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Posted by RJG on December 26th, 2013  •  Recombinant retroviruses in the genomes of modern birds.

Golden-collared toucanet Illustration of a golden-collared toucanet
(Selenidera reinwardtii).

An unusual group of recombinant ERVs identified in avian genomes

The evolutionary relationships of endogenous retroviruses (ERVs) are commonly studied through phylogenetic analysis of the highly conserved polymerase (pol) gene, focusing particularly on the region that encodes the reverse transcriptase (RT) protein. However, the envelope (env) gene, which encodes the glycoprotein used by retroviruses to bind and enter cells, also contains regions of relatively high sequence conservation, and can be used to study the evolutionary relationships of diverse retroviruses [1,2].

Env glycoproteins stud the surface of retroviral particles. They typically comprise two subunits: a surface (SU) subunit that binds a receptor on the exterior surface of a target cell, and a transmembrane (TM) subunit that mediates entry into the interior of that cell. The TM subunit typically exhibits evolutionarily conserved features, and like RT, can be used to construct phylogenetic trees representing the evolutionary relationships between retroviruses.

Combined phylogenetic analysis of the RT and TM domains of retroviral genomes can reveal how diverse retroviruses have 'recombined' during their evolution, swapping genes to generate chimeric retroviruses with novel properties. Recombination can greatly influence the evolutionary trajectories of viruses. For example, a novel env gene acquired through recombination may enable a retrovirus to infect cell types and host species it previously could not.

In a paper published in Journal of Virology this month [3], we describe a novel group of recombinant ERVs in the genomes of birds (class Aves). This group, referred to here as 'Aves ERV-F', is relatively rare, and has an unusual genome structure that appears to have arisen via an ancient recombination event involving highly divergent retroviruses.

In phylogenetic trees based on the RT gene, the Aves ERV-F group forms a sister clade to the Alpharetroviruses. However, trees based on TM reveal that the Aves ERV-F env gene is most closely related to the env genes found in mammalian Gammaretroviruses. These findings indicate not only that the Aves ERV-F group originated through recombination, but also suggest that ‘inter-class’ transmission between mammals and birds occurred in the history of these retroviruses. Current evidence suggests that such 'long-distance' transmission events are rare in retroviruses, but can occur [4].

A complete genome reference sequence for an Aves ERV-F insertion, recovered from the zebrafinch (Taeniopygia guttata) genome, has been added to our retroviral reference sequence library. In addition, an RT fragment previously recovered from the genome of the golden-collared toucanet (Selenidera reinwardtii), ERV-Toucanet-I [5], groups with other Aves ERV-F sequences in RT phylogenies, and has thus been provisionally placed in the Aves ERV-F group.


1.  Bénit L, Dessen P, and T. Heidmann (2001) Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J Virol. 75(23):11709-19. [full text]

2.  Henzy JE and WE Johnson. (2013) Pushing the endogenous envelope. Philos Trans R Soc Lond B Biol Sci. 368(1626):20120506 [full text]

3.  Henzy JE, Gifford RJ, Johnson WE and JM Coffin. (2013) A novel recombinant endogenous retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol. 74(8):3715-30. [abstract]

4.  AM Niewiadomska and RJ Gifford (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biology 11 (8): e1001642 [full text]

5.  Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. (2005) Evolution and distribution of class II-related endogenous retroviruses. J. Virol. 79:6478-86 [full text]