title: Genetic diversity and phenotypic associations of feline caliciviruses from cats in Switzerland.
abstract: Feline calicivirus (FCV) is a common viral pathogen in domestic cats worldwide. The variable regions of the capsid (VP1) gene of FCV have one of the highest recorded rates of molecular evolution. Understanding the genetic diversity and phylogeny of FCV is a prerequisite to exploring the epidemiology and pathogenesis of this virus and to the development of efficacious vaccine strategies. In this study, we undertook a nationwide molecular characterization of FCV using for the first time nearly complete capsid (VP1) gene sequences. Sequences from 66 FCV samples were used to investigate the correlation between viral phylogeny and several traits, including geographic origin, signalment, husbandry, FCV vaccination and co-infections. Codon-based nucleotide alignment showed that individual nucleotides and their corresponding amino acid sites were either invariant or highly variable. Using a threshold of 20 % genetic distance in variable region E, FCV samples were grouped into 52 strains, 10 of which comprised two to three samples. Significant associations between FCV phylogeny and host characteristics were found, specifically the pedigree status of the cats, and two well-supported lineages were identified in which the current FCV strain definition was confounded. No correlation between viral genetic distances and geographic distances was evident. The greater resolution of the FCV phylogeny in this study compared to previous studies can be attributed to our use of more conserved regions of the capsid (VP1) gene; nonetheless, our results were still hampered by sequence saturation. The study highlights the need for whole-genome sequences for FCV phylogeny studies.
authors.affiliation: Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Spiri
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Julien
authors.initials: J
authors.lastname: Thézé
authors.affiliation: Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Marina L
authors.initials: ML
authors.lastname: Meli
authors.affiliation: Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Valentino
authors.initials: V
authors.lastname: Cattori
authors.affiliation: Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Alice
authors.initials: A
authors.lastname: Berger
authors.affiliation: Institute for Veterinary Disease Control Mödling, AGES - Austrian Agency for Health and Food Safety, Mödling, Austria.
authors.forename: Adolf
authors.initials: A
authors.lastname: Steinrigl
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Regina
authors.initials: R
authors.lastname: Hofmann-Lehmann
authors.affiliation: Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.|Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Willi
mesh_terms: D000818:Animals; D017250:Caliciviridae Infections / Q000662:veterinary* / Q000821:virology; D017927:Calicivirus, Feline / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D036022:Capsid Proteins / Q000235:genetics*; D002371:Cat Diseases / Q000821:virology*; D002415:Cats; D014644:Genetic Variation; D010641:Phenotype; D010802:Phylogeny; D013557:Switzerland
chemical_list: D036022:Capsid Proteins