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Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

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Archives of Virology
https://doi.org/10.1007/s00705-018-3723-z
VIROLOGY DIVISION NEWS
Taxonomy ofprokaryotic viruses: 2017 update fromtheICTV Bacterial
andArchaeal Viruses Subcommittee
EvelienM.Adriaenssens1 · JohannesWittmann2 · JensH.Kuhn3 · DannTurner4 · MatthewB.Sullivan5 ·
BasE.Dutilh6,7 · HoBinJang5· LeonardoJ.vanZyl8 · JochenKlumpp9 · MalgorzataLobocka10 ·
AndreaI.MorenoSwitt11 · JanisRumnieks12· RobertA.Edwards13 · JumpeiUchiyama14 ·
PolianeAlfenas‑Zerbini15 · NicolaK.Petty16 · AndrewM.Kropinski17 · JakubBarylski18 · AnnikaGillis19 ·
MarthaR.C.Clokie20 · DavidPrangishvili21 · RobLavigne22 · RamyKaramAziz23 · SiobainDuy24 ·
MartKrupovic21 · MinnaM.Poranen25 · PetarKnezevic26 · FrancoisEnault27 · YigangTong28 ·
HannaM.Oksanen25 · J.RodneyBrister29
Received: 1 December 2017 / Accepted: 15 January 2018
© Springer-Verlag GmbH Austria, part of Springer Nature 2018
The prokaryotic virus community is represented at the Inter-
national Committee on Taxonomy of Viruses (ICTV) by the
Bacterial and Archaeal Viruses Subcommittee. Since our
last report [5], the committee composition has changed,
and a large number of taxonomic proposals (TaxoProps)
were submitted to the ICTV Executive Committee (EC) for
approval.
1. Changes in subcommittee membership. During the
past year we have lost two members. Dr. Hans-Wolfgang
Ackermann, a life member of the ICTV, the father of cau-
dovirus taxonomy [1] and an electron microscopist extraor-
dinaire [24], lamentably died and will be gravely missed.
In addition, Dr. Jens H. Kuhn, who, in spite of protestations
about not being a genuine phage biologist, proved invaluable
Handling Editor: Sead Sabanadzovic.
Electronic supplementary material The online version of this
article (http s://doi.org/10.1007 /s007 05-018-3723 -z) contains
supplementary material, which is available to authorized users.
* Andrew M. Kropinski
Phage.Canada@gmail.com
1 Institute ofIntegrative Biology, University ofLiverpool,
LiverpoolL697ZB, UnitedKingdom
2 Leibniz-Institut DSMZ-Deutsche Sammlung
von Mikroorganismen und Zellkulturen GmbH,
38124Braunschweig, Germany
3 Integrated Research Facility atFort Detrick, National
Institute ofAllergy andInfectious Diseases, National
Institutes ofHealth, Fort Detrick, Frederick, MD21702,
USA
4 Faculty ofHealth andApplied Sciences, UWE Bristol,
Frenchay Campus, BristolBS161QY, UnitedKingdom
5 Department ofMicrobiology, The Ohio State University,
Columbus, OH43210, USA
6 Theoretical Biology andBioinformatics, Utrecht University,
Utrecht, TheNetherlands
7 Centre forMolecular andBiomolecular Informatics,
Radboud University Medical Centre, Nijmegen,
TheNetherlands
8 Department ofBiotechnology, Institute forMicrobial
Biotechnology andMetagenomics (IMBM), University
oftheWestern Cape, Bellville, Cape Town, 7535,
SouthAfrica
9 Institute ofFood, Nutrition andHealth, ETH Zurich,
8092Zurich, Switzerland
10 Department ofMicrobial Biochemistry, Institute
ofBiochemistry andBiophysics ofthePolish Academy
ofSciences, 02-106, Warsaw, Poland
11 Faculty ofEcology andNatural Resources School,
Universidad Andres Bello, 8370146Santiago, Chile
12 Latvian Biomedical Research andStudy Center,
RigaLV-1067, Latvia
13 Departments ofComputer Science andBiology, San Diego
State University, SanDiego, CA92182, USA
E. M. Adriaenssens etal.
1 3
to our discussions and preparation of TaxoProps and manu-
scripts, resigned from the Subcommittee. Both Hans and
Jens are acknowledged for their significant contributions
to prokaryotic virus taxonomy. Furthermore, a number
of current members have new responsibilities; and, in an
effort to increase the geographical diversity of members,
we appointed representatives from South America, Africa,
and Asia (Table1).
2. Changing the names of prokaryotic virus genera. A
significant number of prokaryotic virus genera have either
unpronounceable names (e.g., Pocjvirus, Rdjlvirus) or incor-
porated numerals (e.g., T4virus, D3112virus). In the first
case, these names contravene The International Code of
Virus Classification and Nomenclature (ICVCN, April 2017)
Rule 3.12, which states “Names for taxa shall be easy to use
and easy to remember. Euphonious names are preferred.”
In the latter case, pronunciation is a problem. For example,
is D3112virus pronounced “Dee+three thousand one hun-
dred and twelve+virus” or “Dee+thirty one+twelve+virus”
or “Dee+three+one+one+two+virus”? In addition, this
nomenclature differs drastically from that for other virus
taxa; and, would be incompatible with a Linnaean system
of nomenclature [13]. We identified all prokaryotic taxon
names that are problematic in the ICTV Master Species
List (http s://talk .ictv onli ne.org/file s/mast er-spec ies-list s/m/
msl/6776 ) and suggested alternative names (Supplementary
data file S1). These changes will be proposed officially at the
next meeting of the ICTV EC in 2018.
3. Re-evaluation of the SPO1-like virus taxonomy.
Over the past two years, members of the subcommittee have
re-evaluated the taxonomy of a subset of myoviruses related
to Bacillus phage SPO1. This group, made up of members
of the subfamily Spounavirinae [10] and several genera of
Bacillus-infecting viruses, was represented as a distinct
Table 1 List of current
subcommittee members who
have new responsibilities (*),
along with new members of the
subcommittee
Name Country Position
Evelien Adriaenssens* United Kingdom Chair, Caudovirales phage study group
Dann Turner United Kingdom Chair, Acinetobacter phage study group
Jakub Barylski* Poland Chair, Bacillus phage study group
Jochen Klumpp* Switzerland Chair, Listeria phage study group
Małgorzata Łobocka Poland Chair, Staphylococcus phage study group
Poliane Alfenas-Zerbini Brazil Member
Ramy Aziz Egypt Member
Andrea Moreno Switt Chile Member
Yigang Tong People’s Republic of China Member
Leonardo van Zyl South Africa Member
Jumpei Uchiyama Japan Member
Nicola K. Petty Australia Member
14 School ofVeterinary Medicine, Azabu University, Fuchinobe
1-7-71, Chuo-ku Sagamihara-shi, Kanagawa252-0206, Japan
15 Laboratory ofIndustrial Microbiology,Instituto de
Biotecnologia Aplicada à Agropecuária, Universidade
Federal de Viçosa, Viçosa, MinasGerais, Brazil
16 The ithree institute, University ofTechnology Sydney,
Sydney, NSW2007, Australia
17 Departments ofFood Science, andPathobiology, University
ofGuelph, 50 Stone Rd E, Guelph, ONN1G2W1, Canada
18 Department ofMolecular Virology, Institute ofExperimental
Biology, Adam Mickiewicz University, Poznan, Poland
19 Laboratory ofFood andEnvironmental Microbiology,
Université Catholique de Louvain, 1348Louvain-la-Neuve,
Belgium
20 Department ofInfection, Immunity andInflammation,
University ofLeicester, LeicesterLE19HN, UnitedKingdom
21 Unit ofMolecular Biology oftheGene inExtremophiles,
Department ofMicrobiology, Institut Pasteur, 75015Paris,
France
22 Laboratory ofGene Technology, KU Leuven, 3001Leuven,
Belgium
23 Department ofMicrobiology andImmunology, Faculty
ofPharmacy, Cairo University, Qasr El-Ainy St,
11562Cairo, Egypt
24 Department ofEcology, Evolution andNatural Resources,
Rutgers University, NewBrunswick, NJ08901, USA
25 Department ofBiosciences, University ofHelsinki, Helsinki,
Finland
26 Department ofBiology andEcology, Faculty ofSciences,
University ofNovi Sad, NoviSad, Serbia
27 Université Clermont Auvergne, CNRS, LMGE,
63000Clermont-Ferrand, France
28 Beijing Institute ofMicrobiology andEpidemiology, State
Key Laboratory ofPathogen andBiosecurity, Beijing,
People’sRepublicofChina
29 National Center forBiotechnology Information, National
Library ofMedicine, National Institutes ofHealth, Bethesda,
MD20894, USA
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
1 3
Table 2 Taxonomy proposals (TaxoProps) proposing new taxa (families, subfamilies, genera, species) submitted to the ICTV Executive Com-
mittee in 2017
*taxon established, **previously known as Tectivirus, ***Number in parenthesis indicates the total number of viral species in this genus
Family Subfamily Genus Type species No. of species
in genus***
Ackermannviridae Aglimvirinae Ag3virus Shigella virus AG3 1 (2)
Ackermannviridae Aglimvirinae Limestonevirus Dickeya virus Limestone 1 (2)
Ackermannviridae Cvivirinae Cba120virus Escherichia virus CBA120 4 (9)
Ackermannviridae Cvivirinae Vi1virus* Salmonella virus ViI (5)
Ackermannviridae unassigned unassigned Erwinia virus Ea2809, Serratia virus MAM1, Ser-
ratia virus IME250, Klebsiella virus 0507KN21 4
Myoviridae* Arvunavirus Arthrobacter virus ArV1 2
Myoviridae* Eah2virus Erwinia virus EaH2 2
Myoviridae* Machinavirus Erwinia virus Machina 1
Myoviridae* Ntreusvirus Salmonella virus SPN3US 1
Myoviridae* Svunavirus Geobacillus virus GBSV1 2
Myoviridae* Ampvirinae Chippewavirus Arthrobacter virus BarretLemon 1
Myoviridae* Ampvirinae Jawnskivirus Arthrobacter virus Jawnski 2
Myoviridae* Ampvirinae Sonnyvirus Arthrobacter virus Sonny 3
Podoviridae* Dfl12virus Dinoroseobacter virus DFL12phi1 1
Podoviridae* Jwalphavirus Achromobacter virus JWAlpha 2
Podoviridae* P22virus* Salmonella virus P22 1 (5)
Podoviridae* Sp58virus Salmonella virus SP058 3
Portogloboviridae Alphaportoglobovirus Sulfolobus alphaportoglobovirus 1 1
Siphoviridae* Anatolevirus Propionibacterium virus Anatole 2
Siphoviridae* Attisvirus Gordonia virus Attis 1
Siphoviridae* Doucettevirus Propionibacterium virus Doucette 4
Siphoviridae* Hk97virus Escherichia virus HK97* 9 (11)
Siphoviridae* Lambdavirus* Escherichia virus Lambda 3 (4)
Siphoviridae* Pfr1virus Propionibacterium virus PFR1 1
Siphoviridae* Tp84virus Geobacillus virus TP84 1
Siphoviridae* Trigintaduovirus Mycobacterium virus 32HC 1
Siphoviridae* Wizardvirus Gordonia virus Wizard 2
Siphoviridae* Chebruvirinae Brujitavirus Mycobacterium virus Brujita (2)
Siphoviridae* Chebruvirinae Che9cvirus* Mycobacterium virus Che9c 1 (2)
Siphoviridae* Dclasvirinae Hawkeyevirus Mycobacterium virus Hawkeye 1
Siphoviridae* Dclasvirinae Plotvirus Mycobacterium virus PLot 1
Siphoviridae* Mccleskeyvirinae Lmd1virus Leuconostoc virus Lmd1 6
Siphoviridae* Mccleskeyvirinae Una4virus Leuconostoc virus 1A4 6
Siphoviridae* Nclasvirinae Buttersvirus Mycobacterium virus Butters 2
Siphoviridae* Nclasvirinae Charlievirus Mycobacterium virus Charlie 2 (3)
Siphoviridae* Nclasvirinae Redivirus Mycobacterium virus Redi 3 (4)
Siphoviridae* Nymbaxtervirinae Baxtervirus Gordonia virus BaxterFox 2
Siphoviridae* Nymbaxtervirinae Nymphadoravirus Gordonia virus Nymphadora 3
Cystoviridae* Cystovirus* Pseudomonas virus phi6 6 (7)
Tectiviridae* Alphatectivirus** Pseudomonas virus PRD1 1 (2)
Tectiviridae* Betatectivirus Bacillus virus Bam35 2 (4)
E. M. Adriaenssens etal.
1 3
module in various network analyses published recently [8,
9]. Using a combination of genomic, proteomics, and phylo-
genetic approaches, we have shown that this group of phages
represents a new family, comprising five subfamilies and 13
genera [7]. We therefore suggest that these viruses be moved
from their current taxonomic position in the family Myo-
viridae to a new family included in the order Caudovirales.
4. New taxa. Table2 lists of all new taxa proposed at the
ICTV EC49 meeting in Singapore in 2017. In total, two new
families, eight new subfamilies, 34 new genera, and 91 new
species were proposed. Two significant items are on this
list. The first item is the introduction of two new families of
prokaryotic viruses: Ackermannviridae and Portogloboviri-
dae. With the acceptance of changes to ICVCN Rule 3.11,
the second item is the application of the names of eminent
phage scientists, specifically Hans-Wolfgang Ackermann
(Université Laval) and Charles Shelton McCleskey (Loui-
siana State University) as prefixes for taxon name stems.
5. Updates to taxonomy. As the readership may be
aware, “Virus Taxonomy: The Classification and Nomen-
clature of Viruses - The Online (10th) Report of the ICTV”
is freely accessible at http ://ictv .glob al/repo rt. We would like
to acknowledge the hard work of Hanna M. Oksanen (Corti-
coviridae), Dennis H. Bamford (Pleolipoviridae), and Minna
M. Poranen (Cystoviridae) for completing updates to their
sections. The family Pleolipoviridae is now recognized as
the first virus taxon in the newly established ICTV category
for ssDNA/dsDNA Viruses. The summaries of the ICTV
Report chapters are published in The Journal of General
Virology [6, 11, 12].
Acknowledgements The committee would like to thank Dr. Gra-
ham Hatfull (University of Pittsburgh) for permitting us to use Act-
inobacteriophage Database electron micrographs in 2017’s taxonomy
proposals. The authors thank Laura Bollinger (National Institutes of
Health/National Institute of Allergy and Infectious Diseases, Integrated
Research Facility at Fort Detrick, Frederick, MD, USA) for editing
this paper.
Compliance with ethical standards
The views and conclusions contained in this document are those of the
authors and should not be interpreted as necessarily representing the
official policies, either expressed or implied, of the US Department
of Health and Human Services or of the institutions and companies
affiliated with the authors.
Funding This work was funded in part through Battelle Memorial
Institute’s prime contract with the US National Institute of Allergy and
Infectious Diseases (NIAID) under Contract No. HHSN272200700016I
(J.H.K.). B.E.D. was supported by the Netherlands Organization for
Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was sup-
ported by grant MCB-1330800 from the National Science Founda-
tion. J.R.B. was supported by the Intramural Research Program of
the National Institutes of Health, National Library of Medicine. R.L.
is a member of the phagebiotics research community, supported by
FWO Vlaanderen. M.M.P. was supported by the Academy of Finland
(272507). A.G. was supported by the National Fund for Scientific
Research (FNRS). H.M.O. was supported by University of Helsinki
funding for Instruct-F1 research infrastructure.
Conflict of interest The authors declare that they have no conflict of
interest.
Ethical approval The authors did not perform any studies with human
participants or animals in this article.
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... Members of the B. cereus group are known to be associated with many species-specific temperate (lysogenic) phages, either integrated into their chromosome or as independently replicating linear or circular elements (also known as plasmidial prophages) [5]. To date, temperate phages residing as linear plasmids in the B. cereus group have been identified as belonging to the genus Betatectivirus within the family Tectiviridae [4,[10][11][12]. Betatectiviruses are also closely related to the cryptic linear plasmid pBClin15 of B. cereus type strain ATCC 14579 [13]. ...
... The taxonomical placement of phages Sato and Sole was further investigated taken into account genome organization and sequence identity comparisons (Figure 3 and Figure S1), in combination with phylogenetic analyses (Figure 4), the latter ones including phages belonging to the five currently accepted genera within the family Tectiviridae: Alphatectivirus, Betatectivirus, Gammatectivirus, Deltatectivirus, and Epsilontectivirus [12,24,57,58]. Maximum likelihood assessments with aligned sequences of the three canonical tectiviral proteins (i.e., DNAPolB, packaging ATPase and major capsid protein) showed that Sato and Sole clustered together with phages belonging to the genus Betatectivirus (Figure 4a-c). ...
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Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations to covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. Importance Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome.
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