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Archives of Virology

, Volume 161, Issue 9, pp 2633–2643 | Cite as

Genomoviridae: a new family of widespread single-stranded DNA viruses

  • Mart Krupovic
  • Said A. Ghabrial
  • Daohong Jiang
  • Arvind Varsani
Virology Division News

Abstract

Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that was created recently by the International Committee on Taxonomy of Viruses (ICTV). The family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.

Keywords

Capsid Protein Monophyletic Clade Fungal Virus Replication Initiation Protein ssDNA Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Viruses with single-stranded DNA (ssDNA) genomes infect hosts in all three domains of life and include economically, medically, and environmentally important viral pathogens. Until recently, ssDNA viruses were classified into 10 different taxa—nine families and one genus not assigned to a family [14, 15]. In 2016, the International Committee on Taxonomy of Viruses (ICTV) created two new families for classification of ssDNA viruses, Pleolipoviridae and Genomoviridae [1]. The family Pleolipoviridae includes viruses infecting hyperhalophilic archaea, and it has recently been described elsewhere [25]. Here, we introduce the family Genomoviridae and provide a short overview of the properties of Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), the only cultivated member of the new family, and putative SsHADV-1-like viruses.

SsHADV-1 is the first—and thus far the only—ssDNA virus known to infect fungi (all other fungal viruses have RNA genomes) [10, 33]. SsHADV-1 was isolated from a plant-pathogenic fungus, Sclerotinia sclerotiorum [34]. Another unique property of SsHADV-1 that has not been described for other fungal viruses is its ability to establish infection when applied extracellularly in the form of purified viral particles [35]. Virions can infect the hyphae of virus-free S. sclerotiorum directly when applied to hyphae or sprayed on leaves of Arabidopsis thaliana and Brassica napus infected with S. sclerotiorum. When applied to S. sclerotiorum-infected leaves, the virus can suppress the development of S. sclerotiorum-induced lesions. SsHADV-1 has a narrow host range and, in addition to S. sclerotiorum, can infect the related species S. minor and S. nivalis, but not other relatively closely related fungi, such as Botrytis cinerea [35]. Furthermore, SsHADV-1 has been identified in New Zealand and the USA in environmental samples and insects; however, this is not surprising given the near global distribution of S. sclerotiorum [6, 11].

SsHADV-1 virions are non-enveloped, isometric, 20-22 nm in diameter, and constructed from one capsid protein (CP) [34]. The genome is a circular ssDNA molecule of 2,166 nucleotides and contains two genes – for CP and replication initiation protein (Rep) (Fig. 1). The prediction of the cp gene has been validated by N-terminal sequencing of the CP purified from the virions. The large intergenic region contains a potential stem-loop structure with a nonanucleotide (TAATATTAT) motif at its apex, which is likely to be important for rolling-circle replication. The CP of SsHADV-1 is not recognizably similar to the corresponding proteins from viruses in other taxa.
Fig. 1

Genome map of SsHADV-1. Genes encoding the replication-initiation protein (Rep) and capsid protein (CP) are shown with blue and red arrows, respectively. The position of the nonanucleotide (TAATATTAT) at the apex of a potential stem-loop structure is also indicated

Although SsHADV-1 remains the only isolated member of the group, genomes of more than 100 SsHADV-1-like putative viruses have been reported (see Table 1). These genomes have been sequenced from different environmental samples, and many were identified associated with plant material as well as various animal-associated samples, including cerebrospinal fluid and blood of humans (Table 1 and references therein). Even though the hosts of these putative viruses remain unknown, their diversity suggests that SsHADV-1-like viruses are abundant and widespread in the environment.
Table 1

Genome sequences of putative SsHADV-1-like viruses

GenBank accession no.

Virus/putative virus name

Acronym

Country

Isolation source

Common name

Sample type

Reference

GQ365709

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

China

Sclerotinia sclerotiorum

White mold

Mycelial samples

[34]

KF268025

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

New Zealand

River Sediments

-

River Sediments

[11]

KF268026

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

New Zealand

River Sediments

-

River Sediments

[11]

KF268027

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

New Zealand

River Sediments

-

River Sediments

[11]

KF268028

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

New Zealand

River Sediments

-

River Sediments

[11]

KM598382

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

USA

Ischnura ramburii

Damselfly

Abdomen

[6]

KM598383

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

USA

Erythemis simplicicollis

Dragonfly

Abdomen

[6]

KM598384

Sclerotinia sclerotiorum hypovirulence associated DNA virus 1

SsHADV-1

USA

Pantala hymenaea

Dragonfly

Abdomen

[6]

HQ335086

Mosquito VEM virus SDBVL G

MVemV

USA

Culex erythrothorax

Mosquito

Mosquito samples

[22]

JN704610

Meles meles fecal virus

MmFV

Netherlands

Meles meles

European badger

Rectal swab

[30]

JQ412057

Cassava associated circular DNA virus

CasCV

Ghana

Manihot esculenta

Cassava

Leaf

[5]

JX185428

Dragonfly-associated circular virus 3

DfasCV-3

Tonga

Pantala flavescens

Dragonfly

Abdomen

[26]

JX185429

Dragonfly-associated circular virus 2

DfasCV-2

USA

Erythemis simplicicollis

Dragonfly

Abdomen

[26]

JX185430

Dragonfly-associated circular virus 1

DfasCV-1

USA

Miathyria marcella

Dragonfly

Abdomen

[26]

KF371630

Faecal-associated gemycircularvirus-12

FaGmV-12

New Zealand

Struthio camelus

Ostrich

Faeces

[27]

KF371631

Faecal-associated gemycircularvirus-11

FaGmV-11

New Zealand

Oryctolagus cuniculus

Rabbit

Faeces

[27]

KF371632

Faecal-associated gemycircularvirus-10

FaGmV-10

New Zealand

Sturnus vulgaris

European starling

Faeces

[27]

KF371633

Faecal-associated gemycircularvirus-9

FaGmV-9

New Zealand

Turdus merula

Blackbird

Faeces

[27]

KF371634

Faecal-associated gemycircularvirus-8

FaGmV-8

New Zealand

Petroica traversi

Chatham Island black robin

Faeces

[27]

KF371635

Faecal-associated gemycircularvirus-7

FaGmV-7

New Zealand

Anas platyrhynchos

Mallard duck

Faeces

[27]

KF371636

Faecal-associated gemycircularvirus-6

FaGmV-6

New Zealand

Gerygone albofrontata

Chatham Island warbler

Faeces

[27]

KF371637

Faecal-associated gemycircularvirus-5

FaGmV-5

New Zealand

Gerygone albofrontata

Chatham Island warbler

Faeces

[27]

KF371638

Faecal-associated gemycircularvirus-4

FaGmV-4

New Zealand

Arctocephalus forsteri

New Zealand fur seal

Faeces

[27]

KF371639

Faecal-associated gemycircularvirus-3

FaGmV-3

New Zealand

Gerygone albofrontata

Chatham Island warbler

Faeces

[27]

KF371640

Faecal-associated gemycircularvirus-2

FaGmV-2

New Zealand

Sus scrofa

Domestic pig

Faeces

[27]

KF371641

Faecal-associated gemycircularvirus-1c

FaGmV-1c

New Zealand

Turdus merula

Blackbird

Faeces

[27]

KF371642

Faecal-associated gemycircularvirus-1b

FaGmV-1b

New Zealand

Turdus merula

Blackbird

Faeces

[27]

KF371643

Faecal-associated gemycircularvirus-1a

FaGmV-1a

New Zealand

Ovis aries

Sheep

Faeces

[27]

KF413620

Hypericum japonicum associated circular DNA virus

HJasCV

Viet Nam

Hypericum japonicum

Hypericum

Leaf

[7]

KJ413144

Human genital-associated circular DNA virus-1

HuGaGmC349

South Africa

Homo sapiens

Human

Cervical sample

unpublished

KJ547634

Sewage-associated gemycircularvirus-4

SaGmV-4

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547635

Sewage-associated gemycircularvirus-5

SaGmV-5

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547636

Sewage-associated gemycircularvirus-6

SaGmV-6

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547637

Sewage-associated gemycircularvirus-7a

SaGmV-7a

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547638

Sewage-associated gemycircularvirus-8

SaGmV-8

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547639

Sewage-associated gemycircularvirus-9

SaGmV-9

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547640

Sewage-associated gemycircularvirus-7b

SaGmV-7b

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547641

Sewage-associated gemycircularvirus-11

SaGmV-11

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547642

Sewage-associated gemycircularvirus-2

SaGmV-2

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547643

Sewage-associated gemycircularvirus-3

SaGmV-3

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547644

Sewage-associated gemycircularvirus-10a

SaGmV-10a

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ547645

Sewage-associated gemycircularvirus-10b

SaGmV-10b

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KJ641719

Bat gemycircularvirus 23 GD2012

BtMf-CV-23 GD2012

China

Miniopterus fuliginosus

Bat

Pharyngeal & rectal swabs

[32]

KJ641726

Bat gemycircularvirus 8 NM2013

BtRf-CV-8 NM2013

China

Rhinolophus ferrumequinum

Bat

Pharyngeal & rectal swabs

[32]

KJ641737

Bat gemycircularvirus Tibet2013

BtRh-CV-6 Tibet2013

China

Rhinolophus hipposideros

Bat

Pharyngeal & rectal swabs

[32]

KJ938717

Caribou feces-associated gemycircularvirus

FaGmV-13

Canada

Rangifer tarandus

Caribou

Faeces

[21]

KM510192

Bromus-associated circular DNA virus 3

BasCV-3

New Zealand

Bromus hordeaceus

Soft brome/Bull grass

Leaf

[13]

KM598385

Odonata associated gemycircularvirus-1

OdaGmV-1

USA

Ischnura posita

Damselfly

Abdomen

[6]

KM598386

Odonata associated gemycircularvirus-1

OdaGmV-1

USA

Pantala hymenaea

Dragonfly

Abdomen

[6]

KM598387

Odonata associated gemycircularvirus-2

OdaGmV-2

USA

Aeshna multicolor

Dragonfly

Abdomen

[6]

KM598388

Odonata associated gemycircularvirus-2

OdaGmV-2

USA

Libellula saturata

Dragonfly

Abdomen

[6]

KM821747

Sewage-associated gemycircularvirus-1

SaGmV-1

New Zealand

Sewage oxidation pond

-

Sewage

[12]

KP133075

Gemycircularvirus SL1

GemyCV-SL1

Sri Lanka

Homo sapiens

Human

Cerebrospinal fluid

[24]

KP133076

Gemycircularvirus SL2

GemyCV-SL2

Sri Lanka

Homo sapiens

Human

Cerebrospinal fluid

[24]

KP133077

Gemycircularvirus SL3

GemyCV-SL3

Sri Lanka

Homo sapiens

Human

Cerebrospinal fluid

[24]

KP133078

Gemycircularvirus BZ1

GemyCV-BZ1

Brazil

Homo sapiens

Human

Faeces

[24]

KP133079

Gemycircularvirus BZ2

GemyCV-BZ2

Brazil

Homo sapiens

Human

Faeces

[24]

KP133080

Gemycircularvirus NP

GemyCV-NP

Nepal

Untreated sewage

-

Sewage

[24]

KP263543

Badger faeces-associated gemycircularvirus

BafaGM588

Portugal

Meles meles

European badger

Faeces

[4]

KP263544

Mongoose feces-associated gemycircularvirus a

MoFaGmV181a

Portugal

Herpestes ichneumon

Egyptian mongoose

Faeces

[4]

KP263545

Mongoose feces-associated gemycircularvirus b

MoFaGmV160b

Portugal

Herpestes ichneumon

Egyptian mongoose

Faeces

[4]

KP263546

Mongoose feces-associated gemycircularvirus c

MoFaGmV541c

Portugal

Herpestes ichneumon

Egyptian mongoose

Faeces

[4]

KP263547

Mongoose feces-associated gemycircularvirus d

MoFaGmV478d

Portugal

Herpestes ichneumon

Egyptian mongoose

Faeces

[4]

KP987887

Gemycircularvirus C1c

C1c

France

Homo sapiens

Human

Plasma

[29]

KR912221

Gemycircularvirus gemy-ch-rat1

Gemy-ch-rat1

China

Rattus norvegicus

Rat

Blood

[17]

KT253577

Poaceae associated gemycircularvirus-1

PaGmV-1

Tonga

Brachiaria deflexa

Signalgrass

Leaf

[18]

KT253578

Poaceae associated gemycircularvirus-1

PaGmV-1

Tonga

Brachiaria deflexa

Signalgrass

Leaf

[18]

KT253579

Poaceae associated gemycircularvirus-1

PaGmV-1

Tonga

Saccharum hybrid

Sugarcane

Leaf

[18]

KT309029

Poecile atricapillus GI tract-associated gemycircularvirus

Gitract

USA

Poecile atricapillus

Black-capped chickadee

Buccal and cloacal swab

[9]

KT598248

Soybean leaf-associated gemycircularvirus 1

SlaGemV1

USA

Glycine max

Soybean

Leaf

[20]

KT732790

Pacific flying fox faeces associated gemycircularvirus-1

PfffaGmV-1

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732791

Pacific flying fox faeces associated gemycircularvirus-1

PfffaGmV-1

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732792

Pacific flying fox faeces associated gemycircularvirus-2

PfffaGmV-2

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732793

Pacific flying fox faeces associated gemycircularvirus-2

PfffaGmV-2

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732794

Pacific flying fox faeces associated gemycircularvirus-3

PfffaGmV-3

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732795

Pacific flying fox faeces associated gemycircularvirus-4

PfffaGmV-4

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732796

Pacific flying fox faeces associated gemycircularvirus-4

PfffaGmV-4

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732797

Pacific flying fox faeces associated gemycircularvirus-5

PfffaGmV-5

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732798

Pacific flying fox faeces associated gemycircularvirus-6

PfffaGmV-6

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732799

Pacific flying fox faeces associated gemycircularvirus-6

PfffaGmV-6

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732800

Pacific flying fox faeces associated gemycircularvirus-7

PfffaGmV-7

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732801

Pacific flying fox faeces associated gemycircularvirus-8

PfffaGmV-8

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732802

Pacific flying fox faeces associated gemycircularvirus-8

PfffaGmV-8

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732803

Pacific flying fox faeces associated gemycircularvirus-9

PfffaGmV-9

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732804

Pacific flying fox faeces associated gemycircularvirus-10

PfffaGmV-10

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732805

Pacific flying fox faeces associated gemycircularvirus-10

PfffaGmV-10

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732807

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732808

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732809

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732810

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732811

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732812

Pacific flying fox faeces associated gemycircularvirus-11

PfffaGmV-11

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732813

Pacific flying fox faeces associated gemycircularvirus-12

PfffaGmV-12

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732814

Pacific flying fox faeces associated gemycircularvirus-13

PfffaGmV-13

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT732806

Pacific flying fox faeces associated gemycircularvirus-14

PfffaGmV-14

Tonga

Pteropus tonganus

Bat

Faeces

[19]

KT862238

Faecal-associated gemycircularvirus-14

FaGmV-14

New Zealand

Anas platyrhynchos

Duck

Faeces

[28]

KT862239

Faecal-associated gemycircularvirus-14

FaGmV-14

New Zealand

Anas platyrhynchos

Duck

Faeces

[28]

KT862240

Sewage-associated gemycircularvirus-3

SaGmV-3

New Zealand

Gallus gallus domesticus

Chicken

Faeces

[28]

KT862241

Faecal-associated gemycircularvirus-4

FaGmV-4

New Zealand

Gallus gallus domesticus

Chicken

Faeces

[28]

KT862242

Faecal-associated gemycircularvirus-17

FaGmV-17

New Zealand

Gallus gallus domesticus

Chicken

Faeces

[28]

KT862243

Faecal-associated gemycircularvirus-20

FaGmV-20

New Zealand

Gallus gallus domesticus

Chicken

Faeces

[28]

KT862244

Faecal-associated gemycircularvirus-20

FaGmV-20

New Zealand

Lama glama

Llama

Faeces

[28]

KT862245

Faecal-associated gemycircularvirus-21

FaGmV-21

New Zealand

Lama glama

Llama

Faeces

[28]

KT862246

Faecal-associated gemycircularvirus-20

FaGmV-20

New Zealand

Equus ferus caballus

Horse

Faeces

[28]

KT862247

Faecal-associated gemycircularvirus-21

FaGmV-21

New Zealand

Equus ferus caballus

Horse

Faeces

[28]

KT862248

Faecal-associated gemycircularvirus-18

FaGmV-18

New Zealand

Equus ferus caballus

Horse

Faeces

[28]

KT862249

Faecal-associated gemycircularvirus-16

FaGmV-16

New Zealand

Ovis aries

Sheep

Faeces

[28]

KT862250

Faecal-associated gemycircularvirus-19

FaGmV-19

New Zealand

Sus scrofa domestica

Pig

Faeces

[28]

KT862251

Faecal-associated gemycircularvirus-16

FaGmV-16

New Zealand

Ovis aries

Sheep

Faeces

[28]

KT862252

Sewage-associated gemycircularvirus-3

SaGmV-3

New Zealand

Bos taurus

Cow

Faeces

[28]

KT862253

Faecal-associated gemycircularvirus-22

FaGmV-22

New Zealand

Bos taurus

Cow

Faeces

[28]

KT862254

Faecal-associated gemycircularvirus-15

FaGmV-15

New Zealand

Canis lupus familiaris

Dog

Faeces

[28]

KT862255

Sewage-associated gemycircularvirus-3

SaGmV-3

New Zealand

Lepus europaeus

Hare

Faeces

[28]

LK931483

HCBI8.215 virus

HCBI8_215

Germany

Bos taurus

Cow

Serum

[16]

LK931484

HCBI9.212 virus

HCBI9_212

Germany

Bos taurus

Cow

Serum

[16]

LK931485

MSSI2.225 virus

MSSI2_225

Germany

Homo sapiens

Human

Blood

[16]

All putative SsHADV-1-like viruses encode homologous Rep and CP, and in phylogenetic analyses form monophyletic clades with SsHADV-1 (Figures 2 and 3). Their genomes are of similar size, in the range of 2,089-2,290 nucleotides. Structural and genomic features of SsHADV-1 differ considerably from those of all other currently classified viruses. The Rep of SsHADV-1 is most closely related to the corresponding proteins of members of the family Geminiviridae. It shares with geminiviral proteins two conserved domains, namely geminivirus Rep catalytic domain (Gemini_AL1; PF00799) and geminivirus Rep protein central domain (Gemini_AL1_M; PF08283), with conserved motifs for rolling-circle replication. Notably, similar to some geminiviruses [31], certain SsHADV-1-like viruses also contain introns within their Rep-encoding genes [6, 7, 12, 13, 18, 19, 26, 27, 28, 30]. However, Rep-based phylogenetic analysis shows that SsHADV-1 and other related putative viruses form a well-supported, monophyletic clade, which branches as a sister group to geminiviruses (Fig. 2). Unlike the Rep, the CP of SsHADV-1 (and related viruses) does not display any recognizable sequence similarity to proteins of geminiviruses or any other group of known viruses. Furthermore, all geminiviruses possess distinctive geminate virions constructed from two incomplete T = 1 icosahedra [2, 36], whereas the virion of SsHADV-1 is isometric [34]. Finally, the number of genes and size of the genome differ considerably between SsHADV-1-like viruses and geminiviruses. In particular, all putative SsHADV-1-like viruses lack the movement protein, which is essential for the plant geminiviruses.
Fig. 2

Phylogenetic analysis of the replication-initiation proteins (Reps) of ssDNA viruses. The type species of the proposed genus Gemycircularvirus within the family Genomoviridae is highlighted in boldface. For phylogenetic analysis, protein sequences were aligned using PROMALS3D [23], and columns containing gaps were removed from the alignment using trimAl (strict mode) [3]. Maximum-likelihood phylogenetic analysis was carried out using PhyML 3.1 [8] with the RtREV +G6 +I +F model, which was selected by PhyML as the best-fitting model. Numbers at the branch points represent aBayes local support values. Branches with lower than 60 % support were collapsed. The scale bar represents the number of substitutions per site. For clarity, the tree was mid-point rooted. All taxa are indicated with the corresponding GenBank accession numbers, followed by abbreviated virus names (full virus names are provided in Table 1)

Fig. 3

Phylogenetic analysis of the SsHADV-1-like capsid proteins. The type species of the proposed genus Gemycircularvirus within the family Genomoviridae is highlighted in boldface. For phylogenetic analysis, protein sequences were aligned using PROMALS3D [23], and columns containing gaps were removed from the alignment using trimAl (strictplus mode) [3]. Maximum-likelihood phylogenetic analysis was carried out using PhyML 3.1 [8] with the LG +G6 +F model, which was selected by PhyML as the best-fitting model. Numbers at the branch points represent aBayes local support values. Branches with lower than 60 % support were collapsed. The scale bar represents the number of substitutions per site. The tree was rooted with the capsid proteins of geminiviruses. All taxa are indicated with the corresponding GenBank accession numbers, followed by abbreviated virus names (full virus names are provided in Table 1)

In recognition of the unique features described above, SsHADV-1 has been classified into the species Sclerotinia gemycircularvirus 1 within the new genus Gemycircularvirus (Gemini-like myco-infecting circular virus) [26] within the new family Genomoviridae (sigil: Ge- for geminivirus-like, nomo- for no movement protein).

Although Genomoviridae currently includes only a single representative, new members, possibly including uncultivated viruses, are expected to be added to the family in the near future. Based on the available genetic data and phylogenetic analyses (Figures 2 and 3), it is already clear that many new genera will have to be introduced to adequately reflect the diversity of SsHADV-1-like viruses.

Notes

Compliance with ethical standards

The authors declare that no competing interests exist. This article does not contain any studies with human participants or animals performed by any of the authors.

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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  1. 1.Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Department of MicrobiologyInstitut PasteurParisFrance
  2. 2.Plant Pathology DepartmentUniversity of KentuckyLexingtonUSA
  3. 3.State Key Lab of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  4. 4.School of Biological Sciences and Biomolecular Interaction CentreUniversity of CanterburyChristchurchNew Zealand
  5. 5.Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory SciencesUniversity of Cape TownCape TownSouth Africa
  6. 6.Department of Plant Pathology and Emerging Pathogens InstituteUniversity of FloridaGainesvilleUSA

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