Abstract
The realm Duplodnaviria includes viruses of archaea, bacteria and eukaryotes, with linear dsDNA genomes. Duplodnavirians share a distinct morphogenetic module of four hallmark genes encoding the HK97-fold major capsid protein, a genome packaging ATPase-nuclease (large terminase subunit), a portal protein and a capsid maturation protease. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the realm Duplodnaviria, which is available at ictv.global/report/duplodnaviria.
Keywords: Caudoviricetes, double-stranded DNA viruses, Duplodnaviria, Herviviricetes, HK97-fold major capsid protein, ICTV Report, Peploviricota, Uroviricota, Virus Taxonomy
| Table 1 Characteristics of members of the realm Duplodnaviria | |
| Examples | Escherichia phage T4 (AF158101), species Tequatrovirus T4; Haloferax tailed virus 1 (MG550112), species Retbasiphovirus hantatum; pseudorabies virus (JF797218), species Varicellovirus suidalpha1 |
| Virion | Icosahedral capsids, with or without an envelope, with (bacterial and archaeal viruses) or without (eukaryotic viruses) helical tails |
| Genome | A single linear segment of dsDNA of 11.6–660 kbp. Reiterated sequences are common. Terminase-type DNA packaging. Modular and scattered gene organization |
| Replication | Rolling concatemeric, replicative transposition or protein-primed DNA replication using virus- or host-encoded enzymes. DNA-templated transcription by host- or virus-encoded RNA polymerase may be temporally co-ordinated. |
| Translation | Some mRNAs are spliced |
| Host range | Bacteria, archaea, eukaryotes |
| Taxonomy | The realm includes 1 kingdom, 2 phyla, 2 classes, >10 orders, >100 families, >130 subfamilies, >1700 genera and >5900 species |
Virion
Particles of viruses of the class Herviviricetes (phylum Peploviricota, eukaryotic hosts) are 150–200 nm in diameter and are pleomorphic, mostly spherical, with a glycoprotein-containing lipid envelope that encloses a tegument and an icosahedral capsid.
Particles of viruses of the class Caudoviricetes (phylum Uroviricota, bacterial or archaeal hosts) are head-tailed and do not have an envelope[1,2]. The head is icosahedral and may be isometric or prolate (head diameter 40–200 nm). The tail is typically 10–350 nm in length but can be around 800 nm in some bacterial viruses [3].
The protein composition of mature particles varies greatly among viruses of different families. Only herviviricete particles contain lipids. Carbohydrates have been reported for herviviricete virions [4] and certain caudoviricetes infecting mycobacteria [5].
Genome
All duplodnavirians have linear dsDNA genomes when packaged in the particle. Genome lengths are 108.4–322.3 kbp for herviviricetes and 11.6–>660 kbp for caudoviricetes. Depending on the replication and packaging mechanisms, genomes can have defined termini with reiterated sequences (direct or inverted repeats), cohesive 3′- or 5′-overhangs, or circularly permuted genome architectures [6]. Genes with associated functions are typically clustered, with conserved, essential genes localized internally/centrally in the genome; scattered gene arrangements also occur.
Replication
Duplodnavirians with longer genomes usually encode their own DNA polymerases [7]. Herpesvirals uniformly encode family B DNA polymerases and several other replication proteins, suggesting semiautonomous genome replication [7]. Caudoviricetes can encode DNA polymerases of families A, B (both RNA- and protein-primed) and C [8]. Transposable phages (e.g. coliphage Mu, species Muvirus mu) use a different replication mechanism called replicative transposition, during which the viral genome is copied at various sites of the bacterial chromosome before transcription of structural proteins and packaging.
Taxonomy
Current taxonomy: ictv.global/taxonomy. The realm Duplodnaviria was established in 2020 (Master Species List #35) (Fig. 1). Members have a dsDNA genome encoding a morphogenetic module consisting of the major capsid protein with the HK97 structural fold, a portal protein, the terminase complex and a capsid maturation protease. The module is distinct from that encoded by other known dsDNA viruses, including those in the realm Varidnaviria.
Fig. 1. Current taxonomy of the realm Duplodnaviria.
Resources
Full ICTV Report on the realm Duplodnaviria: ictv.global/report/duplodnaviria.
Acknowledgements
We thank ICTV Report Editors and Donald B. Smith (Managing Editor, ICTV Report).
Footnotes
Funding: Production of this Profile, the ICTV Report and associated resources was supported by the Microbiology Society. E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Microbes and Food Safety BB/X011011/1 and its constituent projects BBS/E/F/000PR13634, BBS/E/F/000PR13635 and BBS/E/F/000PR13636, and by the BBSRC Institute Strategic Programme Food Microbiome and Health BB/X011054/1 and its constituent projects BBS/E/F/000PR13631 and BBS/E/F/000PR13633. E.M.A. and R.C. were funded by the BBSRC grant Bacteriophages for gut health BB/W015706/1. C.L is funded by the UKRI (EP/Y029585/1). E.V.K., Y.I.W and N.Y. are supported by intramural funds of the US Department of Health and Human Services (National Institutes of Health). P.K.V. was funded by a University of Melbourne Postdoctoral Fellowship. This work was supported in part through a Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. 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 U.S. Department of Health and Human Services or of the institutions and companies affiliated with the authors.
Contributor Information
Evelien M. Adriaenssens, Email: Evelien.Adriaenssens@quadram.ac.uk.
Ryan Cook, Email: ryan.cook@quadram.ac.uk.
Valerian Dolja, Email: Valerian.Dolja@oregonstate.edu.
Eugene V. Koonin, Email: koonin@ncbi.nlm.nih.gov.
Mart Krupovic, Email: mart.krupovic@pasteur.fr.
Jens H. Kuhn, Email: jenshkuhn@comcast.net.
Cédric Lood, Email: cedric.lood@biology.ox.ac.uk.
Alejandro Reyes Muñoz, Email: a.reyes@uniandes.edu.co.
Dann Turner, Email: dann2.turner@uwe.ac.uk.
Arvind Varsani, Email: Arvind.Varsani@asu.edu.
Paola K. Vaz, Email: pvaz@unimelb.edu.au.
Thomas Waltzek, Email: thomas.waltzek@wsu.edu.
Yuri I. Wolf, Email: wolf@ncbi.nlm.nih.gov.
Natalya Yutin, Email: yutin@ncbi.nlm.nih.gov.
F. Murilo Zerbini, Email: zerbini@ufv.br.
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