Posted by RJG on October 17, 2011 • Antiretroviral genes variants in Denisovans
Antiretroviral genes variants in Denisovans
Genomics has revealed an unexpected treasure trove of information about the ancient interactions between viruses and hosts. In humans, extremely robust phenotypes of immunity and virulence have been demonstrated for several naturally occurring mutations. Exploring the evolutionary history of these variants can provide fascinating insight into the deep evolutionary history of our interaction with viruses. In a recent publication, Sauter et al. (Hum Mutat 32: 1243–1245, 2011) use a genomic approach to establish a minimum age for a mutation in the antiviral gene tetherin.
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.
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).
The European hare
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.