Endogenous filovirus (EVE) data

We have used GLUE to organise the fossil record of filoviruses. You can access these data in this repository. This website provides a description of Filovirus-GLUE's paleovirus component, and quick links to specific data items.

Species with endogenous filoviruses

Some of the species in which we identified EVEs derived from filoviruses left to right: xxx (xxxx), xxxx (xxx), xxx (family xxxx), xxxx (xxxx).


Relevance to viral metagenomics

The EFV sequences in Filovirus-GLUE can provide a useful resource for those interested in identifying and characterising filoviruses in metagenomic datasets.

Firstly, these sequences be used to exclude any potential 'false positive' hits (i.e. sequences that seem to represent new filoviruses but in fact derive from genomic DNA).

In addition, when new filovirus species are identified, inclusion of EVEs in phylogenetic analyses can often provide useful information about their broader ecology and evolution, including (uniquely) their long-term evolution.


Where do the EFV data come from?

EVE sequences were recovered from whole genome sequence (WGS) assemblies via database-integrated genome screening (DIGS) using the DIGS tool.

All data pertaining to this screen are included in this repository, or in the associated "DIGS-for-EVEs" project.


Paleovirus-specific schema extensions

The paleovirus component of Filovirus-GLUE extends GLUE's core schema to allow the capture of EVE-specific data. These schema extensions are defined in this file and comprise two additional table: 'locus_data' and 'refcon_data'. Both tables are linked to the main 'sequence' table via the 'sequenceID' field.

The 'locus_data' table contains EVE locus information: e.g. species, assembly, scaffold, location coordinates.

The 'refcon_data' table contains summary information for individual EVE insertions. It refers to the reference sequences constructed to represent each insertion, which reflect our best efforts to reconstruct progenitor virus sequences as they might have looked when they initially integrated into the germline of ancestral species.


EVE reference sequences and data

We constructed reference sequences for EVEs using alignments of EVE sequences derived from the same initial germline colonisation event - i.e. orthologous elements in distinct species, and paralogous elements that have arisen via intragenomic duplication of EVE sequences.

Species with endogenous filoviruses


Multiple sequence alignments

Multiple sequence alignment constructed in this study are linked together using GLUE's ‘alignment tree’ data structure. Alignments in the project include:

  1. A single ‘root’ alignment constructed to represent proposed homologies between representative members of major filovirus lineages (including extinct lineages represented only by EVEs).
  2. ‘Genus-level’ alignments constructed to represent proposed homologies between the genomes of representative members of specific filovirus genera and EVE reference sequences.
  3. ‘Tip’ alignments in which all taxa are derived from a single EVE lineage.


Phylogenetic trees

We used GLUE to implement an automated process for deriving midpoint rooted, annotated trees from the alignments included in our project.

Trees were constructed at distinct taxonomic levels:

  1. Recursively populated root phylogeny (Rep)
  2. Genus-level phylogenies
  3. EVE lineage-level phylogenies


Raw EVE sequences and data

These are the raw data generated by database-integrated genome screening (DIGS). The tabular files contain information about the genomic location of each EVE. EVEs were classified by comparison to a polypeptide sequence reference library designed to represent the known diversity of filoviruses - this includes extinct lineages represented only by endogenous viral elements (EVEs).

These data were obtained via DIGS performed in vertebrate genome assemblies downloaded from NCBI genomes (2020-07-15).

Raw data in tabular format are here.

Nucleotide level data in FASTA format (individual files) are here.


Nomenclature for EVEs

We have applied a systematic approach to naming EVE, following a convention developed for endogenous retroviruses. Each element was assigned a unique identifier (ID) constructed from a defined set of components.

EFV Nomenclature

The first component is the classifier ‘EFLN’ (endogenous filo-like nucleoprotein).

The second component is a composite of two distinct subcomponents separated by a period: (i) the name of EVE group; (ii) a numeric ID that uniquely identifies the insertion. The numeric ID is an integer identifies a unique insertion locus that arose as a consequence of an initial germline infection. Thus, orthologous copies in different species are given the same number.

The third component of the ID defines the set of host species in which the ortholog occurs.


Related Publications

Singer JB, Thomson EC, McLauchlan J, Hughes J, and RJ Gifford (2018)
GLUE: A flexible software system for virus sequence data.
BMC Bioinformatics [view]

Zhu H, Dennis T, Hughes J, and RJ Gifford (2018)
Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database. [preprint]

Gifford RJ, Blomberg B, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, and WE Johnson (2018)
Nomenclature for endogenous retrovirus (ERV) loci.
Retrovirology [view]

Katzourakis A. and RJ. Gifford (2010)
Endogenous viral elements in animal genomes.
PLoS Genetics [view]