Posted by RJG on August 1st, 2013 • ERV nomenclature proposal
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.
A peregrine falcon (Falco peregrinus) enjoying the Scottish summer.
Novel ERV and retrovirus genome sequences
In association with an upcoming publication describing our investigation into the origin and evolution of reticuleoendotheliosis virus (REV), we have updated our retroviral reference sequence library to include novel endogenous and exogneous retrovirus genome sequences identified in the course of our study. We sequenced the complete genomes of two unusual endogenous retroviruses (ERVs) in mammalian genomes, and of an isolate of REV obtained in the 1970s (called duck infectious anemia virus [DIAV]). The consensus genome sequences of these viruses have been made available in our online retroviral reference sequence library. In addition we have created reference genome sequences to represent two major lineages of ERV present in avian genomes, including the recently released peregrine falcon (pictured), mallard and rock dove genomes.
Extreme genetic fragility of the HIV-1 capsid
In molecular genetics, robustness or fragility can be defined as the ability, or lack thereof, of a gene to maintain function in the face of molecular sequence changes. Extensive, random mutagenesis of single amino acids in the HIV-1 capsid protein (CA) revealed it to be extremely fragile. In fact, HIV-1 CA was revealed to be the most genetically fragile protein ever analyzed using such an approach. Approximately 70% of single mutations resulted in a non-viable virus.
Although CA participates in several steps in HIV-1 replication, the biological basis for its genetic fragility was primarily the need to participate in the efficient and proper assembly of mature virion particles.
Anna sampling sheep and goats in Lebanon.
Small ruminant lentivirus diversity in the Fertile Crescent
Since the 1950s, a range of lentiviruses that infect livestock have been characterized, including bovine immunodeficiency virus (BIV) in cattle, equine infectious anemia (EIAV) in horses, and 'small ruminant' lentiviruses (SRLVs) in goats and sheep. SRLVs cause persistent infections associated with chronic debilitating diseases that ultimately lead to multi-organ failure and death, and are relatively common in sheep and goat herds throughout the world. However, due to the chronic nature of disease, often marked by long asymptomatic periods, SRLV infection can easily go undetected.
Domestication of sheep and goats is believed to have taken place ~10,000 years ago in the 'Fertile Crescent', an area which includes regions of present day Turkey, Lebanon, Jordan, Iraq and Syria . During the late summer of 2012 we explored the diversity of SRLVs infecting sheep and goats in the Fertile Crescent area, as part of a broader investigation into the origins of the SRLV pandemic.