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Background  Recombination 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).    Results  We 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 .    Conclusions  Our 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 material  The online version of this article (doi:10.1186/s12977-014-0080-1) contains supplementary material, which is available to authorized users.

Feline immunodeficiency virus (FIV) envrecombinants are common in natural infections