HighlightsMulti-cat household animals displayed 63% mortality rate.Lymphoma was the most common cause of death.The CD4:CD8 ratio failed to distinguish cats classified as healthy and not healthy.FIV load failed to distinguish cats classified as healthy and not healthy.Management and housing conditions impact on the progression of FIV infection.

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BackgroundRecombination is a common feature of retroviral biology and one of the most important factors responsible for generating viral diversity at both the intra-host and the population levels. However, relatively little is known about rates and molecular processes of recombination for retroviruses other than HIV, including important model viruses such as feline immunodeficiency virus (FIV).ResultsWe investigated recombination in complete FIV env gene sequences (n = 355) isolated from 43 naturally infected cats. We demonstrated that recombination is abundant in natural FIV infection, with over 41% of the cats being infected with viruses containing recombinant env genes. In addition, we identified shared recombination breakpoints; the most significant hotspot occurred between the leader/signal fragment and the remainder of env.ConclusionsOur results have identified the leader/signal fragment of env as an important site for recombination and highlight potential limitations of the current phylogenetic classification of FIV based on partial env sequences. Furthermore, the presence of abundant recombinant FIV in the USA poses a significant challenge for commercial diagnostic tests and should inform the development of the next generation of FIV vaccines.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-014-0080-1) contains supplementary material, which is available to authorized users.

HighlightsFIV vaccinated cats screened for neutralising antibodiesHomologous neutralisation in 50% of cats testedNo heterologous neutralisation