{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:44:25Z","timestamp":1792806265889,"version":"4.5.0"},"reference-count":39,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:00:00Z","timestamp":1738281600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012768","name":"Long Island University","doi-asserted-by":"publisher","award":["36524"],"award-info":[{"award-number":["36524"]}],"id":[{"id":"10.13039\/100012768","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5\u2019UTR-ORF1ab-S-3abc-M-E-7b-3\u2019UTR-3\u2019), marked differential mutations were observed in the ORF1a\/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it.<\/jats:p>","DOI":"10.3390\/v17020209","type":"journal-article","created":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T05:08:26Z","timestamp":1738300106000},"page":"209","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Comparative Genome Sequencing Analysis of Some Novel Feline Infectious Peritonitis Viruses Isolated from Some Feral Cats in Long Island"],"prefix":"10.3390","volume":"17","author":[{"given":"Abid Ullah","family":"Shah","sequence":"first","affiliation":[{"name":"Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blanca","family":"Esparza","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar","family":"Illanes","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1663-5820","authenticated-orcid":false,"given":"Maged Gomaa","family":"Hemida","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"001843","DOI":"10.1099\/jgv.0.001843","article-title":"ICTV Virus Taxonomy Profile: Coronaviridae 2023","volume":"104","author":"Woo","year":"2023","journal-title":"J. Gen. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/978-1-4615-9373-7_36","article-title":"Pathogenic differences between various feline coronavirus isolates","volume":"173","author":"Pedersen","year":"1984","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_3","unstructured":"Cornell Feline Health Center (2025, January 27). Feline Infectious Peritonitis. Available online: https:\/\/www.vet.cornell.edu\/departments-centers-and-institutes\/cornell-feline-health-center\/health-information\/feline-health-topics\/feline-infectious-peritonitis."},{"key":"ref_4","first-page":"368","article-title":"An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis","volume":"42","author":"Pedersen","year":"1981","journal-title":"Am. J. Vet. Res."},{"key":"ref_5","first-page":"2036","article-title":"Pathogenesis of feline infetious peritonitis: Pathologic changes and immunofluorescence","volume":"42","author":"Weiss","year":"1981","journal-title":"Am. J. Vet. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1177\/1098612X221118761","article-title":"2022 AAFP\/EveryCat Feline Infectious Peritonitis Diagnosis Guidelines","volume":"24","author":"Thayer","year":"2022","journal-title":"J. Feline Med. Surg."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jfms.2005.04.003","article-title":"Prevalence of feline infectious peritonitis in specific cat breeds","volume":"8","author":"Radzai","year":"2006","journal-title":"J. Feline Med. Surg."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Olarte-Castillo, X.A., Goodman, L.B., and Whittaker, G.R. (2024). 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. Microbiol. Spectr., 12.","DOI":"10.1128\/spectrum.00061-24"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.jfms.2008.02.006","article-title":"Pathogenesis of feline enteric coronavirus infection","volume":"10","author":"Pedersen","year":"2008","journal-title":"J. Feline Med. Surg."},{"key":"ref_10","first-page":"229","article-title":"Attempted immunization of cats against feline infectious peritonitis, using avirulent live virus or sublethal amounts of virulent virus","volume":"44","author":"Pedersen","year":"1983","journal-title":"Am. J. Vet. Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"14122","DOI":"10.1128\/JVI.79.22.14122-14130.2005","article-title":"Acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein","volume":"79","author":"Rottier","year":"2005","journal-title":"J. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1177\/0300985814522077","article-title":"Feline infectious peritonitis: Still an enigma?","volume":"51","author":"Kipar","year":"2014","journal-title":"Vet. Pathol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.3201\/eid1509.081573","article-title":"Genetics and pathogenesis of feline infectious peritonitis virus","volume":"15","author":"Brown","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1007\/s11262-013-0972-5","article-title":"Comparative sequence analysis of full-length genome of FIPV at different tissue passage levels","volume":"47","author":"Phillips","year":"2013","journal-title":"Virus Genes"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1354\/vp.42-3-321","article-title":"Morphologic features and development of granulomatous vasculitis in feline infectious peritonitis","volume":"42","author":"Kipar","year":"2005","journal-title":"Vet. Pathol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1111\/1348-0421.12498","article-title":"Determination of the cell tropism of serotype 1 feline infectious peritonitis virus using the spike affinity histochemistry in paraffin-embedded tissues","volume":"61","author":"Cham","year":"2017","journal-title":"Microbiol. Immunol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1099\/vir.0.80985-0","article-title":"Genomic RNA sequence of Feline coronavirus strain FIPV WSU-79\/1146","volume":"86","author":"Dye","year":"2005","journal-title":"J. Gen. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.jfms.2007.10.010","article-title":"Evaluation of real-time RT-PCR for the quantification of FCoV shedding in the faeces of domestic cats","volume":"10","author":"Dye","year":"2008","journal-title":"J. Feline Med. Surg."},{"key":"ref_19","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume":"132","author":"Rozen","year":"2000","journal-title":"Methods Mol. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"110313","DOI":"10.1016\/j.virol.2024.110313","article-title":"Isolation and molecular characterization of an enteric isolate of the genotype-Ia bovine coronavirus with notable mutations in the receptor binding domain of the spike glycoprotein","volume":"603","author":"Shah","year":"2025","journal-title":"Virology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1093\/molbev\/msz312","article-title":"Molecular Evolutionary Genetics Analysis (MEGA) for macOS","volume":"37","author":"Stecher","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"111","DOI":"10.4149\/av_2009_02_111","article-title":"Analysis of putative recombination hot sites in the S gene of canine coronaviruses","volume":"53","author":"Wang","year":"2009","journal-title":"Acta Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1016\/j.cvsm.2011.08.004","article-title":"Feline coronavirus in multicat environments","volume":"41","author":"Drechsler","year":"2011","journal-title":"Vet. Clin. North Am. Small Anim. Pract."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1006\/viro.1998.9045","article-title":"Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses","volume":"243","author":"Vennema","year":"1998","journal-title":"Virology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1099\/vir.0.016485-0","article-title":"Feline infectious peritonitis: Insights into feline coronavirus pathobiogenesis and epidemiology based on genetic analysis of the viral 3c gene","volume":"91","author":"Chang","year":"2010","journal-title":"J. Gen. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.vetmic.2014.07.020","article-title":"Mutations of 3c and spike protein genes correlate with the occurrence of feline infectious peritonitis","volume":"173","author":"Stallkamp","year":"2014","journal-title":"Vet. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"12323","DOI":"10.1128\/JVI.01506-07","article-title":"Localization and membrane topology of coronavirus nonstructural protein 4: Involvement of the early secretory pathway in replication","volume":"81","author":"Oostra","year":"2007","journal-title":"J. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"11518","DOI":"10.1128\/JVI.76.22.11518-11529.2002","article-title":"Generation of a replication-competent, propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome","volume":"76","author":"Ortego","year":"2002","journal-title":"J. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.2460\/ajvr.69.9.1179","article-title":"Evaluation of antibodies against feline coronavirus 7b protein for diagnosis of feline infectious peritonitis in cats","volume":"69","author":"Kennedy","year":"2008","journal-title":"Am. J. Vet. Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.jfms.2008.09.004","article-title":"Field strain feline coronaviruses with small deletions in ORF7b associated with both enteric infection and feline infectious peritonitis","volume":"11","author":"Lin","year":"2009","journal-title":"J. Feline Med. Surg."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"4508","DOI":"10.1128\/JVI.72.5.4508-4514.1998","article-title":"Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus","volume":"72","author":"Herrewegh","year":"1998","journal-title":"J. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Cruz, J.L., Sola, I., Becares, M., Alberca, B., Plana, J., Enjuanes, L., and Zuniga, S. (2011). Coronavirus gene 7 counteracts host defenses and modulates virus virulence. PLoS Pathog., 7.","DOI":"10.1371\/journal.ppat.1002090"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.3201\/eid1807.120143","article-title":"Spike protein fusion peptide and feline coronavirus virulence","volume":"18","author":"Chang","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1297-9716-45-49","article-title":"Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis","volume":"45","author":"Porter","year":"2014","journal-title":"Vet. Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.virol.2017.12.027","article-title":"Feline coronavirus: Insights into viral pathogenesis based on the spike protein structure and function","volume":"517","author":"Jaimes","year":"2018","journal-title":"Virology"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/2\/209\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:24:45Z","timestamp":1760027085000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/2\/209"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,31]]},"references-count":39,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["v17020209"],"URL":"https:\/\/doi.org\/10.3390\/v17020209","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,31]]}}}