 5' UTR gene of FCoV, respectively. The assay distinguished between the two viruses based on the melting curves (melting temperatures 77.0 ± 0.5 °C [FPV] and 80.5 ± 0.5 °C [FCoV]). The minimum limits of FPV and FCoV detection were 4.74 × 10¹ copies/μL and 7.77 × 10¹ copies/μL, respectively. The assay showed excellent reproducibility and reliability, based on the mean coefficient of variation. In conclusion, this novel duplex SYBR Green I-based qPCR assay is sensitive and can specifically, reliably, and rapidly detect FPV and FCoV (co-)infections.

Comparative sequence analysis of the accessory and nucleocapsid genes of feline coronavirus strains isolated from cats diagnosed with effusive feline infectious peritonitis

Feline infectious peritonitis (FIP) is a lethal infectious disease of domestic cats caused by feline coronavirus (FCoV) infection. Feline infectious peritonitis virus (FIPV) is a mutant type of FCoV that is characterized by causing fibrinous serositis with effusions in the pleural and abdominal cavities (wet form) and/or granulomatous-necrotizing inflammatory lesions in several organs (dry form). There have been numerous studies on FIP worldwide, whereas information about this disease in Thailand is still limited. Most studies involving molecular surveillance and evaluation of FCoV field strains have examined the genetic diversity of the spike and accessory ORF3c coding regions. Of these, the S gene is more divergent and is responsible for the two FCoV serotypes, while ORF3c harbors mutations that result either in early termination or destruction of the protein. In this study, we investigated the genetic diversity and genetic relationships among the current Thai and global FCoV strains in the accessory and nucleocapsid genes using a virus-specific PCR method. Comparative sequence analysis suggested that the Thai FCoV isolates were most closely related to strains reported in the Netherlands, the USA, and China. In the ORF3ab sequences, some Thai strains were more than 99% identical to the DF-2 prototype strain. Truncation of the 3a gene product was found in Thai FCoV strains of group 2. Amino acid deletions were observed in the N, ORF3c, and ORF7b proteins of Thai FCoV sequences. The accessory gene sequence divergence may be responsible for driving the periodic emergence and continued persistence of FCoVs in Thai domestic cat populations. Our findings provide updated information about the molecular characteristics of the accessory and nucleocapsid genes of FCoV strains in circulation that were not previously documented in this country.