{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:31:03Z","timestamp":1768505463437,"version":"3.49.0"},"posted":{"date-parts":[[2023,8,2]]},"group-title":"Molecular Biology","reference-count":57,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>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.<\/jats:p>","DOI":"10.1101\/2023.07.31.551356","type":"posted-content","created":{"date-parts":[[2023,8,2]],"date-time":"2023-08-02T15:30:11Z","timestamp":1690990211000},"source":"Crossref","is-referenced-by-count":5,"title":["Intra-host variation in the spike S1\/S2 region of a feline coronavirus type-1 in a cat with persistent infection"],"prefix":"10.64898","author":[{"given":"Ximena A.","family":"Olarte-Castillo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beth. N.","family":"Licitra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole M.","family":"Andr\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria A.","family":"Sierra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher E.","family":"Mason","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8327-3092","authenticated-orcid":false,"given":"Laura B.","family":"Goodman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary R.","family":"Whittaker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023080410400645000_2023.07.31.551356v1.1","doi-asserted-by":"crossref","unstructured":"Addie, D. D. , Bellini, F. , Covell-Ritchie, J. , Crowe, B. , Curran, S. , Fosbery, M. , Hills, S. , Johnson, E. , Johnson, C. , Lloyd, S. , & Jarrett, O. (2023). Stopping Feline Coronavirus Shedding Prevented Feline Infectious Peritonitis. Viruses, 15(4). https:\/\/doi.org\/10.3390\/v15040818","DOI":"10.3390\/v15040818"},{"key":"2023080410400645000_2023.07.31.551356v1.2","doi-asserted-by":"publisher","DOI":"10.1136\/vr.148.21.649"},{"key":"2023080410400645000_2023.07.31.551356v1.3","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.19129-0"},{"issue":"1","key":"2023080410400645000_2023.07.31.551356v1.4","first-page":"2055116919856103","article-title":"Distinct mutation in the feline coronavirus spike protein cleavage activation site in a cat with feline infectious peritonitis-associated meningoencephalomyelitis","volume":"5","year":"2019","journal-title":"JFMS Open Rep"},{"issue":"1","key":"2023080410400645000_2023.07.31.551356v1.5","first-page":"2055116920930582","article-title":"Feline infectious peritonitis virus-associated rhinitis in a cat","volume":"6","year":"2020","journal-title":"JFMS Open Rep"},{"key":"2023080410400645000_2023.07.31.551356v1.6","doi-asserted-by":"crossref","unstructured":"Araujo, G. A. , Matta, E. C. , Lallo, M. A. , Machado, G. F. , & Rocha, P. R. D. (2020). Epicarditis in a cat caused by feline infectious peritonitis virus: case report. Arquivo Brasileiro de Medicina Veterin\u00e1ria e Zootecnia, 72.","DOI":"10.1590\/1678-4162-11359"},{"key":"2023080410400645000_2023.07.31.551356v1.7","doi-asserted-by":"crossref","first-page":"1030440","DOI":"10.3389\/fmicb.2022.1030440","article-title":"Persistent viral infections and their role in heart disease","volume":"13","year":"2022","journal-title":"Front Microbiol"},{"issue":"1","key":"2023080410400645000_2023.07.31.551356v1.8","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13567-017-0467-9","article-title":"Limitations of using feline coronavirus spike protein gene mutations to diagnose feline infectious peritonitis","volume":"48","year":"2017","journal-title":"Vet Res"},{"key":"2023080410400645000_2023.07.31.551356v1.9","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.yasa.2020.07.011","article-title":"Advances in Molecular Diagnostics and Treatment of Feline Infectious Peritonitis","volume":"1","year":"2020","journal-title":"Advances in Small Animal Care"},{"issue":"3","key":"2023080410400645000_2023.07.31.551356v1.10","doi-asserted-by":"crossref","first-page":"e0282151","DOI":"10.1371\/journal.pone.0282151","article-title":"SARS-CoV-2 spike protein-mediated cardiomyocyte fusion may contribute to increased arrhythmic risk in COVID-19","volume":"18","year":"2023","journal-title":"PLoS One"},{"key":"2023080410400645000_2023.07.31.551356v1.11","doi-asserted-by":"publisher","DOI":"10.1056\/nejmsb2104756"},{"key":"2023080410400645000_2023.07.31.551356v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/srep20022"},{"issue":"3","key":"2023080410400645000_2023.07.31.551356v1.13","first-page":"e849","article-title":"Risk Factors for Ebola Virus Persistence in Semen of Survivors in Liberia","volume":"76","year":"2022","journal-title":"Clinical Infectious Diseases"},{"issue":"2","key":"2023080410400645000_2023.07.31.551356v1.14","first-page":"2055116919879256","article-title":"Feline coronavirus-associated myocarditis in a domestic longhair cat","volume":"5","year":"2019","journal-title":"JFMS Open Rep"},{"key":"2023080410400645000_2023.07.31.551356v1.15","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.26587"},{"issue":"1","key":"2023080410400645000_2023.07.31.551356v1.16","doi-asserted-by":"crossref","first-page":"20551169221074226","DOI":"10.1177\/20551169221074226","article-title":"Outbreak of feline infectious peritonitis (FIP) in shelter-housed cats: molecular analysis of the feline coronavirus S1\/S2 cleavage site consistent with a \u2018circulating virulent\u2013avirulent theory\u2019 of FIP pathogenesis","volume":"8","year":"2022","journal-title":"Journal of Feline Medicine and Surgery Open Reports"},{"key":"2023080410400645000_2023.07.31.551356v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/nsb941"},{"key":"2023080410400645000_2023.07.31.551356v1.18","doi-asserted-by":"publisher","DOI":"10.1006\/viro.1997.8663"},{"key":"2023080410400645000_2023.07.31.551356v1.19","doi-asserted-by":"crossref","unstructured":"J\u00e4hne, S. , Felten, S. , Bergmann, M. , Erber, K. , Matiasek, K. , Meli, M. L. , Hofmann-Lehmann, R. , & Hartmann, K. (2022). Detection of Feline Coronavirus Variants in Cats without Feline Infectious Peritonitis. Viruses, 14(8). https:\/\/doi.org\/10.3390\/v14081671","DOI":"10.3390\/v14081671"},{"key":"2023080410400645000_2023.07.31.551356v1.20","doi-asserted-by":"crossref","unstructured":"Jaimes, J. A. , Millet, J. K. , Stout, A. E. , Andre, N. M. , & Whittaker, G. R. (2020). A Tale of Two Viruses: The Distinct Spike Glycoproteins of Feline Coronaviruses. Viruses, 12(1). https:\/\/doi.org\/10.3390\/v12010083","DOI":"10.3390\/v12010083"},{"key":"2023080410400645000_2023.07.31.551356v1.21","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.020214-0"},{"key":"2023080410400645000_2023.07.31.551356v1.22","doi-asserted-by":"publisher","DOI":"10.1053\/rvsc.1999.0368"},{"issue":"11","key":"2023080410400645000_2023.07.31.551356v1.23","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1099\/jgv.0.001481","article-title":"SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected hospitalized COVID-19 patients","volume":"101","year":"2020","journal-title":"J Gen Virol"},{"key":"2023080410400645000_2023.07.31.551356v1.24","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCULATIONAHA.105.548156"},{"key":"2023080410400645000_2023.07.31.551356v1.25","doi-asserted-by":"crossref","unstructured":"Lamers, M. M. , Mykytyn, A. Z. , Breugem, T. I. , Wang, Y. , Wu, D. C. , Riesebosch, S. , van den Doel, P. B. , Schipper, D. , Bestebroer, T. , Wu, N. C. , & Haagmans, B. L. (2021). Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation. Elife, 10. https:\/\/doi.org\/10.7554\/eLife.66815","DOI":"10.7554\/eLife.66815"},{"key":"2023080410400645000_2023.07.31.551356v1.26","first-page":"795449","article-title":"Fatal Pneumonia Associated With a Novel Genotype of Human Coronavirus OC43","volume":"12","year":"2021","journal-title":"Front Microbiol"},{"key":"2023080410400645000_2023.07.31.551356v1.27","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.000084"},{"key":"2023080410400645000_2023.07.31.551356v1.28","doi-asserted-by":"publisher","DOI":"10.3201\/eid1907.121094"},{"key":"2023080410400645000_2023.07.31.551356v1.29","unstructured":"Licitra, B. N. , Sams, K. L. , Lee, D. W. , & Whittaker, G. R. (2014). Feline coronaviruses associated with feline infectious peritonitis have modifications to spike protein activation sites at two discrete positions. arXiv, https:\/\/arxiv.org\/abs\/1412.4034."},{"issue":"7","key":"2023080410400645000_2023.07.31.551356v1.30","doi-asserted-by":"crossref","first-page":"110829","DOI":"10.1016\/j.celrep.2022.110829","article-title":"Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant","volume":"39","year":"2022","journal-title":"Cell Rep"},{"issue":"4","key":"2023080410400645000_2023.07.31.551356v1.31","doi-asserted-by":"crossref","first-page":"e0151422","DOI":"10.1128\/spectrum.01514-22","article-title":"Spike Protein Cleavage-Activation in the Context of the SARS-CoV-2 P681R Mutation: an Analysis from Its First Appearance in Lineage A.23.1 Identified in Uganda","volume":"10","year":"2022","journal-title":"Microbiol Spectr"},{"key":"2023080410400645000_2023.07.31.551356v1.32","doi-asserted-by":"crossref","unstructured":"Lutz, M. , Steiner, A. R. , Cattori, V. , Hofmann-Lehmann, R. , Lutz, H. , Kipar, A. , & Meli, M. L. (2020). FCoV Viral Sequences of Systemically Infected Healthy Cats Lack Gene Mutations Previously Linked to the Development of FIP. Pathogens, 9(8). https:\/\/doi.org\/10.3390\/pathogens9080603","DOI":"10.3390\/pathogens9080603"},{"key":"2023080410400645000_2023.07.31.551356v1.33","doi-asserted-by":"crossref","unstructured":"Malbon, A. J. , Fonfara, S. , Meli, M. L. , Hahn, S. , Egberink, H. , & Kipar, A. (2019). Feline Infectious Peritonitis as a Systemic Inflammatory Disease: Contribution of Liver and Heart to the Pathogenesis. Viruses, 11(12). https:\/\/doi.org\/10.3390\/v11121144","DOI":"10.3390\/v11121144"},{"issue":"5","key":"2023080410400645000_2023.07.31.551356v1.34","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.3390\/v14051069","article-title":"Fecal Feline Coronavirus RNA Shedding and Spike Gene Mutations in Cats with Feline Infectious Peritonitis Treated with GS-441524","volume":"14","year":"2022","journal-title":"Viruses"},{"key":"2023080410400645000_2023.07.31.551356v1.35","doi-asserted-by":"publisher","DOI":"10.1086\/648731"},{"issue":"24","key":"2023080410400645000_2023.07.31.551356v1.36","doi-asserted-by":"crossref","first-page":"e0136821","DOI":"10.1128\/JVI.01368-21","article-title":"Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition","volume":"95","year":"2021","journal-title":"J Virol"},{"key":"2023080410400645000_2023.07.31.551356v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34256-y"},{"key":"2023080410400645000_2023.07.31.551356v1.38","doi-asserted-by":"crossref","first-page":"695206","DOI":"10.3389\/fcvm.2021.695206","article-title":"COVID-19 and Cardiomyopathy: A Systematic Review","volume":"8","year":"2021","journal-title":"Front Cardiovasc Med"},{"key":"2023080410400645000_2023.07.31.551356v1.39","doi-asserted-by":"crossref","unstructured":"Ouyang, H. , Liu, J. , Yin, Y. , Cao, S. , Yan, R. , Ren, Y. , Zhou, D. , Li, Q. , Li, J. , Liao, X. , Ji, W. , Du, B. , Si, Y. , & Hu, C. (2022). Epidemiology and Comparative Analyses of the S Gene on Feline Coronavirus in Central China. Pathogens, 11(4). https:\/\/doi.org\/10.3390\/pathogens11040460","DOI":"10.3390\/pathogens11040460"},{"key":"2023080410400645000_2023.07.31.551356v1.40","first-page":"7","article-title":"An overview of feline enteric coronavirus and infectious peritonitis virus infections","volume":"23","year":"1995","journal-title":"Feline Practice"},{"key":"2023080410400645000_2023.07.31.551356v1.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.tvjl.2014.04.016"},{"key":"2023080410400645000_2023.07.31.551356v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.tvjl.2014.04.017"},{"key":"2023080410400645000_2023.07.31.551356v1.43","doi-asserted-by":"publisher","DOI":"10.1002\/PRO.3943"},{"key":"2023080410400645000_2023.07.31.551356v1.44","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0446-y"},{"key":"2023080410400645000_2023.07.31.551356v1.45","doi-asserted-by":"crossref","unstructured":"Pirofski, L. A. , & Casadevall, A. (2020). Pathogenesis of COVID-19 from the Perspective of the Damage-Response Framework. mBio, 11(4). https:\/\/doi.org\/10.1128\/mBio.01175-20","DOI":"10.1128\/mBio.01175-20"},{"issue":"12","key":"2023080410400645000_2023.07.31.551356v1.46","doi-asserted-by":"crossref","first-page":"3180","DOI":"10.1128\/jcm.34.12.3180-3184.1996","article-title":"Two related strains of feline infectious peritonitis virus isolated from immunocompromised cats infected with a feline enteric coronavirus","volume":"34","year":"1996","journal-title":"J Clin Microbiol"},{"key":"2023080410400645000_2023.07.31.551356v1.47","doi-asserted-by":"crossref","unstructured":"Saito, A. , Irie, T. , Suzuki, R. , Maemura, T. , Nasser, H. , Uriu, K. , Kosugi, Y. , Shirakawa, K. , Sadamasu, K. , Kimura, I. , Ito, J. , Wu, J. , Iwatsuki-Horimoto, K. , Ito, M. , Yamayoshi, S. , Loeber, S. , Tsuda, M. , Wang, L. , Ozono, S. , \u2026 The Genotype to Phenotype Japan, C. (2021). Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature. https:\/\/doi.org\/10.1038\/s41586-021-04266-9","DOI":"10.1038\/s41586-021-04266-9"},{"key":"2023080410400645000_2023.07.31.551356v1.48","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009233"},{"key":"2023080410400645000_2023.07.31.551356v1.49","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75"},{"key":"2023080410400645000_2023.07.31.551356v1.50","doi-asserted-by":"crossref","unstructured":"Sweet, A. , Andre, N. M. , & Whittaker, G. R. (2022). RNA in-situ hybridization for pathology-based diagnosis of feline infectious peritonitis (FIP): current diagnostics for FIP and comparison to the current gold standard. Qeios. https:\/\/doi.org\/10.32388\/NUN8KB","DOI":"10.32388\/NUN8KB"},{"issue":"9","key":"2023080410400645000_2023.07.31.551356v1.51","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1177\/1098612X221118761","article-title":"2022 AAFP\/EveryCat Feline Infectious Peritonitis Diagnosis Guidelines","volume":"24","year":"2022","journal-title":"J Feline Med Surg"},{"key":"2023080410400645000_2023.07.31.551356v1.52","doi-asserted-by":"publisher","DOI":"10.1006\/viro.1998.9045"},{"key":"2023080410400645000_2023.07.31.551356v1.53","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2205690119"},{"key":"2023080410400645000_2023.07.31.551356v1.54","doi-asserted-by":"crossref","unstructured":"Whittaker, G. R. , Andre, N. M. , & Millet, J. K. (2018). Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species. mSphere, 3(1). https:\/\/doi.org\/10.1128\/mSphereDirect.00463-17","DOI":"10.1128\/mSphereDirect.00463-17"},{"key":"2023080410400645000_2023.07.31.551356v1.55","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1908898117"},{"key":"2023080410400645000_2023.07.31.551356v1.56","first-page":"148","article-title":"Two Feline Cases of Dilated Cardiomyopathy-like Disease Caused by Feline Infectious Peritonitis","volume":"25","year":"2016","journal-title":"J. Anim. Clin. Med"},{"issue":"1","key":"2023080410400645000_2023.07.31.551356v1.57","doi-asserted-by":"crossref","first-page":"vead019","DOI":"10.1093\/ve\/vead019","article-title":"Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes","volume":"9","year":"2023","journal-title":"Virus Evol"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.07.31.551356","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:01:04Z","timestamp":1768453264000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.07.31.551356"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,2]]},"references-count":57,"URL":"https:\/\/doi.org\/10.1101\/2023.07.31.551356","relation":{},"subject":[],"published":{"date-parts":[[2023,8,2]]},"subtype":"preprint"}}