title: Feline immunodeficiency virus (FIV) env recombinants are common in natural infections.
abstract: 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.
authors.forename: Paweł M
authors.initials: PM
authors.lastname: Bęczkowski
authors.forename: Joseph
authors.initials: J
authors.lastname: Hughes
authors.forename: Roman
authors.initials: R
authors.lastname: Biek
authors.forename: Annette
authors.initials: A
authors.lastname: Litster
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Willett
authors.forename: Margaret J
authors.initials: MJ
authors.lastname: Hosie
mesh_terms: D000818:Animals; D002415:Cats; D006023:Glycoproteins / Q000235:genetics*; D016089:Immunodeficiency Virus, Feline / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011995:Recombination, Genetic; D014759:Viral Envelope Proteins / Q000235:genetics*
chemical_list: D006023:Glycoproteins; D014759:Viral Envelope Proteins; C445079:envelope protein, Feline immunodeficiency virus