Welcome to the GitHub repository for Lentivirus-GLUE-ERV: an extension to Lentivirus-GLUE.
This project layer extends Lentivirus-GLUE through the incorporation of endogenous retrovirus (ERV) sequence data.
For many years, the scientific consensus was that lentiviruses---the retroviral genus that includes HIV---did not leave a fossil record in the genomes of their hosts. Endogenous retroviruses (ERVs) derived from other retroviral genera, such as Gammaretrovirus and Betaretrovirus, are widespread and well-documented, but no evidence of lentiviral ERVs had been found. This absence, combined with the extraordinary evolutionary speed observed in HIV during the HIV/AIDS pandemic, led many researchers to infer that lentiviruses were a relatively recent addition to the retroviral family, and might possibly have emerged within a timescale of thousands, rather than millions of years.
This view began to shift in 2007 with the publication of the European rabbit genome, which revealed the presence of rabbit endogenous lentivirus K (RELIK). RELIK was not an isolated curiosity; its presence in multiple leporid species demonstrated that this lentivirus had integrated into the genome of an ancient common ancestor at least 12 million years ago. This discovery provided definitive proof that lentiviruses have existed for far longer than previously assumed, upending the idea that they were a recent evolutionary phenomenon.
Since the discovery of RELIK, additional endogenous lentiviruses have been identified in a variety of mammals, including lemurs, mustelids, colugos, and springhares. These findings have painted a more nuanced picture of lentiviral evolution. While endogenous lentiviruses remain rare compared to those of other retroviral genera, their existence shows that lentiviruses have been infecting mammals for millions of years, occasionally leaving behind genomic fossils that offer invaluable insights into their ancient diversity and host-virus interactions.
The rarity of endogenous lentiviruses raises intriguing questions about their biology and evolutionary history. Perhaps their genomic integration is less frequent or less likely to be preserved than that of other retroviruses. Alternatively, their sequences may degrade more rapidly due to evolutionary pressures, or their presence may be underrepresented in the genomes that have been studied to date. Regardless, the identification of these rare remnants has fundamentally reshaped our understanding of the lentivirus genus, pushing its origins back into deep evolutionary time.
For more details please see the Lentivirus-GLUE User Guide.
To install Lentivirus-GLUE-ERV, follow the instructions provided in the User Guide.
You can choose between:
- Docker-based installation for ease of deployment.
- Native installation for traditional setup.
Lentivirus-GLUE-ERV can be installed as a prebuilt database for quick setup or constructed from scratch via (a project build process) for more customization.
Lentivirus-GLUE-ERV is constructed using sequence data obtained from NCBI Nucleotide.
We welcome contributions from the community! If you're interested in contributing to Lentivirus-GLUE-ERV, please review our Contribution Guidelines.
The project is licensed under the GNU Affero General Public License v. 3.0
For questions, issues, or feedback, please open an issue on the GitHub repository.