Quasispecies and naturally occurring superinfection in feline immunodeficiency virus infection

Analysis of individual clones containing the V1 and V2 domains of the segment of the FIV env gene present in a naturally infected cat (T) was carried out. The polymerase chain reaction (PCR) was used to amplify proviral FIV DNA extracted from peripheral blood mononuclear cells (PBMCs) obtained in October 1994 from this cat. The PCR products were cloned and the DNA sequences determined for 11 clones. Sequences obtained were aligned with sequences corresponding to FIV isolates (T90, T91, T92) previously obtained from the same cat in 1990, 1991 and 1992. Phylogenetic analysis was performed which included consensus sequences of another Australian isolate, N91, as well as UK, US, Swiss and Japanese isolates of FIV. All clones varied from each other, and none of these clones was identical to the consensus sequences of the isolates obtained previously from the same cat (the T-series). However, most of these clones appeared to have originated from the ancestor of the most recent isolate (T92). In addition, 2 of the clones (7&11) are closely related to another Australian isolate N91, obtained from a different cat (N) in 1991. Because these two cats (T and N) were housed together for at least 3 years (1990-1993) it is suggested that the first cat (T) has become superinfected with an isolate from a second cat (N) under natural conditions. The identification of clones of differing sequences, which were not identical to each other nor to their ancestors, emphasises the rapid mutation of lentiviruses within the env region, and the difficulty of developing an effective FIV vaccine. More importantly, the possibility of natural superinfection with FIV in cats has implications for the development of a successful lentiviral vaccine.