EVE Nomenclature - giffordlabcvr/Parvovirus-GLUE GitHub Wiki

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

EPV Nomenclature

The first component is the classifier ‘EPV’ (endogenous parvovirus element).

The second component is a composite of two distinct subcomponents separated by a period:

(i) the name of EPV group;
(ii) a numeric ID that uniquely identifies the insertion. The numeric ID is an integer identifying 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.

This systematic naming approach facilitates clear identification and comparison of EVEs across different species and research contexts.

Please note the following:

  1. EVEs were assigned to virus taxonomic groups as accurately as possible based on phylogenetic/genomic analysis. For EVEs that could not be confidently assigned to a subgroup, the lowest taxonomic rank possible for the EVE type is given (i.e. family).
  2. We grouped sets of orthologous EVEs using shared numeric IDs. However, some orthologous relationships might have been missed, and some EVEs may have been incorrectly grouped as orthologs when they are actually distinct, paralogous loci.
  3. When EVEs occur in a single species, the corresponding Latin binomial species name is provided. When EVEs occur as orthologs in multiple species, we provide the taxonomic name of the species group. If the species set corresponds to an unranked clade, we use the name of the closest named group at a lower rank and add the abbreviation 'UR' (unranked) to indicate that no named clade perfectly captures the range of species in which the EVE is found.