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Aerial view of Madagascar

Posted by RJG on September 10th, 2013  •  EAV-HP and oocyan in chickens

blue egg Oocyan (blue eggshell color) is caused by an ERV insertion upstream of the SLCO1B3 gene in chickens.

Parallel ERV-mediated evolution of blue egg color in chickens

The delightful word 'oocyan' refers to the trait of blue-green eggshell color that occurs in native chickens of Chile (Mapuche fowl) and some of their descendants in North America and Europe, as well as certain Asian chicken breeds (e.g. Dongxiang, Lushi).

Oocyan is an autosomal dominant trait, and recent papers in PLoS Genetics and PLoS ONE have established that it's occurrence in chickens from different geographical regions is due to an endogenous retrovirus (ERV) insertion upstream of the SLCO1B3 gene [1, 2].

Remarkably, the ERV insertions responsible for oocyan appear to represent separate integration events in Chinese versus American/European chicken breeds - thus it appears that the oocyan phenotype has evolved on two separate occasions, via the same ERV-mediated mechanism, in distinct populations of chickens.

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Posted by RJG on September 2nd, 2013  •  Aquatic mammal ERVs

Endogenous retroviruses in aquatic mammal genomes

The first aquatic mammal ERV sequence was described in 1996, recovered from the genome of a 'hook-nosed sea pig' (Halichoerus grypus) by Tristem [1].

In 2005, I reported the first cetacean ERV sequence - this betaretroviral ERV sequence fragment spanned the protease (PR) and reverse transcriptase (RT) genes, and was recovered from the Risso's dolphin genome [2].

The sequence of a complete ERV provirus from a cetacean was described shortly afterwards - this time an endogenous gammaretrovirus, identified in the killer whale (Orcinus orca) genome [3]. Recently, another gammaretroviral provirus sequence was recovered from the bottlenose dolphin (Tursiops truncatus), along with several other ERV PR-RT sequence fragments from cetacean genomes [4]. This most recent set of cetacean ERV sequences has been incorporated into our online retroviral reference sequence library.

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Posted by RJG and AMN on August 27th, 2013  •  Origin and evolution of reticuloendotheliosis virus (REV)

Bronx Zoo, c1911. Digital ID: 810170. New York Public Library Visitors arriving at the gates of the New York Zoological Park in 1911

The extraordinary evolutionary history of the REVs

Their story unites mammals from Madagascar with birds from South East Asia, and links the distant evolutionary past to a more recent history of environmental and technological change.

The reticuloendotheliosis viruses (REVs) are retroviruses that were identified in the 1950s as the agents of virulent disease in gamebirds and waterfowl. Remarkably, DNA sequences derived from REVs are present in the genomes of two other, unrelated viruses - gallid herpesvirus-2 (GHV-2), the cause of Marek's disease, and fowlpox virus (FWPV), the cause of fowlpox.

In a study published today in PLoS Biology [1], we shed new light on the origin and evolution of REVs, accounting for their unusual distribution in nature.

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Posted by RJG on August 1st, 2013  •  ERV nomenclature proposal

Orion's belt The "three kings" of Orion's belt - Alnitak, Alnilam and Mintaka

An integrated taxonomy for ERVs and exogenous retroviruses


Historically, endogenous retroviruses (ERVs) have been grouped into three ‘classes’ (I, II and III), based on their relatedness in the reverse transcriptase (RT) gene to the exogenous Gammaretrovirus, Betaretrovirus and Spumavirus genera respectively [1,2]. Individual ERV lineages (i.e. groups of ERVs that are assumed to derive from a single germline invasion event) have historically been referred to as 'families'.

However, the terms ‘class’ and ‘family’ have specific taxonomic meanings, and their use in ERV nomenclature is problematic because it conflicts with retroviral taxonomy - in the classification system adopted by the International Committee on Taxonomy of Viruses (ICTV), the highest level of classification is 'order' (below 'class') and the retroviruses as a whole have family status (family Retroviridae). Today we are releasing an updated version of our retrovirus reference sequence library, annotated using a propositional taxonomy that integrates ERVs with the previously established taxonomy of exogenous retroviruses.

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