Filovirus Coordinates and Naming
Coordinate Numbering
All Filoviridae coordinate numbering in the LANL Ebola HFV Database is assigned using reference sequence Yambuku-Mayinga (accession NC_002549).
Sequence Naming
For our sequence downloads and curated alignments, two names are offered for each sequence:
-
Modified Standard Name
Example: EBOV/H.sap-wt/SLE/14/Makona-G3846/KM233109
Name fields:
Virus (4-5 letters)/ Host-isolation (8 letters) /Country (3 letters)/Year (2 letters)/Variant-Isolate /Accession
This name is based on the latest nomenclature (see references below). We modified these names slightly to allow for computer analysis:
- The shortened name was used as a basis (Kuhn et al., 2014).
- The isolation type is used as defined in Kuhn et al., 2013:
- wt: virus directly sequenced from a clinical specimen
- tc: virus has undergone tissue/cell culture passaging
- lab: virus was adapted in the laboratory to cells or animals it would not normally infect
- frag: virus is known from sequence fragments only
- hist: virus has been lost
- hist_lab: virus was adapted to a non-natural host but is not available for study any more
- Blank spaces have been eliminated.
- The host species name is shortened ("H.sap" for H. sapiens, for example).
- Accession numbers have been added at the end of the name to allow accurate linkage to sequences.
Name Convenient for Analysis
Example: EV.SL.061814.d.Hsap-wt.Makona_Jawie-G3846.KM233109
This name is based on the standard name, but further modified for convenience:
- The virus name has been abbreviated to 2 letters (see abbreviations below).
- Most of the fields have a consistent number of characters, to aid in parsing. Each field has been kept as short as possible.
- The slash symbol "/" is replaced with the period "." because the slash symbol is problematic for some bioinformatics tools.
- The period was removed from host species name (i.e., Hsap) to allow for accurate parsing of names into fields.
- The isolation type has been shortened to 2 characters. The 2-letter isolation types are:
- wt: virus directly sequenced from a clinical specimen
- tc: virus has undergone tissue/cell culture passaging
- la: virus was adapted in the laboratory to cells or animals it would not normally infect
- fr: virus is known from sequence fragments only
- hi: virus has been lost
- hl: virus was adapted to a non-natural host but is not available for study any more
- The country name has been shortened to the ISO standard 2-letter country code (see 2-letter County Codes).
- The date field has been expanded to include the full date, when known. (6 digits, with 2 digits each for month, day, and year). For example, 061814 is 6/18/2014 (month/day/year). "xx" is used for unknown. For example, xxxx76 stands for sampling made in 1976, with unknown month and day.
- The name includes a field for the patient's survival status (s = survived; d = died). When the survival status is unknown, or the host species is non-human, this field contains "x".
- The most distinguishing geographical location is noted in the name (region, chiefdom, city, village). In the example above, the geographic location Jawie is added to the variant-isolate name "Makona-G3846", resulting in "Makona_Jawie-G3846" in the "name convenient for analysis".
Filovirus Species Abbreviations
The following abbreviations and taxonomy are used in our alignments and sequence data:
2-letter
|
4-letter
|
Virus
|
Species
|
Genus |
Family |
EV
|
EBOV
|
Ebola virus
|
Zaire ebolavirus
|
Ebolavirus
|
Filoviridae
|
SV
|
SUDV
|
Sudan virus
|
Sudan ebolavirus
|
Ebolavirus
|
Filoviridae
|
RV
|
RESTV
|
Reston virus
|
Reston ebolavirus
|
Ebolavirus
|
Filoviridae
|
TV
|
TAFV
|
Taï Forest virus
|
Taï Forest ebolavirus
|
Ebolavirus
|
Filoviridae
|
BV
|
BDBV
|
Bundibugyo virus
|
Bundibugyo ebolavirus
|
Ebolavirus
|
Filoviridae
|
MV
|
MARV
|
Marburg virus
|
Marburg marburgvirus
|
Marburgvirus
|
Filoviridae
|
MR
|
RAVV
|
Ravn virus
|
Marburg marburgvirus
| Marburgvirus
|
Filoviridae
|
LV
|
LLOV
|
Lloviu virus
|
Lloviu cuevavirus
|
Cuevavirus
|
Filoviridae
|
Nomenclature References
Kuhn et al. 2014. Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA. Arch Virol 2014 May 159(5):1229-37. (PMID: 24190508)
Kuhn et al. 2013. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. Arch Virol 2013 Jan 158(1):301-11. (PMID: 23001720)
Questions or comments? Contact us at
hfv-info@lanl.gov