Seq/ICTV/MSL and VMR

International Committee on Taxonomy of Viruses (ICTV) [1] maintains a database [2] of virus taxonomic classification [3]. The Master Species Lists (MSL) [4] provides “the official, current virus taxonomy approved by the ICTV”. The Virus Metadata Resource (VMR) [5] provides “exemplars and additional isolates for each virus species”.

An Example

ICTV provides MSL downloads in .xlsx [4], web version of interactive search [6], and visual taxonomy browser [7]. For example, if we are interested in studying the virus causing feline acquired immunodeficiency syndrome [8], we can find the following taxonomy information in the ICTV MSL:

Column name	value	taxon-specific suffix *
Realm	Riboviria	…viria
Subrealm		…vira
Kingdom	Pararnavirae	…virae
Subkingdom		…virites
Phylum	Artverviricota	…viricota
Subphylum		…viricotina
Class	Revtraviricetes	…viricetes
Subclass		…viricetidae
Order	Ortervirales	…virales
Suborder		…virineae
Family	Retroviridae	…viridae
Subfamily	Orthoretrovirinae	…virinae
Genus	Lentivirus	…virus
Subgenus		…virus
Species	Lentivirus felimdef
Genome	ssRNA-RT
Last Change	Renamed,
MSL of Last Change	39
Proposal for Last Change	2023.009D.Retroviridae_68rensp.zip
Taxon History URL	ictv.global=202305029

^* [15]

From the taxon history, we can see that the species name was Feline immunodeficiency virus (FIV) in the previous releases, and changed to Lentivirus felimdef in the 2023 release [9]. The reasons of changes proposed are included in the Proposal for Last Change link. Additional information about FIV, for example, about the genus Lentivirus, can be found in ICTV report [10].

How to

The module mtbp3.seq.ictvmsiview accept a csv file exported from the MSL tab of MSL download file. The csv file path can be assigned using the option msl_file_path. For demonstration, a small subset of MSL is shipped with this module. When using the option msl_file_path = "", the example file will be loaded.

To load a MSL csv file:

from mtbp3.seq import ictvmslview
msl = ictvmslview.ictvmsl(msl_file_path = "")

File supp_seq/ICTV_MSL39v4_example.csv has been loaded
Column names: ['Sort', 'Realm', 'Subrealm', 'Kingdom', 'Subkingdom', 'Phylum', 'Subphylum', 'Class', 'Subclass', 'Order', 'Suborder', 'Family', 'Subfamily', 'Genus', 'Subgenus', 'Species', 'Genome', 'Last Change', 'MSL of Last Change', 'Proposal for Last Change ', 'Taxon History URL']
Total number of rows: 65

Please note that the column names will be used as search_rank in this module and those are case sensitive. The search_strings is not case sensitive, as shown below.

To view the first row of loaded file:

print(msl.msl.iloc[0].transpose())

Sort                                                      13664
Realm                                                 Riboviria
Subrealm                                                    NaN
Kingdom                                            Pararnavirae
Subkingdom                                                  NaN
Phylum                                           Artverviricota
Subphylum                                                   NaN
Class                                           Revtraviricetes
Subclass                                                    NaN
Order                                              Ortervirales
Suborder                                                    NaN
Family                                             Retroviridae
Subfamily                                     Orthoretrovirinae
Genus                                           Alpharetrovirus
Subgenus                                                    NaN
Species                           Alpharetrovirus avicarmilhil2
Genome                                                 ssRNA-RT
Last Change                                            Renamed,
MSL of Last Change                                           39
Proposal for Last Change     2023.009D.Retroviridae_68rensp.zip
Taxon History URL                         ictv.global=202304982
Name: 0, dtype: object

To view the unique values of ‘Realm’ in the file and number of species under each realm:

msl.msl['Realm'].value_counts()

Realm
Riboviria    65
Name: count, dtype: int64

The counts above are from the example file.

The full MSL 39v4 includes the following realms and kingdoms:

    Virus:
    ├── Adnaviria:
    │   └── Zilligvirae (32 Species)
    ├── Duplodnaviria:
    │   └── Heunggongvirae (4973 Species)
    ├── Monodnaviria:
    │   ├── Loebvirae (60 Species)
    │   ├── Sangervirae (22 Species)
    │   ├── Shotokuvirae (1930 Species)
    │   └── Trapavirae (16 Species)
    ├── NA:
    │   └── NA (636 Species)
    ├── Riboviria:
    │   ├── NA (17 Species)
    │   ├── Orthornavirae (6423 Species)
    │   └── Pararnavirae (272 Species)
    ├── Ribozyviria:
    │   └── NA (21 Species)
    └── Varidnaviria:
        ├── Bamfordvirae (279 Species)
        └── Helvetiavirae (9 Species)

To count species within a subset:

print('\n'.join(msl.count_species(count_rank='Phylum', outfmt="tree", search_within_subset={'Kingdom': 'Bamfordvirae'}))

Output:

    Virus:
    └── [Realm] Varidnaviria:
        └── [Kingdom] Bamfordvirae:
            ├── [Phylum] NA (1 Species)
            ├── [Phylum] Nucleocytoviricota (132 Species)
            └── [Phylum] Preplasmiviricota (146 Species)

Search within MSL

To search for rows with “lentivirus fel” included in a species name:

print(msl.find_rows_given_str(search_strings="lentivirus fel", color="red").iloc[0].transpose())

Sort                                                      13704
Realm                                                 Riboviria
Subrealm                                                    NaN
Kingdom                                            Pararnavirae
Subkingdom                                                  NaN
Phylum                                           Artverviricota
Subphylum                                                   NaN
Class                                           Revtraviricetes
Subclass                                                    NaN
Order                                              Ortervirales
Suborder                                                    NaN
Family                                             Retroviridae
Subfamily                                     Orthoretrovirinae
Genus                                                Lentivirus
Subgenus                                                    NaN
Species                            Lentivirus felimdef
Genome                                                 ssRNA-RT
Last Change                                            Renamed,
MSL of Last Change                                           39
Proposal for Last Change     2023.009D.Retroviridae_68rensp.zip
Taxon History URL                         ictv.global=202305029
Name: 40, dtype: object

To search for rows with “lentivirus” included in species:

print(msl.find_rows_given_str(search_strings="lentivirus", search_rank="Species", color="red", narrow=True)[['Genus', 'Species','Genome']])

         Genus                        Species    Genome
36  Lentivirus   Lentivirus bovimdef  ssRNA-RT
37  Lentivirus     Lentivirus bovjem  ssRNA-RT
38  Lentivirus  Lentivirus capartenc  ssRNA-RT
39  Lentivirus  Lentivirus equinfane  ssRNA-RT
40  Lentivirus   Lentivirus felimdef  ssRNA-RT
41  Lentivirus  Lentivirus humimdef1  ssRNA-RT
42  Lentivirus  Lentivirus humimdef2  ssRNA-RT
43  Lentivirus  Lentivirus ovivismae  ssRNA-RT
44  Lentivirus        Lentivirus pum  ssRNA-RT
45  Lentivirus   Lentivirus simimdef  ssRNA-RT

To search for genus Lentivirus using exact=True option (partly exact, the searching is still not case sensitive):

print('\n'.join(msl.find_rows_given_str(search_strings="lentivirus", search_rank="Genus", color="red", outfmt='tree', exact=True)))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    └── [Family] Retroviridae; [Subfamily] Orthoretrovirinae:
                        └── [Genus] Lentivirus:
                            ├── [Species] Lentivirus bovimdef
                            ├── [Species] Lentivirus bovjem
                            ├── [Species] Lentivirus capartenc
                            ├── [Species] Lentivirus equinfane
                            ├── [Species] Lentivirus felimdef
                            ├── [Species] Lentivirus humimdef1
                            ├── [Species] Lentivirus humimdef2
                            ├── [Species] Lentivirus ovivismae
                            ├── [Species] Lentivirus pum
                            └── [Species] Lentivirus simimdef

There are more than one virus species in family Retroviridae that can infect feline. To search for virus within family Retroviridae that can infect feline:

print('\n'.join(msl.find_rows_given_str(search_strings=" fel", search_rank="Species", color="red", outfmt='tree', search_within_subset={"Family":"Retroviridae"})))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    ├── [Family] Retroviridae; [Subfamily] Orthoretrovirinae:
                    │   ├── [Genus] Gammaretrovirus:
                    │   │   └── [Species] Gammaretrovirus felleu
                    │   └── [Genus] Lentivirus:
                    │       └── [Species] Lentivirus felimdef
                    └── [Family] Retroviridae; [Subfamily] Spumaretrovirinae:
                        └── [Genus] Felispumavirus:
                            └── [Species] Felispumavirus felcat

To search for two known virus species:

print('\n'.join(msl.find_rows_given_str(search_strings=["Gammaretrovirus felleu", "Lentivirus felimdef"], search_rank="Species", color="red", outfmt='tree')))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    └── [Family] Retroviridae; [Subfamily] Orthoretrovirinae:
                        ├── [Genus] Gammaretrovirus:
                        │   └── [Species] Gammaretrovirus felleu
                        └── [Genus] Lentivirus:
                            └── [Species] Lentivirus felimdef

The tree above always shows 8 ranks.

There are two more types of tree available, including a tree with nonempty rank:

print('\n'.join(msl.find_rows_given_str(search_strings=["Gammaretrovirus felleu", "Lentivirus felimdef"], search_rank="Species", color="red", outfmt='tree', tree_style="drop")))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    └── [Family] Retroviridae:
                        └── [Subfamily] Orthoretrovirinae:
                            ├── [Genus] Gammaretrovirus:
                            │   └── [Species] Gammaretrovirus felleu
                            └── [Genus] Lentivirus:
                                └── [Species] Lentivirus felimdef

and a tree with full 15 ranks:

print('\n'.join(msl.find_rows_given_str(search_strings=["Gammaretrovirus felleu", "Lentivirus felimdef"], search_rank="Species", color="red", outfmt='tree', tree_style="full")))

    [Realm] Riboviria:
    └── [Subrealm] NA:
        └── [Kingdom] Pararnavirae:
            └── [Subkingdom] NA:
                └── [Phylum] Artverviricota:
                    └── [Subphylum] NA:
                        └── [Class] Revtraviricetes:
                            └── [Subclass] NA:
                                └── [Order] Ortervirales:
                                    └── [Suborder] NA:
                                        └── [Family] Retroviridae:
                                            └── [Subfamily] Orthoretrovirinae:
                                                ├── [Genus] Gammaretrovirus:
                                                │   └── [Subgenus] NA:
                                                │       └── [Species] Gammaretrovirus felleu
                                                └── [Genus] Lentivirus:
                                                    └── [Subgenus] NA:
                                                        └── [Species] Lentivirus felimdef

Download Updated MSL

To download the current release, use msl.update_msl(version="current"). That will return output:

File of version current has been loaded
Column names: ['Sort', 'Realm', 'Subrealm', 'Kingdom', 'Subkingdom', 'Phylum', 'Subphylum', 'Class', 'Subclass', 'Order', 'Suborder', 'Family', 'Subfamily', 'Genus', 'Subgenus', 'Species', 'Genome', 'Last Change', 'MSL of Last Change', 'Proposal for Last Change ', 'Taxon History URL']
Total number of rows: 14690

To see versions available to download:

msl.update_msl(version="")

Version '' is not supported. Supported versions are: current, 39.v4, 39.v3, 39.v2, 39.v1, 38.v3, 38.v2, 38.v1, 2021.v3, 2021.v2, 2021.v1, 2020, 2019, 2018b.v2, 2018a, 2017, 2016.v1.3, 2015, 2014.v4, 2013.v2, 2012.v4, 2011.v2, 2009.v10, 2008, 2005.v1

Subtypes within Species

ICTV MSL focuses on “taxa at and above the species rank” [11]. Classification below the species are often related to species specific characteristics [12].

Species Exemplar

ICTV VMR provides one exemplar (and may be more additional isolates) for each species in VMR, with Genebak accession number and direct link to NCBI database.

To load a VRM table extracted from VRM download file:

from mtbp3.seq import ictvvmrview
vmr = ictvvmrview.ictvvmr(vmr_file_path = "")

File supp_seq/ICTV_VMR_MSL39v4_example.csv has been loaded
Column names: ['Isolate ID', 'Species Sort', 'Isolate Sort', 'Realm', 'Subrealm', 'Kingdom', 'Subkingdom', 'Phylum', 'Subphylum', 'Class', 'Subclass', 'Order', 'Suborder', 'Family', 'Subfamily', 'Genus', 'Subgenus', 'Species', 'Exemplar or additional isolate', 'Virus name(s)', 'Virus name abbreviation(s)', 'Virus isolate designation', 'Virus GENBANK accession', 'Genome coverage', 'Genome', 'Host source', 'Accessions Link']
Total number of rows: 65

When the path is empty, an example file will be used for illustration. Similarily, use vmr.update_vmr(version="current"). to download the current version from ICTV.

To search for exemplars including “feline” using search_rank_or_exemplar="Virus name(s)":

print('\n'.join(vmr.find_rows_given_str(search_strings="feline", search_rank_or_exemplar="Virus name(s)", color="red", outfmt='tree', tree_style="drop")))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    └── [Family] Retroviridae:
                        ├── [Subfamily] Orthoretrovirinae:
                        │   ├── [Genus] Gammaretrovirus:
                        │   │   ├── [Species] Gammaretrovirus felleu (ssRNA-RT):
                        │   │   │   └── [E] feline leukemia virus (Rickard subgroup A) (Genebank: AF052723)
                        │   │   ├── [Species] Gammaretrovirus hazufelsar (ssRNA-RT):
                        │   │   │   └── [E] Hardy-Zuckerman feline sarcoma virus (Genebank: X03711)
                        │   │   └── [Species] Gammaretrovirus snythefelsar (ssRNA-RT):
                        │   │       └── [E] Snyder-Theilen feline sarcoma virus (Genebank: M22820)
                        │   └── [Genus] Lentivirus:
                        │       └── [Species] Lentivirus felimdef (ssRNA-RT):
                        │           └── [E] feline immunodeficiency virus (Petaluma) (Genebank: M25381)
                        └── [Subfamily] Spumaretrovirinae:
                            └── [Genus] Felispumavirus:
                                └── [Species] Felispumavirus felcat (ssRNA-RT):
                                    └── [E] feline foamy virus Felis catus (FUV7) (Genebank: Y08851)

To search for genus Lentivirus:

print('\n'.join(vmr.find_rows_given_str(search_strings="lentivirus", search_rank_or_exemplar="Genus", color="red", outfmt='tree', exact=True, tree_style="drop")))

    [Realm] Riboviria:
    └── [Kingdom] Pararnavirae:
        └── [Phylum] Artverviricota:
            └── [Class] Revtraviricetes:
                └── [Order] Ortervirales:
                    └── [Family] Retroviridae:
                        └── [Subfamily] Orthoretrovirinae:
                            └── [Genus] Lentivirus:
                                ├── [Species] Lentivirus bovimdef (ssRNA-RT):
                                │   └── [E] bovine immunodeficiency virus (HXB3) (Genebank: M32690)
                                ├── [Species] Lentivirus bovjem (ssRNA-RT):
                                │   └── [E] Jembrana disease virus (Tabanan_87) (Genebank: U21603)
                                ├── [Species] Lentivirus capartenc (ssRNA-RT):
                                │   └── [E] caprine arthritis encephalitis virus (Clements) (Genebank: M33677)
                                ├── [Species] Lentivirus equinfane (ssRNA-RT):
                                │   └── [E] equine infectious anemia virus (Genebank: U01866)
                                ├── [Species] Lentivirus felimdef (ssRNA-RT):
                                │   └── [E] feline immunodeficiency virus (Petaluma) (Genebank: M25381)
                                ├── [Species] Lentivirus humimdef1 (ssRNA-RT):
                                │   └── [E] human immunodeficiency virus 1 (Genebank: AF033819)
                                ├── [Species] Lentivirus humimdef2 (ssRNA-RT):
                                │   └── [E] human immunodeficiency virus 2 (BEN) (Genebank: M30502)
                                ├── [Species] Lentivirus ovivismae (ssRNA-RT):
                                │   └── [E] Visna_maedi virus (kv1772) (Genebank: L06906)
                                ├── [Species] Lentivirus pum (ssRNA-RT):
                                │   └── [E] puma lentivirus (14) (Genebank: U03982)
                                └── [Species] Lentivirus simimdef (ssRNA-RT):
                                    └── [E] simian immunodeficiency virus (Genebank: M58410)

Other Resource

NCBI:

• Explore Virus Data [13]

• NCBI Visual Data Dashboard [14]

Reference

---

[1]

ICTV. (2024). About Virus Taxonomic Classification. (web page)

[2]

Elliot J Lefkowitz, Donald M Dempsey, Robert Curtis Hendrickson, Richard J Orton, Stuart G Siddell, Donald B Smith, Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV), Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D708–D717, (web page)

[3]

wiki. (year). Virus classification. (web page)

[4] (1,2)

ICTV. (2024). Master Species Lists (MSL). (web page)

[5]

ICTV. (2024). Virus Metadata Resource (VMR). (web page)

[6]

ICTV. (2024). Current ICTV Taxonomy Release. (web page)

[7]

ICTV. (2024). Visual Taxonomy Browser. (web page)

[8]

Sykes J. E. (2014). Feline Immunodeficiency Virus Infection. Canine and Feline Infectious Diseases, 209–223. (web page)

[9]

ICTV. (2023). History of the taxon. (web page)

[10]

ICTV. (year). The ICTV Report on Virus Classification and Taxon Nomenclature. (web page)

[11]

Siddell, S. G., Smith, D. B., Adriaenssens, E., Alfenas-Zerbini, P., Dutilh, B. E., Garcia, M. L., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Lefkowitz, E. J., Łobocka, M., Mushegian, A. R., Oksanen, H. M., Robertson, D. L., Rubino, L., Sabanadzovic, S., Simmonds, P., Suzuki, N., Van Doorslaer, K., … Zerbini, F. M. (2023). Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). The Journal of general virology, 104(5), 001840. (web page)

[12]

Kuhn, J. H., Bao, Y., Bavari, S., Becker, S., Bradfute, S., Brister, J. R., Bukreyev, A. A., Chandran, K., Davey, R. A., Dolnik, O., Dye, J. M., Enterlein, S., Hensley, L. E., Honko, A. N., Jahrling, P. B., Johnson, K. M., Kobinger, G., Leroy, E. M., Lever, M. S., Mühlberger, E., … Nichol, S. T. (2013). Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. Archives of virology, 158(1), 301–311. (web page)

[13]

NCBI. (2024). Explore Virus Data: Feline immunodeficiency virus. (web pate)

[14]

NCBI. (2024). NCBI Visual Data Dashboard. (web page)

[15]

ICTV. (year). Taxon names are written differently from virus names. (web page)