Mapping the virus 'fossil record'

This repository contains an organised catalog of endogenous viral element (EVE) sequences recovered from published genome sequence data via database-integrated genome screening (DIGS). DIGS is an approach for systematically screening whole genome sequence (WGS) data in silico.

WGS assemblies screened in this project were obtained from the NCBI Genome resource.

DIGS was performed using the DIGS tool, an open software framework available here.

For more information please see the Project Documentation.

References

Investigations of data generated in this project have been reported in the following open access publications:

  1. Blanco-Melo, D., et al. (2024). A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’. Genome Biology, 25, Article number: 120
  2. Campbell, M.A., et al. (2022). Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates. PLoS Biol, 20(11): p. e3001867.
  3. Bamford, C.G.G., et al. (2022). Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol, 8(2): p. veac085.
  4. Lytras, S., G. Arriagada, and R.J. Gifford. (2021). Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. Virus Evol, 7(1): p. veab012.
  5. Dennis, T.P.W., et al. (2019). The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Res, 262: p. 15-23.
  6. Dennis, T.P.W., et al. (2018). Insights into Circovirus host range from the genomic fossil record. J Virol, 92(16).
  7. Pénzes, J.J., et al. (2018). Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evol, 4(2): p. vey026.
  8. Blanco-Melo, D., R.J. Gifford, and P.D. Bieniasz (2018). Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology, 15(1): p. 34.
  9. Souza, W.M., et al. (2017). Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. J Gen Virol, 98(2): p. 225-229.
  10. Blanco-Melo, D., R.J. Gifford, and P.D. Bieniasz (2017) Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. Elife, 6.

Contributing

We welcome contributions from the EVE research community! If you're interested in contributing to DIGS-for-EVEs, please review our Contribution Guidelines.

Contributor Covenant

License

The project is licensed under the GNU Affero General Public License v. 3.0

Contact

For questions, issues, or feedback, please open an issue on the GitHub repository.