Co-infection with different subtypes of feline immunodeficiency virus can complicate subtype assignment by phylogenetic analysis.

Phylogenetic analyses of the V3-V5 region of the env gene are used to determine Feline immunodeficiency virus (FIV) subtypes but can be complicated by co-infection with different subtypes or the presence of recombinant subtypes. FIV in blood samples from 30 domestic cats in New Zealand was subtyped by sequencing three overlapping fragments of the V3-V5 region of the env gene and 467 bp of the gag gene. Phylogenetic analyses revealed that the isolates clustered with subtype A and C viruses. Seven samples showed discrepancies in subtype assignment from analyses of their env gene sequences. Nucleotide differences of 19.6% and 20.9% in overlapping regions in two cats suggest co-infection with subtypes A and C.