Nucleotide sequence of UK and Australian isolates of feline calicivirus (FCV) and phylogenetic analysis of FCVs

We have determined the first complete genome sequence and capsid gene seque nces of feline calicivirus (FCV) isolates from the UK and Australia. These were compared with other previously published sequences. The viruses used i n the comparisons were isolated between 1957 and 1995 from various geograph ical locations and obtained from cats showing a range of clinical signs. De spite these diverse origins, comparisons between all strains showed a simil ar degree of sequence variation within both ORF1 (non-structural polyprotei n) and ORF2 (major capsid protein) (amino acid distances of 7.7-13.0% and 8 .8-18.6%, respectively). In contrast, ORF3 (putative minor structural prote in) sequences indicated a more heterogenous distribution of FCV relatedness (amino acid distances of 1.9-17.9%). Phylogenetic analysis suggested that, unlike some other caliciviruses, FCV isolates within the current data set fall into one diverse genogroup. Within this group, there was an overall la ck of geographic or temporal clustering which may be related to the epidemi ology of FCV infection in cats. Analysis of regions of variability in the g enome has shown that, as well as the previously identified variable regions in ORF2, similar domains exist within ORFs 1 and 3 also, although to a les ser extent. In ORF1, these variable domains largely fall between the putati ve nonstructural protein functional domains. (C) 1999 Elsevier Science B.V. All rights reserved.