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Aerial view of Madagascar

Posted by RJG and AK on November 18, 2010  •  Endogenous viral elements in animal genomes.

A mosquito Aedes aegyptii mosquitoes have diverse viral genes inserted into their genomes.

The expanding reach of paleovirology

The presence of retrovirus sequences in animal genomes has been recognised since the 1970s, but is readily explained by the fact that these viruses integrate into chromosomal DNA as part of their normal replication cycle. Unexpectedly, however, when we conducted a systematic in silico screen of animal genomes, we discovered a large and diverse population of sequences derived from non-retroviral viruses.

Phylogenetic and genomic analysis of these endogenous viral elements (EVEs) reveals new information about the evolutionary history of diverse virus groups, often providing the first and only direct evidence for an ancient origin. The diversity of endogenous viral elements revealed by our screen indicates that it will eventually be possible to recover genomic fossils for many, if not all virus families, thus greatly broadening the scope of paleovirological studies.

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Posted by AK on September 17, 2010  •  Functional analysis of ancient lentiviruses.

RELIK capsid protein
Complex of RELIK capsid with cyclophilin A [view on NCBI]

Structural and functional analysis of endogenous lentiviruses uncovers an ancient molecular interface.

RELIK and PSIV capsid proteins were reconstructed in collaboration with researchers at the National Institute for Medical Research. Chimeric lentiviruses bearing ancestral PSIV and RELIK capsids were shown to contain functional binding loops for cyclophilin-A, a cellular molecule involved in interactions between lentiviral capsid proteins and the innate antiviral protein TRIM5-alpha. These data provide evidence for an ancient capsid-cyclophilin interaction preserved throughout lentiviral evolution.

 [pubmed link]

Posted by RJG and AK on October 15, 2009  •  An endogenous foamy virus in the sloth genome.

two-toed sloth Hoffmann's two-toed sloth (Choloepus hoffmanni)

An endogenous foamy virus reveals the deep co-evolutionary history of retroviruses and mammals.

Foamy viruses (also called spumaviruses) are complex retroviruses that asymptomatically infect a wide range of mammals, and are considered promising candidate vectors for stem cell gene therapy. We identified an endogenous foamy virus - the first to be reported - in the genome of Hoffmann's two-toed sloth (Choloepus hoffmanni).

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Posted by RJG on February 15, 2009  •  RELIK orthologs in the rabbit and hare genomes.

European hare The European hare
(Lepus europaeus)

Invasion of the lagomorph germ line by lentiviruses took place prior to the divergence of rabbits and hares.

Following our discovery of RELIK - an endogenous lentivirus - in the genome of the European rabbit, we sought to investigate the distribution of endogenous lentiviruses throughout the order Lagomorpha (rabbits, hares, and pikas).

The general perception of lagomorphs as fecund is misleading. In fact, many species are threatened, and some - such as the riverine rabbit - are critically endangered. Consequently, broad screening of lagomorph genomes on a species-by-species basis is impractical. Nevertheless, in a collaboration with researchers at University College London, we demonstrated the presence of lentivirus insertions in a wide range of lagomorph species, including those that are too rare to sample.

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