Identification of conserved and variable regions in the envelope glycoprotein sequences of two feline immunodeficiency viruses isolated in Zurich, Switzerland

Abstract

The nucleotide sequences of the envelope (env) coding regions of two strains of the feline immunodeficiency virus isolated in Zurich, Switzerland (FIVZ1, FIVZ2) have been analysed. In addition, the complete sequence of the FIVZ1 isolate has been determined. Comparisons have been made with the previously published sequences of three North American isolates (PPR and the Petaluma strains FIV34TF10 and FIV14). The isolate FIVZ1 was very similar to the Petaluma strains of FIV and may represent a clonal derivative acquired by 'contamination'. Overall there are between 2.6% and 15.1% amino acid changes in the env gene products of the five isolates. Of the Zurich isolates, FIVZ2 exhibited the greatest divergence to the other viruses and based on its genotype, phenotype and origins probably represents a new isolate of FIV. Possibly the viruses diverged only recently from a common ancestor. Some 31 of the 33 cysteine residues and 17 of the 21 potential N-linked glycosylation sites of the FIV34TF10 env gene product were conserved among all five isolates. The open reading frame 3 (ORF3, or D) which overlaps the env gene (but is encoded in a different frame) has an ATG codon downstream of a potential splice acceptor site in all five isolates, supporting the view that it encodes a viral gene product. In ORF3 of FIVZ1 a stop codon was located 16 amino acids upstream of the stop codon of ORF3 of the other isolates. The ORF4 (or G) of isolate FIVZ2, thought to be the second coding exon of an FIV rev-like gene, contained a nucleotide deletion in amino acid 45 of ORF4, resulting in a--1 frameshift at this position. Comparison of the LTR sequences of the five isolates identified conserved promoter/enhancer elements. A potential stem-loop structure was identified in the R region of the LTRs of all the isolates, despite the heterogeneity of nucleotide sequences in that region. Such structures (TAR) are present in analogous regions of other lentiviruses and are responsible for tat-mediated trans-activation.