Nomenclature for endogenous retrovirus (ERV) loci

Retrovirology

Table 2 Application of the proposed nomenclature to example ERV loci

Example description	Locus ID
ERV-L insertion identified in all eutherian mammals^a	ERV-L.1-Eutheria
Human copy of ERV-L.1-Eutheria	ERV-L.1-Homo sapiens
	ERV-L.1-HomSap*
	ERV-L.1-Hsa*
	L.1-Hsa**
HERV.K (HML2) 113	ERV-K(HML2).113-Hsa^b
Chimpanzee ortholog of HERV.K (HML2) 113	ERV-K(HML2).113-Ptr
All copies of HERV.K (HML2) 113 found in great apes (Hominidae)	ERV-K(HML2).113-Hominidae
Human copy HERV-K(HML2) 4q35.2	ERV-K(HML2).4352-Hsa^c
Polytropic murine leukemia virus ERV 1 (Pmv-1) in mouse	ERV-Pmv.1-Mus musculus
Xenotropic murine leukemia virus ERV 8 (Xmv-8) in mouse	ERV-Xmv.8-Mmu
Mouse mammary tumour virus (MMTV) locus 9 (Mtv9)	ERV-MMTV.8-Mmu
Xmv-8 in inbred mouse strain C57L	ERV-Xmv.8-Mmu.C57L
Copy 2 of rabbit endogenous lentivirus K (RELiK) in rabbit	ERV-RELiK.2-Oryctolagus cuniculus
Copy 2 of rabbit endogenous lentivirus K (RELiK) in rabbit	ERV-RELiK.2-OryCun*
Copy 2 of rabbit endogenous lentivirus K (RELiK) in hare	ERV-RELiK.2-Lepus europaeus
	ERV-RELiK.2-LepEur*
	RELiK.2-OryCun**
Macaque copy #183 of an unclassified Betaretrovirus-like virus	ERV-AB.183-Macaca mulatta
Peregrine falcon copy #25 of avian ‘Betaretrovirus-like lineage 3′	ERV-AB3.25-Falco peregrinus
Use of trailing element to indicate alternative alleles of a polymorphic insertion	ERV-K(HML2).113-Hsa.a^d
	ERV-K(HML2).113-Hsa.b^d
Use of trailing element to indicate alternative genome structures of a polymorphic insertion	ERV-K(HML2).113-Hsa.provirus^d
	ERV-K(HML2).113-Hsa.LTR^d

*Alternative versions using an abbreviation to designate the host species component of the ID
**A shorter form of the ID can be used when it is clear from the context—or from the lineage component of the ID—that an ERV is being referred to
^aFor reference, see [35]
^bWe propose that where established numeric IDs are already in use, they should be preserved, as is the case for many representatives of the well researched HERV-K(HML2) lineage
^cIn this example, an ID is assigned to an ERV locus that has only previously been referred to via its cytogenetic location—a numeric ID is therefore proposed that preserves a mnemonic link to this cytogenetically-based identifier, without preserving the information about cytogenetic location. This follows a principle of our proposal wherein the numeric ID component of the overall ERV ID can retain mnemonic links to previous IDs, but all auxiliary information associated with ERV loci is obtained from a database via a unique ID, rather than encoded into the ID itself
^dHowever, where it aids discussion such information can be appended to the ERV ID stem (e.g. to distinguish distinct alleles and genome structures)

ISSN: 1742-4690