Abstract
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.
Highlights
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
These sequences were combined with 19 reference sequences and used to construct a further Maximum Likelihood (ML) tree which was rooted on the reference clade C env sequence [Figure 1]
Based on the ML phylogeny and the recombination analyses of sequences from both cohorts, we propose that the following groups of mosaic viruses represent putative circulating recombinant forms (CRF) of feline immunodeficiency virus (FIV): 1) M47, M50, 2) M20, M48, 3) P14, P8A
Summary
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. Recombination, together with point mutations introduced by the error prone reverse transcriptase (RT) [1] and the activity of host restriction factors [2], is regarded as the most important mechanism for generating genetic diversity among retroviruses [3,4]. Two features of the retroviral life cycle facilitate recombination: 1) the presence of two RNA genomes within each viral particle and 2) the tendency of RT to switch between those RNA molecules during provirus synthesis [5,6]. This can result in the synthesis of recombinant DNA of mixed ancestry, originating from both RNA molecules [7]. Recombination can occur between virions of the same or different subtypes, resulting in the generation
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
