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Pecon-Slattery, J.; McCracken, C.L.; Troyer, J.L.; VandeWoude, S.; Roelke, M.; Sondgeroth, K.; Winterbach, C.; Winterbach, H.; O'Brien, S.J.
Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild
2008  BMC Genomics (9): 66-78

Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (_Felis catus_) and serves as a natural model for HIV infection in humans. In African lions (_Panthera leo_) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion. In this study, comparative genomic methods are used to evaluate the full proviral genome of two geographically distinct FIV subtypes isolated from free-ranging lions. Genome organization of FIV_Ple _subtype B (9891 bp) from lions in the Serengeti National Park in Tanzania and FIV_Ple _subtype E (9899 bp) isolated from lions in the Okavango Delta in Botswana, both resemble FIV genome sequence from puma, Pallas cat and domestic cat across 5' LTR, _gag, pol, vif, orfA, env, rev _and 3'LTR regions. Comparative analyses of available full-length FIV consisting of subtypes A, B and C from FIV_Fca_, Pallas cat FIV_Oma _and two puma FIV_Pco _subtypes A and B recapitulate the species-specific monophyly of FIV marked by high levels of genetic diversity both within and between species. Across all FIV_Ple _gene regions except _env_, lion subtypes B and E are monophyletic, and marginally more similar to Pallas cat FIV_Oma _than to other FIV. Sequence analyses indicate the SU and TM regions of _env _vary substantially between subtypes, with FIV_Ple _subtype E more related to domestic cat FIV_Fca _than to FIV_Ple _subtype B and FIV_Oma _likely reflecting recombination between strains in the wild. This study demonstrates the necessity of whole-genome analysis to complement population/ gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion lentiviruses are integral to the advancement of comparative genomics of human pathogens, as well as emerging disease in wild populations of endangered species.

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