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Virus TaxonomyThe ICTV Report on Virus Classification and Taxon
Nomenclature
Herelleviridae Chapter
Herelleviridae
Jakub Barylski, Andrew M. Kropinski, Nabil-Fareed Alikhan, and
Evelien M. Adriaenssens
The citation for this ICTV Report chapter is the summary
published as Barylski et al., (2020):ICTV Virus Taxonomy Profile:
Herelleviridae, Journal of General Virology, 101, 362–363
Corresponding author: Evelien M Adriaenssens
([email protected])Edited by: Andrew M. Kropinski
and Stuart G. SiddellPosted: July 2020, updated September 2020
Summary
Members of the family Herelleviridae are bacterial viruses
infecting members of the phylum Firmicutes (Table
1.Herelleviridae). In the ninth reportof the ICTV, this group was
reported as the genus SPO1-like viruses. The virions have myovirus
morphology, i.e., a head-tail structure with along, contractile
tail, and an icosahedral head. Genomes are dsDNA of 125–170 kb.
Table 1.Herelleviridae. Characteristics of members of the family
Herelleviridae
Characteristic Description
Typicalmember Bacillus phage SPO1 (FJ230960.1), species Bacillus
virus SPO1 genus Okubovirus
Virion Head-tail morphology with contractile tail, heads
generally isometric with diameters of 85–100 nm showing
capsomers,uncontracted tails of 130–185 nm in length
Genome Linear, terminally redundant, non-permuted dsDNA of
125–170 kbp
Replication Phage-encoded DNA polymerase
Translation Bacterial translation
Host range Bacteria of the phylum Firmicutes
Taxonomy Realm Duplodnaviria, kingdom Heunggongvirae, phylum
Uroviricota, class Caudoviricetes, order Caudovirales, 5
subfamilies,19 genera and 82 species
Virion
Morphology
Virions have isometric, icosahedral heads of 85–100 nm in
diameter. The heads show clear capsomers, i.e. the subunits of the
capsid arearranged in pentons and hexons that are assembled into
the isometric, icosahedral capsid. The uncontracted tails are
130–185 nm in length. Thetails have a baseplate of approximately 60
nm and a small collar (Table 1.Herelleviridae, Figure
1.Herelleviridae).
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Figure 1.Herelleviridae. Transmission electron micrograph of
Bacillus phage phiAGATE, a member of the family Herelleviridae
(subfamilyBastillevirinae). Virions were concentrated from
bacteria-free lysates and stained with 2% uranyl acetate.
Negatively-stained phage particleswere visualized using a JEOL
JEM-1400 transmission electron microscope at 120 kV.
Physicochemical and physical properties
Bacillus phage SPO1 buoyant density in CsCl is 1.54 g/cm .
Nucleic acid
The genomes of herelleviruses consist of linear dsDNA with long
terminal repeats of 3–16 kbp ( Perkus and Shub 1985, Klumpp et al.,
2008,Łobocka and Szybalski 2012). Genomes are of 125–170 kbp. tRNAs
are encoded by some members. The genome of Bacillus phage SPO1
hasthymidine replaced with 5-hydroxymethyluridine and this
modification or a similar one could be present in all members of
the family (Okubo et al.,1972, Parker and Eiserling 1983, Klumpp et
al., 2010).
Proteins
The virion of Bacillus phage SPO1 comprises at least 35 proteins
as judged from electropherograms of purified particles ( Parker and
Eiserling1983).
Lipids
No lipids reported.
Carbohydrates
No carbohydrates reported.
Genome organization and replication
The genomes of herelleviruses are linear dsDNA with long
terminal repeats of various lengths. Genomes are of 125–170 kbp and
encode 165–301genes, including 0–24 tRNAs. For Bacillus phage SPO1,
the majority of the coding sequences are in the same orientation;
two islands encodinghypothetical proteins are transcribed from the
opposite strand (Figure 2.Herelleviridae). The terminal repeat of
SPO1 contain a host-takeovermodule involved in phage propagation.
Transcription is mediated by phage-encoded sigma factors that
co-opt the host RNA polymerase (Stewartet al., 2009). Introns have
been identified in a number of herellevirus genomes (
Goodrich-Blair et al., 1990, Lavigne and Vandersteegen 2013).
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Figure 2.Herelleviridae. Genome organisation of Bacillus phage
SPO1, the typical member of the family Herelleviridae. The terminal
repeatarea is indicated with a blue arc, structural modules with a
cyan arcs. The predicted coding sequences on the plus-strand are in
purple, those onthe minus-strand in teal. The five predicted tRNAs
are indicated in black. This figure was generated with BRIG
(Alikhan et al., 2011).
Table 2.Herelleviridae. Core genes with predicted functions
shared among all members of the family*
Gene Prokaryotic virus orthologous group numberDnaB-like
helicase VOG0025, VOG4691baseplate J-like protein VOG4644tail
sheath protein VOG0067terminase large subunit (intron-invaded)
VOG0051major capsid protein VOG0061prohead protease VOG4568portal
protein VOG4556DNA primase VOG4551DNA polymerase I VOG0668RNA
polymerase VOG0118recombination exonuclease VOG4575recombination
endonuclease VOG0083tail tape measure protein VOG0069tail tube
protein VOG0068
* at a 50% amino acid sequence identity threshold at minimum 50%
gene coverage or by prokaryotic Virus Orthologous Group
(pVOG)analysis (Barylski et al., 2020)
Biology
The phages belonging to this family are reported to be
obligately lytic, but some may be able to cause persistent
infection, pseudolysogenicinfection or a carrier state (Schuch and
Fischetti 2009, Yuan et al., 2015). Herelleviruses infect bacteria
belonging to the phylum Firmicutes andhave a worldwide
distribution.
Derivation of names
Herelleviridae – named in honour of the 100 anniversary of the
discovery of bacteriophages by Félix d’ Hérelle in 1917.
Subfamily demarcation criteria
Subfamilies (Table 3.Herelleviridae) are identified as
well-supported monophyletic groups based on phylogenetic analysis
of concatenated coregene markers and single core genes (Figure
3.Herelleviridae). Within a subfamily, members are 20–25% identical
in translated nucleotide contentas calculated with the tBLASTx
algorithm. Between members of different subfamilies, there is
little to no nucleotide sequence identity across thegenome
length.
th
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Table 3.Herelleviridae. The subfamilies of Herelleviridae.
Subfamily Genera Host Genome (kbp) Terminal
repeats*Bastillevirinae 7 Bacillus sp. 146–167 LongBrockvirinae 2
Enterococcus sp. 140–155 NDJasinkavirinae 1 Listeria monocytogenes
131–138 NDSpounavirinae 2 Bacillus sp. 132–146 LongTwortvirinae 7
Staphylococcus and Lactobacillus 135–150 ND
*ND Not Determined for all members
Genus demarcation criteria
The Herelleviridae genera are well-supported monophyletic clades
in genome-based phylogenies and in (concatenated) marker
genephylogenies. Members of the genus share at least 60% nucleotide
identity across the genome length. The genome organisation is
conserved.Members of the same genus generally infect members of the
same bacterial genus.
Species demarcation criteria
The species demarcation criteria are the same for all species
within this family. Members of the same species are more than 95%
identical ingenome nucleotide sequence, including the terminal
repeat region. Phages with genomes that differ in more than 5% are
assigned to differentspecies.
Relationships within the family
Phylogenetic analysis of 10 core gene products shared among all
herelleviruses ( Barylski et al., 2020) has identified five
subfamilies, 19 generaand 82 species, of which three species have
not been assigned to a genus or subfamily (Figure
3.Herelleviridae). The relationships are largelyconserved in single
marker gene phylogenies, however, shuffling between subfamilies has
been observed for the tail tube protein (Barylski et al.,2020).
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Figure 3.Herelleviridae. Phylogenetic analysis of members of the
family Herelleviridae. Amino acid sequences of the major capsid
proteins ofall herelleviruses exemplar isolates were downloaded
from NCBI. Amino acid sequences were aligned with MAFFT (Katoh and
Standley 2013)and trimmed with TrimAl using the gappyout setting
(Capella-Gutiérrez et al., 2009). The displayed maximum likelihood
tree was generated withthe IQ-TREE pipeline including ModelFinder
(Katoh and Standley 2013, Kalyaanamoorthy et al., 2017) and rooted
at midpoint. Ultrafastboostraps (UFBOOT) scores out of 100 indicate
branch support (Kalyaanamoorthy et al., 2017). Coloured circles
indicate members of the samegenus, while black circles are
asssigned to a speces but not a genus. * The genus Harbinvirus was
mistakenly assigned to thesubfamily Twortvirinae; the Taxonomic
Proposal 2020.072B.N.V1.Herelleviridae has been submitted to the
ICTV to change it to an orphan genusin the family. This
phylogenetic tree and corresponding sequence alignment are
available to download from the Resources page.
Relationships with other taxa
Herelleviruses share morphological similarity with other
myoviruses, i.e. bacteriophages with long contractile tails.
Species unassigned to a subfamily
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★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Brochothrix virus A9 Brochothrix phage A9 HM242243 NC_015253
Complete genome★ Lactobacillus virus Lb338-1 Lactobacillus phage
Lb338-1 FJ822135 NC_012530 Complete genome★ Lactobacillus virus
LP65 Lactobacillus phage LP65 AY682195 NC_006565 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
Member taxa
BastillevirinaeAgatevirusBastillevirusBequatrovirusCaeruleovirusNitunavirusTsarbombavirusWphvirusBrockvirinaeKochikohdavirusSchiekvirusJasinkavirinaePecentumvirusSpounavirinaeOkubovirusSiminovitchvirusTwortvirinaeBaoshanvirusHarbinvirusKayvirusSciuriunavirusSepunavirusSilviavirusTwortvirus
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https://www.ncbi.nlm.nih.gov/nuccore/HM242243https://www.ncbi.nlm.nih.gov/nuccore/NC_015253https://www.ncbi.nlm.nih.gov/nuccore/FJ822135https://www.ncbi.nlm.nih.gov/nuccore/NC_012530https://www.ncbi.nlm.nih.gov/nuccore/AY682195https://www.ncbi.nlm.nih.gov/nuccore/NC_006565https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1267/subfamily-bastillevirinaehttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1268/genus-agatevirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1269/genus-bastillevirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1270/genus-bequatrovirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1271/genus-caeruleovirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1272/genus-nitunavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1273/genus-tsarbombavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1274/genus-wphvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1275/subfamily-brockvirinaehttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1276/genus-kochikohdavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1381/genus-schiekvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1277/subfamily-jasinkavirinaehttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1278/genus-pecentumvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1264/subfamily-spounavirinaehttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1265/genus-okubovirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1266/genus-siminovitchvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1279/subfamily-twortvirinaehttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1378/genus-baoshanvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1379/genus-harbinvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1280/genus-kayvirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1380/genus-sciuriunavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1282/genus-sepunavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1281/genus-silviavirushttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae/1283/genus-twortvirus
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Subfamily: Bastillevirinae
Distinguishing features
Members of this subfamily infect Bacillus sp. including B.
cereus, B. subtilis, B. thuringiensis, B. pumilis and B.
megatherium. Genomes are of146–167 kbp and have long terminal
repeats.
Derivation of names
Bastillevirinae, Bastillevirus: from Bacillus phage Bastille
Genus demarcation criteria
The Bastillevirinae genera are well-supported monophyletic
clades in genome-based phylogenies and in (concatenated) marker
genephylogenies. Members of the genera share at least 60%
nucleotide identity across the genome length. The genome
organisation is conserved.Members of the same genus generally
infect members of the same bacterial genus.
Species unassigned to a genus
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Mater Bacillus phage Mater KM236245 NC_027366
Complete genome★ Bacillus virus Moonbeam Bacillus phage Moonbeam
KM236246 NC_027374 Complete genome★ Bacillus virus SIOphi Bacillus
phage SIOphi KC699836 NC_042133 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
Member taxa
AgatevirusBastillevirusBequatrovirusCaeruleovirusNitunavirusTsarbombavirusWphvirus
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Genus: Agatevirus
Distinguishing features
Members of this genus infect Bacillus thuringiensis and Bacillus
pumilis. The type species is Bacillus virus Agate . The
non-redundant part of thegenome of the exemplar isolate, Bacillus
virus Agate, is approximately 150 kbp, with 210 gene coding
sequences as well as 4 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus thuringiensis and B.
pumilis.
Derivation of names
Agatevirus: derived from the name of the exemplar isolate,
Bacillus phage phiAGATE, of the type species, Bacillus virus
Agate.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Agate Bacillus phage phiAGATE JX238501
NC_020081 Complete genome★ Bacillus virus Bobb Bacillus phage Bobb
KM051843 NC_024792 Complete genome★ Bacillus virus Bp8pC Bacillus
phage Bp8p-C KJ010547 NC_029121 Complete genome
Bacillus virus Bp8pC Bacillus phage Bp8p-T KJ010548 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Bastillevirus
Distinguishing features
Members of this genus infect Bacillus cereus and Bacillus
thuringiensis. The type species is Bacillus virus Bastille. No
terminal repeats have beenreported for these genomes. The genome of
the exemplar isolate is 154 kbp, with 273 gene coding sequences as
well as 7 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus and Bacillus
thuringiensis.
Derivation of names
Bastillevirus: derived from the name of the exemplar isolate,
Bacillus phage Bastille, of the type species, Bacillus virus
Bastille.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Bastille Bacillus phage Bastille JF966203
NC_018856 Complete genome★ Bacillus virus CAM003 Bacillus phage
CAM003 KJ489397 NC_024216 Complete genome★ Bacillus virus Evoli
Bacillus phage Evoli KJ489398 NC_024207 Complete genome★ Bacillus
virus HoodyT Bacillus phage Hoody T KJ489400 NC_024205 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Bequatrovirus
Distinguishing features
Members of this genus infect Bacillus cereus and Bacillus
thuringiensis. The type species is Bacillus virus B4. Terminal
repeats have beenreported for some bequatrovirus genomes. The
unique sequence of the genome of the exemplar isolate, of the type
species is 163 kbp, with 277gene coding sequences. No encoded tRNAs
have been reported.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus and Bacillus
thuringiensis.
Derivation of names
Bequatrovirus: derived from the name of the exemplar isolate,
Bacillus phage B4, of the type species (phonetic B [Be] followed by
quatro, derivedfrom Italian for four, quattro).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus AvesoBmore Bacillus phage AvesoBmore KT307976
NC_028887 Complete genome★ Bacillus virus B4 Bacillus phage B4
JN790865 NC_018863 Complete genome
Bacillus virus B4 Bacillus phage B5S JN797796 Complete genome★
Bacillus virus Bigbertha Bacillus phage BigBertha KF669647
NC_022769 Complete genome★ Bacillus virus Riley Bacillus phage
Riley KJ489402 NC_024788 Complete genome★ Bacillus virus Spock
Bacillus phage Spock KF669662 NC_022763 Complete genome★ Bacillus
virus Troll Bacillus phage Troll KF208639 NC_022088 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Caeruleovirus
Distinguishing features
Members of this genus infect Bacillus cereus and Bacillus
megatherium. The type species is Bacillus virus Bc431. The genome
of the exemplarisolate of the type species is 159 kbp, with 238
gene coding sequences as well as 21 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus and Bacillus
megatherium.
Derivation of names
Caeruleovirus: derived by association with the name of one of
the member species, Bacillus virus Deepblue, caerulean being a
shade of blue.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Bc431 Bacillus phage vB_BceM_Bc431v3 JX094431
NC_020873 Complete genome★ Bacillus virus Bcp1 Bacillus phage Bcp1
KJ451625 NC_024137 Complete genome★ Bacillus virus BCP82 Bacillus
phage BCP8-2 KJ081346 NC_027355 Complete genome★ Bacillus virus
BM15 Bacillus phage BM15 KT995480 NC_042140 Complete genome★
Bacillus virus Deepblue Bacillus phage Deep Blue KU577463 NC_031056
Complete genome★ Bacillus virus JBP901 Bacillus phage JBP901
KJ676859 NC_027352 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Nitunavirus
Distinguishing features
Members of this genus infect Bacillus subtilis. The type species
is Bacillus virus NIT1. Terminal repeats have been reported for
some nitunavirusgenomes. The unique sequence of the genome of the
exemplar isolate of the type species is 153 kbp, containing
terminal repeats of about 4 kbp,with 252 gene coding sequences as
well as 3 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus subtilis.
Derivation of names
Nitunavirus: derived phonetically from the name of the exemplar
isolate, Bacillus phage phiNIT1, of the type species (i.e. nit
followed by unameaning one).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Grass Bacillus phage Grass KF669652 NC_022771
Complete genome★ Bacillus virus NIT1 Bacillus phagephiNIT1 AP013029
NC_021856 Complete genome
★ Bacillus virus SPG24 Bacillus phage SPG24 AB930182 NC_030903
Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Tsarbombavirus
Distinguishing features
Members of this genus infect Bacillus cereus and Bacillus
thuringiensis. The type species is Bacillus virus Tsarbomba. No
terminal repeats havebeen reported for tsarbombavirus genomes. The
genome of the exemplar isolate of the type species is 156 kbp, with
227 gene coding sequencesas well as 18 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus and Bacillus
thuringiensi.
Derivation of names
Tsarbombavirus: derived from the name of the exemplar isolate,
Bacillus phage TsarBomba, of the type species.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus BCP78 Bacillus phage BCP78 JN797797 NC_018860
Complete genomeBacillus virus BCP78 Bacillus phage BCU4 JN797798
Complete genome
★ Bacillus virus TsarBomba Bacillus phage TsarBomba KT224359
NC_028890 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Wphvirus
Distinguishing features
Members of this genus infect Bacillus cereus. The type species
is Bacillus virus WPh. The genome of the exemplar isolate of the
type species is157 kbp, with 274 gene coding sequences and no
encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus.
Derivation of names
Wphvirus: derived from the name of the exemplar isolate Bacillus
phage W.Ph., of the type species.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus BPS13 Bacillus phage BPS13 JN654439 NC_018857
Complete genome★ Bacillus virus BPS10C Bacillus phage BPS10C
KC430106 NC_023501 Complete genome★ Bacillus virus Hakuna Bacillus
phage Hakuna KJ489399 NC_024213 Complete genome★ Bacillus virus
Megatron Bacillus phage Megatron KJ489401 NC_024211 Complete
genome
Bacillus virus Megatron Bacillus phage Eyuki KT207918 Complete
genome★ Bacillus virus WPh Bacillus phage W.Ph. HM144387 NC_016563
Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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Subfamily: Brockvirinae
Distinguishing features
Members of this subfamily generally infect Enterococcus sp. with
known isolates infecting E. faecalis and E. faecium. Virus genomes
are of 140–155 kbp.
Derivation of names
Brockvirinae: named in honour of Thomas D. Brock (1926–), the
eminent American microbiologist and educator known for his
discovery ofhyperthermophiles, who worked on Streptococcus phages
early in his career.
Genus demarcation criteria
The single genus in the Brockvirinae is a well-supported
monophyletic clade in genome-based phylogenies and in
(concatenated) marker genephylogenies. Members of the genus share
at least 60% nucleotide identity across the genome length, a
conserved genome organisation andgenerally infect members of the
same bacterial genus.
Member taxa
KochikohdavirusSchiekvirus
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Genus: Kochikohdavirus
Distinguishing features
Members of this genus infect Enterococcus faecalis. The type
species is Enterococcus virus EF24C . The genome of the exemplar
isolate of thetype species is 142 kbp, with 221 gene coding
sequences as well as 5 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Enterococcus faecalis.
Derivation of names
Kochikohdavirus: derived from the place of origin of the
exemplar isolate, Enterococcus phage phiEF24C, of the type species
(isolated in Kohda,Kochi City, Japan).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Enterococcus virus ECP3 Enterococcus phage ECP3 KJ801817
NC_027335 Complete genome★ Enterococcus virus EF24C Enterococcus
phage EF24C AP009390 NC_009904 Complete genome
Enterococcus virus EF24C Enterococcus phage phiEF24C-P2 AB609718
Complete genome★ Enterococcus virus EFLK1 Enterococcus phage EFLK1
KR049063 NC_029026 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Schiekvirus
Distinguishing features
Members of this genus infect Enterococcus faecalis. The type
species is Enterococcus virus EFDG1 . The genome of the exemplar
isolate of thetype species is 148 kbp, with 216 gene coding
sequences as well as 24 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Enterococcus faecalis.
Derivation of names
Schiekvirus: named after the German virologist Wolfgang Schiek
(Hygiene-Institut, University of Göttingen) who was one of the
first scientists towork on Enterococcus phages.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Enterococcus virus EFDG1 Enterococcus phage EFDG1 KP339049
NC_029009 Complete genome★ Enterococcus virus EFP01 Enterococcus
phage EFP01 KY549443 NC_047796 Complete genome★ Enterococcus virus
EfV12 Enterococcus phage EfV12-phi1 MH880817 NC_048087 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/KP339049https://www.ncbi.nlm.nih.gov/nuccore/NC_029009https://www.ncbi.nlm.nih.gov/nuccore/KY549443https://www.ncbi.nlm.nih.gov/nuccore/NC_047796https://www.ncbi.nlm.nih.gov/nuccore/MH880817https://www.ncbi.nlm.nih.gov/nuccore/NC_048087
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Subfamily: Jasinkavirinae
Distinguishing features
Members of this subfamily generally infect Listeria
monocytogenes strains and have genomes of 131–138 kbp.
Derivation of names
Jasinkavirinae: named in honour of Stanisława
Jasińska-Lewandowska (1921–1998), a Polish scientist who was one of
the first to study Listeriaand their viruses.
Genus demarcation criteria
The single genus in the Jasinkavirinae is a well-supported
monophyletic clade in genome-based phylogenies and in
(concatenated) marker genephylogenies. Members of the genus share
at least 60% nucleotide identity across the genome length, a
conserved genome organisation and infectmembers of the same
bacterial genus.
Member taxa
Pecentumvirus
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Genus: Pecentumvirus
Distinguishing features
The genus description and subfamily description are currently
the same, i.e. the subfamily only contains one genus and there are
no unassignedspecies.
Members of this genus infect Listeria monocytogenes. The type
species is Listeria virus P100. The genome of the exemplar isolate
of the typespecies is 131 kbp, with 193 gene coding sequences, as
well as 18 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Listeria monocytogenes.
Derivation of names
Pecentumvirus: derived phonetically from the name of the
exemplar isolate, Listeria phage P100, of the type species (“pe”
followed by centummeaning 100 in Latin).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Listeria virus A511 Listeria phage A511 DQ003638 NC_009811
Complete genome★ Listeria virus AG20 Listeria phage vB_LmoM_AG20
JQ797329 NC_020871 Complete genome★ Listeria virus List36 Listeria
phage List-36 KJ535721 NC_024364 Complete genome★ Listeria virus
LMSP25 Listeria phage LMSP-25 KJ535722 NC_024360 Complete
genome
Listeria virus LMSP25 Listeria phage LMTA-57 KJ591605 Complete
genomeListeria virus LMSP25 Listeria phage LMTA-94 KJ586795
Complete genome
★ Listeria virus LMTA34 Listeria phage LMTA-34 KJ586794
NC_042048 Partial genome★ Listeria virus LMTA148 Listeria phage
LMTA-148 KJ591604 NC_024787 Complete genome★ Listeria virus LP048
Listeria phage LP-048 KJ094033 NC_024359 Complete genome★ Listeria
virus LP064 Listeria phage LP-064 KJ094029 NC_041862 Complete
genome
Listeria virus LP064 Listeria phage LP-124 KJ094031 Complete
genome★ Listeria virus LP083-2 Listeria phage LP-083-2 KJ094030
NC_024383 Complete genome
Listeria virus LP083-2 Listeria phage LP-125 JX126918 Complete
genome★ Listeria virus P100 Listeria phage P100 DQ004855 NC_007610
Complete genome★ Listeria virus WIL1 Listeria phage WIL-1 KM373208
NC_025440 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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Subfamily: Spounavirinae
Distinguishing features
Members of this subfamily infect Bacillus sp. including B.
cereus and B. subtilis. Virus genomes are of 132–146 kbp and have
long terminalrepeats.
Derivation of names
Spounavirinae – derived from Bacillus phage SPO1 (i.e. spo and
una, meaning one), the first recognised isolate of this
subfamily.
Genus demarcation criteria
The Spounavirinae genera are well-supported monophyletic clades
in genome-based phylogenies and in (concatenated) marker
genephylogenies. Members of the genera share at least 60%
nucleotide identity across the genome length. The genome
organisation is conserved.Members of the same genus generally
infect members of the same bacterial genus.
Member taxa
OkubovirusSiminovitchvirus
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Genus: Okubovirus
Distinguishing features
Members of this genus infect Bacillus subtilis. The type species
is Bacillus virus SPO1. The non-redundant portion of the genome of
the exemplarisolate, Bacillus phage SPO1, is 133 kbp, with 204 gene
coding sequences as well as 5 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus subtilis.
Derivation of names
Okubovirus: named in honour of Shunzo Okubo (1930–1978), former
Professor of Genetics at Osaka University who isolated phage SPO1
in1964 and carried out the original studies on the exemplar isolate
of the genus.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus Camphawk Bacillus phage CampHawk KF669649
NC_022761 Complete genome★ Bacillus virus SPO1 Bacillus phage SPO1
FJ230960 NC_011421 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Genus: Siminovitchvirus
Distinguishing features
Members of this genus infect Bacillus cereus. The type species
is Bacillus virus CP51. The non-redundant part of the genome of the
exemplarisolate, Bacillus virus CP5, is 139 kbp, with 221 gene
coding sequences.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Bacillus cereus.
Derivation of names
Siminovitchvirus: named in honour of Louis Siminovitch (1920 –
), a Canadian molecular biologist who studied phages early in his
academiccareer.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Bacillus virus CP51 Bacillus phage CP-51 KF554508 NC_025423
Complete genome★ Bacillus virus JL Bacillus phage JL KC595512
NC_028982 Complete genome★ Bacillus virus Shanette Bacillus phage
Shanette KC595513 NC_028983 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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Subfamily: Twortvirinae
Distinguishing features
Members of this subfamily generally infect Staphylococcus and
Lactobacillus strains, and have genomes of 135–150 kbp.
Derivation of names
Twortvirinae: named in honour of Frederick William Twort
(1877–1950), the English bacteriologist who discovered prokaryotic
viruses in 1915.
Genus demarcation criteria
The Twortvirinae genera are well-supported monophyletic clades
in genome-based phylogenies and in (concatenated) marker gene
phylogenies.Members of the genera share at least 60% nucleotide
identity across the genome length. The genome organisation is
conserved. Members of thesame genus generally infect members of the
same bacterial genus.
Note that the genus Harbinvirus has been misplaced in the
subfamily Twortvirinae; the Taxonomic Proposal
2020.072B.N.V1.Herelleviridae hasbeen submitted to the ICTV to
change it to an orphan genus in the family.
Member taxa
BaoshanvirusHarbinvirusKayvirusSciuriunavirusSepunavirusSilviavirusTwortvirus
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Genus: Baoshanvirus
Distinguishing features
Members of this genus infect Staphylococcus sp. The type species
is Staphylococcus virus BS2. The genome of the exemplar isolate of
the typespecies is 149 kbp, with a total of 210 predicted gene
coding sequences and 1 encoded tRNA.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sp. mainly S.
aureus.
Derivation of names
Baoshanvirus: derived from the place of origin of the type
isolate, the Chinese district Boashan.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virus BS1 Staphylococcus phage phiSA_BS1
MH078572 NC_047945 Complete genome phiSA_BS1★ Staphylococcus virus
BS2 Staphylococcus phage phiSA_BS2 MH028956 NC_047948 Complete
genome phiSA_BS2
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/MH078572https://www.ncbi.nlm.nih.gov/nuccore/NC_047945https://www.ncbi.nlm.nih.gov/nuccore/MH028956https://www.ncbi.nlm.nih.gov/nuccore/NC_047948
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Genus: Harbinvirus
Distinguishing features
The genus Harbinvirus has been misplaced in the subfamily
Twortvirinae; the Taxonomic Proposal 2020.072B.N.V1.Herelleviridae
has beensubmitted to the ICTV to change it to an orphan genus in
the family. Members of this genus infect Lactobacillus plantarum.
The type species isLactobacillus virus Lpa804 . The genome of the
exemplar isolate of the type species is 142 kbp, with a total of
105 predicted gene codingsequences and 9 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Lactobacillus plantarum.
Derivation of names
Harbinvirus: derived from the place of isolation of the type
species exemplar isolate, Harbin, the capital of Heilongjiang and
the location of theNortheast Agricultural University.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Lactobacillus virus Bacchae Lactobacillus phage Bacchae
MG765277 NC_047924 Complete genome★ Lactobacillus virus Bromius
Lactobacillus phage Bromius MH809531 NC_048085 Complete genome★
Lactobacillus virus Iacchus Lactobacillus phage Iacchus MH809529
NC_048084 Complete genome★ Lactobacillus virus Lpa804 Lactobacillus
phage Lpa804 MG557979 NC_048134 Complete genome★ Lactobacillus
virus Semele Lactobacillus phage Semele MG765279 NC_047926 Complete
genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/MG765277https://www.ncbi.nlm.nih.gov/nuccore/NC_047924https://www.ncbi.nlm.nih.gov/nuccore/MH809531https://www.ncbi.nlm.nih.gov/nuccore/NC_048085https://www.ncbi.nlm.nih.gov/nuccore/MH809529https://www.ncbi.nlm.nih.gov/nuccore/NC_048084https://www.ncbi.nlm.nih.gov/nuccore/MG557979https://www.ncbi.nlm.nih.gov/nuccore/NC_048134https://www.ncbi.nlm.nih.gov/nuccore/MG765279https://www.ncbi.nlm.nih.gov/nuccore/NC_047926
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Genus: Kayvirus
Distinguishing features
Members of this genus infect Staphylococcus sp. mainly S.
aureus. The type species is Staphylococcus virus K. The genome of
the exemplarisolate of the type species is 142 kbp, with 8 kb
terminal repeats, and with a total of 233 gene coding sequencess as
well as 4 encoded tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sp. mainly S.
aureus.
Derivation of names
Kayvirus: derived phonetically from the name of the exemplar
isolate, Staphylococcus phage K, of the type species.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virus G1 Staphylococcus phage G1 AY954969
NC_007066 Complete genomeStaphylococcus virus G1 Staphylococcus
phage 676Z JX080302 Complete genomeStaphylococcus virus G1
Staphylococcus phage A3R JX080301 Complete genomeStaphylococcus
virus G1 Staphylococcus phage A5W EU418428 Complete
genomeStaphylococcus virus G1 Staphylococcus phage Fi200W JX080303
Complete genomeStaphylococcus virus G1 Staphylococcus phage IME-SA1
KP687431 Complete genomeStaphylococcus virus G1 Staphylococcus
phage IME-SA118 KR902361 Complete genomeStaphylococcus virus G1
Staphylococcus phage IME-SA119 KR908644 Complete
genomeStaphylococcus virus G1 Staphylococcus phage IME-SA2 KP687432
Complete genomeStaphylococcus virus G1 Staphylococcus phage ISP
FR852584 Complete genomeStaphylococcus virus G1 Staphylococcus
phage MSA6 JX080304 Complete genomeStaphylococcus virus G1
Staphylococcus phage P4W JX080305 Complete genomeStaphylococcus
virus G1 Staphylococcus phage SA5 JX875065 Complete
genomeStaphylococcus virus G1 Staphylococcus phage Staph1N JX080300
Complete genomeStaphylococcus virus G1 Staphylococcus phage Team1
KC012913 Complete genome
★ Staphylococcus virus G15 Staphylococcus phage G15 JQ686190
NC_019448 Complete genome★ Staphylococcus virus JD7 Staphylococcus
phage JD007 JX878671 NC_019726 Complete genome★ Staphylococcus
virus K Staphylococcus phage K KF766114 NC_005880 Complete genome★
Staphylococcus virus MCE2014 Staphylococcus phage MCE-2014 KJ888149
NC_025416 Complete genome★ Staphylococcus virus P108 Staphylococcus
phage P108 KM216423 NC_025426 Complete genome★ Staphylococcus virus
Rodi Staphylococcus phage phiIPLA-RODI KP027446 NC_028765 Complete
genome★ Staphylococcus virus S253 Staphylococcus phage S25-3
AB853330 NC_022920 Complete genome★ Staphylococcus virus S25-4
Staphylococcus phage S25-4 AB853331 NC_022918 Complete genome★
Staphylococcus virus SA12 Staphylococcus phage phiSA12 AB903967
NC_023573 Complete genome★ Staphylococcus virus Sb1 Staphylococcus
phage Sb-1 HQ163896 NC_023009 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/AY954969https://www.ncbi.nlm.nih.gov/nuccore/NC_007066https://www.ncbi.nlm.nih.gov/nuccore/JX080302https://www.ncbi.nlm.nih.gov/nuccore/JX080301https://www.ncbi.nlm.nih.gov/nuccore/EU418428https://www.ncbi.nlm.nih.gov/nuccore/JX080303https://www.ncbi.nlm.nih.gov/nuccore/KP687431https://www.ncbi.nlm.nih.gov/nuccore/KR902361https://www.ncbi.nlm.nih.gov/nuccore/KR908644https://www.ncbi.nlm.nih.gov/nuccore/KP687432https://www.ncbi.nlm.nih.gov/nuccore/FR852584https://www.ncbi.nlm.nih.gov/nuccore/JX080304https://www.ncbi.nlm.nih.gov/nuccore/JX080305https://www.ncbi.nlm.nih.gov/nuccore/JX875065https://www.ncbi.nlm.nih.gov/nuccore/JX080300https://www.ncbi.nlm.nih.gov/nuccore/KC012913https://www.ncbi.nlm.nih.gov/nuccore/JQ686190https://www.ncbi.nlm.nih.gov/nuccore/NC_019448https://www.ncbi.nlm.nih.gov/nuccore/JX878671https://www.ncbi.nlm.nih.gov/nuccore/NC_019726https://www.ncbi.nlm.nih.gov/nuccore/KF766114https://www.ncbi.nlm.nih.gov/nuccore/NC_005880https://www.ncbi.nlm.nih.gov/nuccore/KJ888149https://www.ncbi.nlm.nih.gov/nuccore/NC_025416https://www.ncbi.nlm.nih.gov/nuccore/KM216423https://www.ncbi.nlm.nih.gov/nuccore/NC_025426https://www.ncbi.nlm.nih.gov/nuccore/KP027446https://www.ncbi.nlm.nih.gov/nuccore/NC_028765https://www.ncbi.nlm.nih.gov/nuccore/AB853330https://www.ncbi.nlm.nih.gov/nuccore/NC_022920https://www.ncbi.nlm.nih.gov/nuccore/AB853331https://www.ncbi.nlm.nih.gov/nuccore/NC_022918https://www.ncbi.nlm.nih.gov/nuccore/AB903967https://www.ncbi.nlm.nih.gov/nuccore/NC_023573https://www.ncbi.nlm.nih.gov/nuccore/HQ163896https://www.ncbi.nlm.nih.gov/nuccore/NC_023009
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Genus: Sciuriunavirus
Distinguishing features
Members of this genus infect Staphylococcus sciuri. The type
species is Staphylococcus virus SscM1. The genome of the exemplar
isolate of thetype species is 140 kbp, with a 202 predicted gene
coding sequences and no tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sciuri.
Derivation of names
Sciuriunavirus: derived from the species epithet of the host of
the type species exemplar and the second part of the exemplar
isolate name (Ssc-1).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virus SscM1 Staphylococcus phage vB_SscM-1
KX171212 NC_047767 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/KX171212https://www.ncbi.nlm.nih.gov/nuccore/NC_047767
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Genus: Sepunavirus
Distinguishing features
Members of this genus infect Staphylococcus sp. including S.
epidermis. The type species is Staphylococcus virus SEP1. The
genome of theexemplar isolate of the type species is 140 kbp, with
a total of 200 gene coding sequences and no tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sp. including S.
epidermis.
Derivation of names
Sepunavirus: derived from the name of the exemplar isolate,
Staphylococcus phage phiIBB-SEP1, of the type species (i.e. sep
followed by una,meaning one).
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virus IPLAC1C Staphylococcus phage vB_SepM_
phiIPLA-C1C KP027447 NC_028962 Complete genome★ Staphylococcus
virus SEP1 Staphylococcus phage phiIBB-SEP1 KF021268 NC_041928
Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/KP027447https://www.ncbi.nlm.nih.gov/nuccore/NC_028962https://www.ncbi.nlm.nih.gov/nuccore/KF021268https://www.ncbi.nlm.nih.gov/nuccore/NC_041928
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Genus: Silviavirus
Distinguishing features
Members of this genus infect Staphylococcus sp. mainly S.
aureus. The type species is Staphylococcus virus Remus. The genome
of theexemplar isolate of the type species is 135 kbp, with a total
of 174 gene coding sequences as well as 1 encoded tRNA.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sp. mainly S.
aureus.
Derivation of names
Silviavirus: indirectly derived from the exemplar isolate,
Staphylococcus phage Remus, of the type species. In Roman
mythology, Silvia was themother of Romulus and Remus, after which
two phage strains belonging to the type species were named.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virus Remus Staphylococcus phage vB_SauM_Remus
JX846612 NC_022090 Complete genomeStaphylococcus virus Remus
Staphylococcus phage vB_SauM_Romulus JX846613 Complete genome
★ Staphylococcus virus SA11 Staphylococcus phage SA11 JX194239
NC_019511 Complete genome★ Staphylococcus virus Stau2
Staphylococcus phage Stau2 KP881332 NC_030933 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/JX846612https://www.ncbi.nlm.nih.gov/nuccore/NC_022090https://www.ncbi.nlm.nih.gov/nuccore/JX846613https://www.ncbi.nlm.nih.gov/nuccore/JX194239https://www.ncbi.nlm.nih.gov/nuccore/NC_019511https://www.ncbi.nlm.nih.gov/nuccore/KP881332https://www.ncbi.nlm.nih.gov/nuccore/NC_030933
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Genus: Twortvirus
Distinguishing features
Members of this genus infect Staphylococcus sp. The type species
is Staphylococcus virus Twort. The genome of the exemplar isolate
of the typespecies is 130 kbp, with a total of 195 gene coding
sequences and no tRNAs.
Virion
See discussion under family description.
Genome organisation and replication
See discussion under family description.
Biology
Members of the genus infect Staphylococcus sp.
Derivation of names
Twortvirus: derived from the name of the exemplar isolate,
Staphylococcus phage Twort, of the type species, itself named after
Frederick WilliamTwort (1877–1950), the English bacteriologist who
discovered prokaryotic viruses in 1915.
Species demarcation criteria
Members of the same species are more than 95% identical in
genome nucleotide sequence, including the terminal repeat region.
Phages withgenomes that differ by more than 5% are assigned to
different species.
Member species
★ Exemplar isolate of the speciesSpecies Virus name Isolate
Accession number RefSeq number Available sequence Virus Abbrev.
★ Staphylococcus virusTwortStaphylococcus phageTwort AY954970
NC_007021 Complete genome
Virus names, the choice of exemplar isolates, and virus
abbreviations, are not official ICTV designations.
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https://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Virionhttps://talk.ictvonline.org/ictv-reports/ictv_online_report/dsdna-viruses/w/herelleviridae#Genomehttps://www.ncbi.nlm.nih.gov/nuccore/AY954970https://www.ncbi.nlm.nih.gov/nuccore/NC_007021
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Authors: Herelleviridae
Jakub Barylski Bacillus phage Study Group Chair Department of
Molecular Virology Institute of Experimental Biology Faculty of
Biology Adam Mickiewicz University in Poznan Collegium Biologicum -
Umultowska 89 61-614 Poznan Poland E-mail:
[email protected]
Andrew M. Kropinski Department of Pathobiology University of
Guelph 50 Stone Road E Guelph Ontario N1G 2W1 Canada Tel: +1 519
780-0877 E-mail: [email protected]
Nabil-Fareed Alikhan Quadram Institute Bioscience Norwich
Research Park Norwich NR4 7UQ UK Tel: +44 01603255000 E-mail:
[email protected]
Evelien M. Adriaenssens* Chair Caudovirales Study Group Quadram
Institute Bioscience Norwich Research Park Norwich NR4 7UQ UK Tel:
+44 01603255000 E-mail: [email protected]
* to whom correspondence should be addressed
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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Resources: Herelleviridae
A detailed analysis phylogenetic and phylogenomic relationships
among members of the family Herelleviridae is published in
(Barylski et al.,2020), for which supplementary data can be found
in the Dryad repository https://doi.org/10.5061/dryad.106q6g6.
Sequence alignments and tree files:
Figure 3.Herelleviridae
Tree file (newick format)
Alignment file (FASTA format)
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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https://www.ncbi.nlm.nih.gov/pubmed/31127947https://doi.org/10.5061/dryad.106q6g6https://talk.ictvonline.org/cfs-file/__key/communityserver-wikis-components-files/00-00-00-01-44/ODD.Herelle.Fig3.v4.treefile.nwk.txthttps://talk.ictvonline.org/cfs-file/__key/communityserver-wikis-components-files/00-00-00-01-44/ODD.Herelle.Fig3.v4.alignment.fst
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Further reading: Herelleviridae
Asare, P. T., T. Y. Jeong, S. Ryu, J. Klumpp, M. J. Loessner, B.
D. Merrill and K. P. Kim (2015). Putative type 1 thymidylate
synthase anddihydrofolate reductase as signature genes of a novel
Bastille-like group of phages in the subfamily Spounavirinae. BMC
Genomics 16: 582.[PubMed]
Barylski, J., G. Nowicki and A. Goździcka-Józefiak (2014) . The
discovery of phiAGATE, a novel phage infecting Bacillus pumilus,
leads to newinsights into the phylogeny of the subfamily
Spounavirinae. PLoS One 9: e86632. [PubMed]
Klumpp, J., M. Schmuki, S. Sozhamannan, W. Beyer, D. E. Fouts,
V. Bernbach, R. Calendar and M. J. Loessner (2014). The odd one
out:Bacillus ACT bacteriophage CP-51 exhibits unusual properties
compared to related Spounavirinae W.Ph. and Bastille. Virology
462-463: 299-308.[PubMed]
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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https://www.ncbi.nlm.nih.gov/pubmed/26250905https://www.ncbi.nlm.nih.gov/pubmed/24466180https://www.ncbi.nlm.nih.gov/pubmed/25010479
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References: Herelleviridae
Alikhan, N. F., N. K. Petty, N. L. Ben Zakour and S. A. Beatson
(2011). BLAST Ring Image Generator (BRIG): simple prokaryote
genomecomparisons. BMC Genomics 12: 402. [PubMed]
Barylski, J., F. Enault, B. E. Dutilh, M. B. P. Schuller, R. A.
Edwards, A. Gillis, J. Klumpp, P. Knezevic, M. Krupovic, J. H.
Kuhn, R. Lavigne,H. M. Oksanen, M. B. Sullivan, H. B. Jang, P.
Simmonds, P. Aiewsakun, J. Wittmann, I. Tolstoy, J. R. Brister, A.
M. Kropinski and E. M.Adriaenssens (2020). Analysis of
spounaviruses as a case study for the overdue reclassification of
tailed phages. Syst. Biol. [PubMed]
Goodrich-Blair, H., V. Scarlato, J. M. Gott, M. Q. Xu and D. A.
Shub (1990). A self-splicing group I intron in the DNA polymerase
gene ofBacillus subtilis bacteriophage SPO1. Cell 63: 417-424.
[PubMed]
Klumpp, J., J. Dorscht, R. Lurz, R. Bielmann, M. Wieland, M.
Zimmer, R. Calendar and M. J. Loessner (2008). The terminally
redundant,nonpermuted genome of Listeria bacteriophage A511: a
model for the SPO1-like myoviruses of gram-positive bacteria. J.
Bacteriol. 190: 5753-5765. [PubMed]
Klumpp, J., R. Lavigne, M. J. Loessner and H. W. Ackermann
(2010). The SPO1-related bacteriophages. Arch. Virol. 155:
1547-1561.[PubMed]
Lavigne, R. and K. Vandersteegen (2013). Group I introns in
Staphylococcus bacteriophages. Future Virology 8: 997–1005.
[PMID
Łobocka, M. and W. T. Szybalski (2012). Phages (Preface). Adv.
Virus Res. 83: xvii-xviii. [PubMed]
Okubo, S., T. Yanagida, D. J. Fujita and B. M. Olsson-Wilhelm
(1972). The genetics of bacteriophage SPO1. Biken journal 15:
81-97.[PubMed]
Parker, M. L. and F. A. Eiserling (1983). Bacteriophage SPO1
structure and morphogenesis. III. SPO1 proteins and synthesis. J.
Virol. 46: 260-269. [PubMed]
Perkus, M. E. and D. A. Shub (1985). Mapping the genes in the
terminal redundancy of bacteriophage SPO1 with restriction
endonucleases. J.Virol. 56: 40-48. [PubMed]
Schuch, R. and V. A. Fischetti (2009). The secret life of the
anthrax agent Bacillus anthracis: bacteriophage-mediated ecological
adaptations.PLoS One 4: e6532. [PubMed]
Stewart, C. R., S. R. Casjens, S. G. Cresawn, J. M. Houtz, A. L.
Smith, M. E. Ford, C. L. Peebles, G. F. Hatfull, R. W. Hendrix, W.
M. Huangand M. L. Pedulla (2009). The genome of Bacillus subtilis
bacteriophage SPO1. J. Mol. Biol. 388: 48-70. [PubMed]
Yuan, Y., Q. Peng, D. Wu, Z. Kou, Y. Wu, P. Liu and M. Gao
(2015). Effects of actin-like proteins encoded by two Bacillus
pumilus phages onunstable lysogeny, revealed by genomic analysis.
Appl. Environ. Microbiol. 81: 339-350. [PubMed]
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
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https://www.ncbi.nlm.nih.gov/pubmed/21824423https://www.ncbi.nlm.nih.gov/pubmed/31127947https://www.ncbi.nlm.nih.gov/pubmed/2119891https://www.ncbi.nlm.nih.gov/pubmed/18567664https://www.ncbi.nlm.nih.gov/pubmed/20714761https://www.ncbi.nlm.nih.gov/pubmed/22748816https://www.ncbi.nlm.nih.gov/pubmed/4628367https://www.ncbi.nlm.nih.gov/pubmed/6827651https://www.ncbi.nlm.nih.gov/pubmed/3928902https://www.ncbi.nlm.nih.gov/pubmed/19672290https://www.ncbi.nlm.nih.gov/pubmed/19285085https://www.ncbi.nlm.nih.gov/pubmed/25344242
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Citation: Herelleviridae
A summary of this ICTV Report chapter has been published as an
ICTV Virus Taxonomy Profile article in the Journal of General
Virology, andshould be cited when referencing this online chapter
as follows:
Jakub Barylski, Andrew M. Kropinski, Nabil-Fareed Alikhan,
Evelien M. Adriaenssens and ICTV Report Consortium. 2020, ICTV
Virus TaxonomyProfile: Herelleviridae, Journal of General Virology,
101:362–363
Funding support
Support for the preparation of this ICTV Report chapter and
associated Journal of General Virology taxonomy profile, was funded
by a grant fromthe Wellcome Trust (WT108418AIA).
InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global
www.ictv.global/report/herelleviridae 35
https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001392https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001392
Virus Taxonomy The ICTV Report on Virus Classification and Taxon
Nomenclature Herelleviridae
ChapterHerelleviridaeSummaryVirionMorphologyPhysicochemical and
physical propertiesNucleic acidProteinsLipidsCarbohydrates
Genome organization and replication* at a 50% amino acid
sequence identity threshold at minimum 50% gene coverage or by
prokaryotic Virus Orthologous Group (pVOG) analysis (Barylski et
al., 2020)
BiologyDerivation of namesSubfamily demarcation criteria*ND Not
Determined for all members
Genus demarcation criteriaSpecies demarcation
criteriaRelationships within the familyRelationships with other
taxaSpecies unassigned to a subfamilyVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Member taxa
Subfamily: BastillevirinaeDistinguishing featuresDerivation of
namesGenus demarcation criteriaSpecies unassigned to a genusVirus
names, the choice of exemplar isolates, and virus abbreviations,
are not official ICTV designations.
Member taxa
Genus: AgatevirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: BastillevirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: BequatrovirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: CaeruleovirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: NitunavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: TsarbombavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: WphvirusDistinguishing featuresVirionGenome organisation
and replicationBiologyDerivation of namesSpecies demarcation
criteriaMember speciesVirus names, the choice of exemplar isolates,
and virus abbreviations, are not official ICTV designations.
Subfamily: BrockvirinaeDistinguishing featuresDerivation of
namesGenus demarcation criteriaMember taxa
Genus: KochikohdavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: SchiekvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Subfamily: JasinkavirinaeDistinguishing featuresDerivation of
namesGenus demarcation criteriaMember taxa
Genus: PecentumvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Subfamily: SpounavirinaeDistinguishing featuresDerivation of
namesGenus demarcation criteriaMember taxa
Genus: OkubovirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: SiminovitchvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Subfamily: TwortvirinaeDistinguishing featuresDerivation of
namesGenus demarcation criteriaMember taxa
Genus: BaoshanvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: HarbinvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: KayvirusDistinguishing featuresVirionGenome organisation
and replicationBiologyDerivation of namesSpecies demarcation
criteriaMember speciesVirus names, the choice of exemplar isolates,
and virus abbreviations, are not official ICTV designations.
Genus: SciuriunavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: SepunavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: SilviavirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Genus: TwortvirusDistinguishing featuresVirionGenome
organisation and replicationBiologyDerivation of namesSpecies
demarcation criteriaMember speciesVirus names, the choice of
exemplar isolates, and virus abbreviations, are not official ICTV
designations.
Authors: HerelleviridaeResources: HerelleviridaeSequence
alignments and tree files:Figure 3.Herelleviridae
Further reading: HerelleviridaeReferences:
HerelleviridaeCitation: HerelleviridaeFunding support