Sequence-based taxonomic framework for the classification ... taxonomic...Sequence-based taxonomic...

Sequence-based taxonomic framework for the

classification of uncultured single-stranded DNA

viruses of the family GenomoviridaeArvind Varsani12dagger and Mart Krupovic3Dagger

1The Biodesign Center for Fundamental and Applied Microbiomics School of Life sciences Center forEvolution and Medicine Arizona State University Tempe AZ 85287 USA 2Structural Biology Research UnitDepartment of Clinical Laboratory Sciences University of Cape Town Observatory 7700 South Africa and3Unite Biologie moleculaire du Gene chez les Extremophiles Department of Microbiology Institut Pasteur 25rue du Docteur Roux Paris 75015 France

Corresponding authors E-mails krupovicpasteurfr arvindvarsaniasuedudaggerhttporcidorg0000-0003-4111-2415Daggerhttporcidorg0000-0001-5486-0098

Abstract

With the advent of metagenomics approaches a large diversity of known and unknown viruses has been identified in varioustypes of environmental plant and animal samples One such widespread virus group is the recently established familyGenomoviridae which includes viruses with small (2ndash24 kb) circular ssDNA genomes encoding rolling-circle replication initia-tion proteins (Rep) and unique capsid proteins Here we propose a sequence-based taxonomic framework for classification of121 new virus genomes within this family Genomoviruses display47 sequence diversity which is very similar to thatwithin the well-established and extensively studied family Geminiviridae (46 diversity) Based on our analysis we establish a78 genome-wide pairwise identity as a species demarcation threshold Furthermore using a Rep sequence phylogeny-basedanalysis coupled with the current knowledge on the classification of geminiviruses we establish nine genera within theGenomoviridae family These are Gemycircularvirus (nfrac1473) Gemyduguivirus (nfrac141) Gemygorvirus (nfrac149) Gemykibivirus (nfrac1429)Gemykolovirus (nfrac143) Gemykrogvirus (nfrac143) Gemykroznavirus (nfrac141) Gemytondvirus (nfrac141) Gemyvongvirus (nfrac141) The presentedtaxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an ex-ample for future classification of other groups of uncultured viruses discovered using metagenomics approaches

Key words Genomoviridae CRESS DNA viruses replication-associated protein ssDNA viruses

1 Introduction

Viral metagenomics fostered by powerful high-throughput se-quencing methods has recently revolutionized our perception ofvirus diversity in the environment Many novel groups of unculti-vated viruses have been discovered during the past decade in-cluding viruses with small moderately-sized and even largegenomes (Yau et al 2011 Roux et al 2012 Labonte and Suttle

2013 Dutilh et al 2014 Yutin et al 2015 Zhou et al 2015et alDayaram et al 2016 Steel et al 2016) Many of these virus groupsremain unclassified To embrace the constantly growing outputfrom viral metagenomics studies virus taxonomy is increasinglyswitching from the traditional classification guided by biologicalfeatures such as serology virion morphology or host range topredominantly sequence-guided practices (Simmonds et al 2017)Sequence-guided virus classification is relatively straightforward

VC The Author 2017 Published by Oxford University PressThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (httpcreativecommonsorglicensesby-nc40) which permits non-commercial re-use distribution and reproduction in any medium provided the original work is properly citedFor commercial re-use please contact journalspermissionsoupcom

1

Virus Evolution 2017 3(1) vew037

doi 101093vevew037Reflections

when the new viruses fall into existing taxa with well-defined de-marcation criteria However in the absence of isolated representa-tives and established taxonomic framework rational definition ofappropriate taxonomic ranks such as families genera and spe-cies for novel groups of uncultured viruses might be considerablymore complex Solutions to this problem are perhaps most ur-gently needed in the case of single-stranded (ss) DNA viruseswhich are extremely widespread in nature Due to their small ge-nomes sizes high mutation and recombination rates (Duffy andHolmes 2008 Duffy and Holmes 2009 Firth et al 2009 Harkinset al 2009 2014 Grigoras et al 2010 Martin et al 2011 Streck et al2011 Nguyen et al 2012 Cadar et al 2013 Roux et al 2013) andrelative ease of genome amplification an incredible diversity ofthese viruses has been discovered through metagenomics studiesin all conceivable habitats ssDNA viruses infect cells from allthree domains of life and are currently classified by theInternational Committee on Taxonomy of Viruses (ICTV) intoeleven families and one unassigned genus Members of the fami-lies Microviridae and Inoviridae infect bacteria viruses of the fami-lies Spiraviridae and Pleolipoviridae prey on archaea whereaseukaryotes host viruses classified into the families AnelloviridaeBidnaviridae Circoviridae Geminiviridae Genomoviridae Nanoviridaeand Parvoviridae and the unassigned genus Bacilladnavirus In addi-tion several widespread groups of uncultured viruses discoveredby viral metagenomics remain unclassified predominantly thosethat are circular replication-associated protein encoding single-stranded (CRESS) DNA viruses (Simmonds et al 2017)

The Genomoviridae family is one of the most recently establishedfamilies of ssDNA viruses (Adams et al 2016 Krupovic et al 2016)The family currently includes a single genus Gemycircularviruswhich contains a single species Sclerotinia gemycircularvirus 1 en-compassing a single isolate Sclerotinia sclerotiorumhypovirulence-associated DNA virus 1 (SsHADV-1) SsHADV-1 wasisolated from a plantndashpathogenic fungus Sclerotinia sclerotiorum andis the only ssDNA virus known to infect fungi (Yu et al 2010 2013)Recently Liu et al (2016) have shown that SsHADV-1 is able to in-fect a mycophagous insect (Lycoriella ingenua) which acts as a trans-mission vector SsHADV-1 virions are non-enveloped isometric20ndash22 nm in diameter and assembled from a single capsid protein(CP) (Yu et al 2010) The genome is a circular ssDNA molecule of2166 nucleotides and contains two genesmdashfor CP and rolling-circlereplication initiation protein (Rep) Like in many other ssDNA vi-ruses with circular genomes the large intergenic region ofSsHADV-1 contains a potential stem-loop structure with a nonanu-cleotide (TAATATTAT) motif at its apex which is likely to be im-portant for rolling-circle replication initiation The CP of SsHADV-1is not recognizably similar to the corresponding proteins from vi-ruses in other taxa Although SsHADV-1 remains the only isolatedand classified member of the Genomoviridae 121 viral genomeswith varying degree of similarity to that of SsHADV-1 have been re-covered and sequenced from various environmental plant- andanimal-associated samples indicating that these viruses are wide-spread and abundant in the environment (Table 1) However aproper taxonomic framework and demarcation criteria necessaryto accommodate these viruses within the family Genomoviridae arelacking Here we explore the diversity and evolution of unculturedSsHADV-1-like viruses and attempt to establish a framework fortheir classification based on sequence data alone

2 Genomoviridae diversity and speciesclassification

At the time of the analysis (August 2016) there were 121SsHADV-1-like genome sequences in the GenBank database

Each of these genomes encodes two putative proteins homolo-gous to the CP and Rep of SsHADV-1 highlighting strongcoherence of this virus assemblage Nevertheless there is a con-siderable sequence divergence within the group (SupplementaryFig S1) To investigate the extent of genomoviral sequence diver-sity we analyzed the distribution of genome-wide pairwiseidentities (one minus Hamming distances of pairwise alignedsequences with pairwise deletion of gaps) across all 121 availablegenomes (Fig 1A) using SDT v12 (Muhire Varsani and Martin2014) Most of the virus genomes in our dataset share 56ndash66genome-wide pairwise identities and only a handful containednearly identical relatives (98 identity) indicating that se-quence diversity among SsHADV-1-like viruses remains largelyunexplored

Pairwise comparison of the Rep and CP protein sequencesrevealed a broader distribution of identity values (Fig 1B and C)Notably the CPs were considerably more divergent that theReps with the highest proportion of pairwise identities being33 (versus 48 for the Rep) This observation is in line withfunctional differences of the two proteins and the fact that viralCPs often encompass host recognition determinants which areunder constant pressure to co-evolve with the cellular receptors(Kolawole et al 2014 Shangjin Cortey and Segales 2009) Basedon the analysis of distribution of the pairwise identities acrossgenomes CPs and Reps we consider a threshold of 78 to be aconservative value for species demarcation Thus all viral ge-nomes showing identities higher than this value should be con-sidered as variants of the existing species Nonetheless theremay be situations where it is difficult to assign species becausea particular new sequence is

1 gt78 similar to sequences from a particular species butislt 78 similar to other variants of that same species

2 gt78 similar to sequences from two or more differentspecies

To resolve the above conflicts we suggest adopting a similarapproach proposed for geminiviruses (Muhire et al 2013Varsani et al 2014a b Brown et al 2015) To resolve conflict 1we suggest that the new sequence be classified within any spe-cies in which it sharesgt78 identity to any one variant for-merly classified as belonging to that species even if it islt78identical to other viruses within that species To resolve conflict2 we suggest that the new sequence be considered as belongingto the species with sequences with which it shares the highestdegree of similarity

3 Rep-based approach for creation of genera

Maximum likelihood phylogenetic analyses based on the Rep of121 genomoviruses revealed several well-supported clades thatcould be considered as genera within the family (Fig 2) Wenote that the clades obtained in the Rep-based phylogeny arenot fully consistent with those obtained in the phylogeneticanalysis of the full genome or the more diverse CP sequences(Figs 3 and 4) This is most explicit in the case of the newly pro-posed genus Gemykolovirus (see below) In the Rep-based treecorresponding sequences form a sister clade to the single repre-sentative of the genus Gemyduguivirus (Fig 2) In contrast in thewhole-genome-based phylogeny gemykoloviruses form a sistergroup to members of the genus Gemycircularvirus (Fig 3) Thereason for this incongruence is likely to be intra-familial recom-bination between different genomovirus genomes resulting inchimeric entities encoding Rep and CP with different evolution-ary histories (Kraberger et al 2015a) Indeed in the CP-based

2 | Virus Evolution 2017 Vol 3 No 1

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09Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

) (co

nti

nu

ed)

A Varsani and M Krupovic | 3

Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

09T

bat

H10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

10T

bat

H10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

11T

bat

L10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

12T

bat

L10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us8

KT

7328

06T

bat

3157

9Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us9

KT

7327

95T

bat

2138

3Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us10

KT

7327

94T

bat

H10

3958

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rat

asso

ciat

edge

myc

ircu

larv

irus

1K

R91

2221

Ch

-zjr

at-0

1R

attu

sno

rveg

icus

Rat

Blo

od

Ch

ina

Liet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

GQ

3657

09Ss

HA

DV

-1C

NSc

lero

tini

asc

lero

tior

umSc

lero

tin

iaM

ycel

ials

amp

les

Ch

ina

Yu

etal

(20

10)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

5Ss

HA

DV

-1N

ZH

620

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

6Ss

HA

DV

-1N

ZSR

120

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

7Ss

HA

DV

-1N

ZSR

320

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

8Ss

HA

DV

-1N

ZSR

520

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

82Ss

HA

DV

-1-U

S-54

9LB

-12

Isch

nura

ram

buri

iD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

83Ss

HA

DV

-1-U

S-54

9DFS

-12

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

84Ss

HA

DV

-1-U

S-54

9SR

-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KJ5

4763

8B

S391

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KM

8217

47Sa

Gm

V-1

NZ

-BS3

970-

2012

Sew

age

oxid

atio

npo

ndndash

Sew

age

New

Zea

lan

dK

rabe

rger

etal

(20

15a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us2

KJ5

4764

1B

S411

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us3

KJ5

4763

6B

S401

4Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4763

7B

S393

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4764

0B

S397

2Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us5

KJ5

4763

9B

S397

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4947

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5151

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Soyb

ean

asso

ciat

edge

myc

ircu

larv

irus

1K

T59

8248

SlaG

emV

1-1

Gly

cine

max

Soyb

ean

Leaf

USA

Mar

zan

oan

dD

om

ier

(201

6)

Gem

ydug

uiv

irus

Dra

gonfl

yas

soci

ated

gem

ydug

uivi

rus

1JX

1854

28T

O-D

FS3B

2-20

10Pa

ntal

afla

vesc

ens

Dra

gon

fly

Abd

om

enT

on

gaR

osa

rio

etal

(20

12)

Gem

ygor

viru

sC

anin

eas

soci

ated

gem

ygor

viru

s1

KT

8622

5453

Fec7

do

gC

anis

lupu

sfa

mili

aris

Do

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1JN

7046

10V

S470

0006

Mel

esm

eles

Euro

pea

nba

dge

rR

ecta

lsw

abN

eth

erla

nd

sva

nd

enB

ran

det

al(

2012

)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2238

4Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2239

24Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2790

Tba

tA

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2791

Tba

tH

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Sew

age

deri

ved

gem

ygor

viru

s1

KJ4

1314

434

9H

omo

sapi

ens

Hu

man

Cer

vica

lsam

ple

Sou

thA

fric

a

Sew

age

deri

ved

gem

ygor

viru

s1

KJ5

4763

5B

S396

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Star

ling

asso

ciat

edge

myg

orvi

rus

1K

F371

632

P14

Stur

nus

vulg

aris

Euro

pea

nst

arli

ng

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Gem

ykib

ivir

usBa

dger

asso

ciat

edge

myk

ibiv

irus

1K

P263

543

588t

Mel

esm

eles

Euro

pea

nba

dge

rFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Blac

kro

bin

asso

ciat

edge

myk

ibiv

irus

1K

F371

634

P21

Petr

oica

trav

ersi

Ch

ath

amIs

lan

d

blac

kro

bin

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ykib

ivir

us

1K

F371

633

P22

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Bovi

neas

soci

ated

gem

ykib

ivir

us1

LK93

1483

HC

BI8

215

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Dra

gonfl

yas

soci

ated

gem

ykib

ivir

us1

JX18

5430

FL1-

2X-2

010

Mia

thyr

iam

arce

llaD

rago

nfl

yA

bdo

men

USA

Ro

sari

oet

al(

2012

)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

4B

S398

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

5B

S384

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KP9

7469

4D

B2

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)

Hum

anas

soci

ated

gem

ykib

ivir

us1

LK93

1485

MSS

I22

25H

omo

sapi

ens

Hu

man

Blo

od

Ger

man

yLa

mbe

rto

etal

(20

14)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

5SL

1H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

6SL

2H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

7SL

3H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

(co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

8B

Z1

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

9B

Z2

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3308

0N

PU

ntre

ated

sew

age

ndashSe

wag

eN

epal

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP2

6354

654

1cH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP9

8788

7G

emyC

1cH

omo

sapi

ens

Hu

man

Plas

ma

Fran

ceU

chet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us4

KT

3638

39G

eTz1

Hom

osa

pien

sH

um

anC

ereb

rosp

inal

flu

idC

hin

aZ

ho

uet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us5

KU

3431

37H

V-G

cV2

Hom

osa

pien

sH

um

anPe

rica

rdia

lflu

idFr

ance

Hal

ary

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ykib

ivir

us1

KP2

6354

516

0bH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Pter

opu

sas

soci

ated

gem

ykib

ivir

us1

KT

7328

13T

bat

A64

418

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

J641

737

BtR

h-C

V-6

Tib

et20

13R

hino

loph

ushi

ppos

ider

osB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

P263

544

181a

Her

pest

esic

hneu

mon

Egyp

tian

mo

ngo

ose

Faec

esPo

rtu

gal

Co

nce

icao

-Net

oet

al(

2015

)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

2K

J641

726

BtR

f-C

V-8

NM

2013

Rhi

nolo

phus

ferr

umeq

uinu

mB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Sew

age

deri

ved

gem

ykib

ivir

us1

KJ5

4764

3B

S414

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

4027

BS1

4149

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5252

BS1

4149

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5556

BS1

4149

har

eLe

pus

euro

paeu

sH

are

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us2

KJ5

4764

2B

S391

1Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykol

ovir

us

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

98T

bat

A10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

99T

bat

H10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myk

olov

irus

2K

T73

2800

Tba

tH

1039

21Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Gem

ykro

gvir

usB

ovin

eas

soci

ated

gem

ykro

gvir

us1

LK93

1484

HC

BI9

212

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Car

ibou

asso

ciat

edge

myk

rogv

irus

1K

J938

717

FaG

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tree gemykoloviruses are firmly nested within the large cladeincluding the majority of gemycircularviruses (Fig 4) Giventhat CP sequences of genomoviruses are considerably more di-vergent than the Rep sequences (Fig 1) it appears reasonable toestablish a higher (ie above the species level) taxonomicframework using the Rep (Fig 2) The latter protein is also

conserved in other eukaryotic ssDNA viruses (which is not thecase for the CP) and can thus be used to assess the place ofgenomoviruses within the larger community of ssDNA viruses

To evaluate the taxonomic structure of the Genomoviridaewe took advantage of the fact that in Rep-based phylogeneticanalyses genomoviruses consistently form a sister group to

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Percentage identity

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Figure 1 Distribution of (A) genome-wide (B) Rep and (C) CP pairwise identities (121 taxa) of genomoviruses calculated using SDT v12 (Muhire Varsani and Martin

2014)


members of the Geminiviridae (Krupovic et al 2016) a compre-hensively characterized family of plant viruses with circularssDNA genomes (Varsani et al 2014b) Thus using the estab-lished taxonomic framework of the Geminiviridae overlaid on theRep-based phylogeny as a guide we could define five cladesand four additional singletons within the Genomoviridae branch(Fig 2) The defined groups displayed equivalent intra-family di-vergence as the established genera within the familyGeminiviridae (Varsani et al 2014b) The nine groups were sup-ported in both nucleotide and protein sequence inferred phylog-enies (Supplementary Fig S2) Consequently in addition to theexisting genus Gemycircularvirus we propose establishing eightnew genera within the family Genomoviridae The details of thenine genera are summarized in Fig 5 and briefly outlinedbelow

31 Gemycircularvirus

This genus has the largest number of new species (nfrac14 43 sev-enty-three genomes Table 1) and includes SsHADV-1 thefounding member of the family Members of the genus display44 diversity Viruses within the forty-three species clusterwith 99 and 96 branch support values in phylogenetic treesconstructed from either Rep or full genome sequences respec-tively (Figs 2 and 3)

32 Gemykibivirus

This is the second most populated genus (nfrac14 16 twenty-nine ge-nomes Table 1) in the family with 43 diversity among its mem-bers The name of the genus is an acronym of words geminivirus-like and myco-like kibi virus (kibi means circular in Amharic)Sequences within the fifteen species cluster with 93 branch sup-port within phylogenetic trees constructed from Rep (Fig 2) andtwo well-supported clades (100 and 96) within trees constructedfrom full genome sequences (Fig 3) suggesting that recombinationhas played an important role in the evolution of this group

33 Gemygorvirus

Members of this genus (nfrac14 5 nine genomes Table 1) display49 diversity The name of the genus is an acronym of wordsgeminivirus-like and myco-like gor virus (gor means round inHindi) Sequences within the five species cluster with 100 and99 branch support within phylogenetic trees constructed fromeither Rep or full genome sequences respectively (Figs 2 and 3)

34 Gemykolovirus

Members of this genus (nfrac14 2 three genomes Table 1) display37 diversity The name of the genus is an acronym of wordsgeminivirus-like and myco-like kolo virus (kolo means round inCzech) Sequences within the two species cluster with 100 and89 branch support within phylogenetic trees constructed fromeither Rep or full genome sequences respectively (Figs 2 and 3)

35 Gemykrogvirus

Members of this genus (nfrac14 3 three genomes Table 1) display33 diversity The name of the genus is an acronym of wordsgeminivirus-like and myco-like krog virus (krog means round inSlovenian) Sequences within the three species cluster with 99and 100 branch support within phylogenetic trees constructedfrom either Rep or full genome sequences respectively (Figs 2and 3)

JQ412056 Cassava associated gemycircularvirus 1 JQ412057 Cassava associated gemycircularvirus 1 KT862253 Bovine associated gemycircularvirus 1 KF413620 Hypericum associated gemycircularvirus 1 KT732797 Pteropus associated gemycircularvirus 3 JX185429 Dragonfly associated gemycircularvirus 1 KM598385 Odonata associated gemycircularvirus 1 KM598386 Odonata associated gemycircularvirus 1 KT862245 Lama associated gemycircularvirus 1 KT862247 Lama associated gemycircularvirus 1 KJ547637 Sewage derived gemycircularvirus 4 KM510192 Bromus associated gemycircularvirus 1 KM821747 Sewage derived gemycircularvirus 1 KJ547639 Sewage derived gemycircularvirus 5 KJ547638 Sewage derived gemycircularvirus 1 KJ547640 Sewage derived gemycircularvirus 4 KJ547641 Sewage derived gemycircularvirus 2 KJ547636 Sewage derived gemycircularvirus 3 KM598384 Sclerotinia gemycircularvirus 1 KF268028 Sclerotinia gemycircularvirus 1 KF268027 Sclerotinia gemycircularvirus 1 KM598383 Sclerotinia gemycircularvirus 1 KF268026 Sclerotinia gemycircularvirus 1 KF268025 Sclerotinia gemycircularvirus 1 GQ365709 Sclerotinia gemycircularvirus 1 KM598382 Sclerotinia gemycircularvirus 1 KT732792 Pteropus associated gemycircularvirus 2 KT732793 Pteropus associated gemycircularvirus 2 KT862246 Chicken associated gemycircularvirus 1 KT862243 Chicken associated gemycircularvirus 1 KT862244 Chicken associated gemycircularvirus 1 KT732814 Pteropus associated gemycircularvirus 4 KT862249 Sheep associated gemycircularvirus 1 KT862251 Sheep associated gemycircularvirus 1 KF371636 Gerygone associated gemycircularvirus 1 KP263547 Mongoose associated gemycircularvirus 1 KF371637 Gerygone associated gemycircularvirus 2 KT862242 Chicken associated gemycircularvirus 2 KT598248 Soybean associated gemycircularvirus 1 KF371641 Blackbird associated gemycircularvirus 1 KF371642 Blackbird associated gemycircularvirus 1 KF371643 Blackbird associated gemycircularvirus 1 KF371639 Gerygone associated gemycircularvirus 3 KF371640 Porcine associated gemycircularvirus 2 KF371638 Fur seal associated gemycircularvirus 1 KT862241 Fur seal associated gemycircularvirus 1 KJ641719 Miniopterus associated gemycircularvirus 1 KT732795 Pteropus associated gemycircularvirus 9 KT732796 Pteropus associated gemycircularvirus 9 KT253578 Poaceae associated gemycircularvirus 1 KT253577 Poaceae associated gemycircularvirus 1 KT253579 Poaceae associated gemycircularvirus 1 KT732794 Pteropus associated gemycircularvirus 5 KT862248 Equine associated gemycircularvirus 1 KT862250 Porcine associated gemycircularvirus 1 KT732804 Pteropus associated gemycircularvirus 1 KT732805 Pteropus associated gemycircularvirus 1 KT309029 Chickadee associated gemycircularvirus 1 KT732801 Pteropus associated gemycircularvirus 5 KT732802 Pteropus associated gemycircularvirus 5 KT732803 Pteropus associated gemycircularvirus 6 KM598387 Odonata associated gemycircularvirus 2 KM598388 Odonata associated gemycircularvirus 2 KR912221 Rat associated gemycircularvirus 1 HQ335086 Mosquito associated gemycircularvirus 1 KF371635 Mallard associated gemycircularvirus 1 KT732806 Pteropus associated gemycircularvirus 8 KT732809 Pteropus associated gemycircularvirus 7 KT732810 Pteropus associated gemycircularvirus 7 KT732807 Pteropus associated gemycircularvirus 7 KT732808 Pteropus associated gemycircularvirus 7 KT732811 Pteropus associated gemycircularvirus 7 KT732812 Pteropus associated gemycircularvirus 7 KT862252 Sewage derived gemykibivirus 1 KT862240 Sewage derived gemykibivirus 1 KT862255 Sewage derived gemykibivirus 1 KJ547643 Sewage derived gemykibivirus 1 KF371634 Black robin associated gemykibivirus 1 KU343137 Human associated gemykibivirus 5 JX185430 Dragonfly associated gemykibivirus 1 KJ547642 Sewage derived gemykibivirus 2 KJ641726 Rhinolophus associated gemykibivirus 2 LK931485 Human associated gemykibivirus 1 KJ547645 Human associated gemykibivirus 1 KP974694 Human associated gemykibivirus 1 KJ547644 Human associated gemykibivirus 1 KT732813 Pteropus associated gemykibivirus 1 KF371633 Blackbird associated gemykibivirus 1 KT363839 Human associated gemykibivirus 4 KP263546 Human associated gemykibivirus 3 KP987887 Human associated gemykibivirus 3 KP263545 Mongoose associated gemykibivirus 1 LK931483 Bovine associated gemykibivirus 1 KP263543 Badger associated gemykibivirus 1 KJ641737 Rhinolophus associated gemykibivirus 1 KP263544 Rhinolophus associated gemykibivirus 1 KP133080 Human associated gemykibivirus 2 KP133076 Human associated gemykibivirus 2 KP133075 Human associated gemykibivirus 2 KP133077 Human associated gemykibivirus 2 KP133078 Human associated gemykibivirus 2 KP133079 Human associated gemykibivirus 2 KF371632 Starling associated gemygorvirus 1 KT862254 Canine associated gemygorvirus 1 JN704610 Mallard associated gemygorvirus 1 KT862238 Mallard associated gemygorvirus 1 KT862239 Mallard associated gemygorvirus 1 KT732790 Pteropus associated gemygorvirus 1 KT732791 Pteropus associated gemygorvirus 1 KJ413144 Sewage derived gemygorvirus 1 KJ547635 Sewage derived gemygorvirus 1 KT732798 Pteropus associated gemykolovirus 1 KT732799 Pteropus associated gemykolovirus 1 KT732800 Pteropus associated gemykolovirus 2 JX185428 Dragonfly associated gemyduguivirus 1 KP974693 Human associated gemyvongvirus 1 KJ547634 Sewage derived gemykrogvirus 1 KJ938717 Caribou associated gemykrogvirus 1 LK931484 Bovine associated gemykrogvirus 1 KF371630 Ostrich associated gemytondvirus 1 KF371631 Rabbit associated gemykroznavirus 1 HQ443515 Becurtovirus KP410285 Becurtovirus JQ920490 Citrus (unclassified) KR131749 Mulberry (unclassified) JX094280 Capulavirus KT214386 Capulavirus KT214373 Capulavirus KT214389 Capulavirus JX559642 Grablovirus KF147918 Grablovirus EF536860 Mastrevirus AF003952 Mastrevirus DQ458791 Mastrevirus KJ437671 Mastrevirus FJ665630 Eragrovirus FJ665634 Eragrovirus U49907 Curtovirus GU734126 Curtovirus JF502373 Begomovirus FM877473 Begomovirus KM386645 Apple (unclassified) FJ665283 Begomovirus KC706535 Begomoviurs X84735 Topocuvirus AF379637 Curtovirus EU921828 Curtovirus KT388088 Turncurtovirus KT388086 Turncurtovirus GU456685 Turncurtovirus KC108902 Turncurtovirus

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GemyduguivirusGemycircularvirus

GemykibivirusGemygorvirus

Gemyvongvirus

Gemykolovirus

GemytondvirusGemykroznavirusGemykrogvirus

Figure 2 Maximum likelihood phylogenetic tree of the Rep amino acid se-

quences inferred using PHYML (Guindon et al 2010) with LGthornGthornI substitution

model and rooted with geminivirus sequences The sequences of geminiviruses

labeled with the corresponding genera names are used as a guide to identify

genera within the Genomoviridae family The cyan line shows a proposed demar-

cation of genera for both Genomoviridae and Geminiviridae Branches withlt75

SH-like branch support have been collapsed


KJ547637 Sewage derived gemycircularvirus 4 KJ547640 Sewage derived gemycircularvirus 4


KM821747 Sewage derived gemycircularvirus 1 KM510192 Bromus associated gemycircularvirus 1

KT862245 Lama associated gemycircularvirus 1 KT862247 Lama associated gemycircularvirus 1


KT862244 Chicken associated gemycircularvirus 1 KT862243 Chicken associated gemycircularvirus 1 KT862246 Chicken associated gemycircularvirus 1 KF413620 Hypericum associated gemycircularvirus 1

KT732797 Pteropus associated gemycircularvirus 3 KM598382 Sclerotinia gemycircularvirus 1 KM598383 Sclerotinia gemycircularvirus 1 GQ365709 Sclerotinia gemycircularvirus 1

KF268025 Sclerotinia gemycircularvirus 1 KM598384 Sclerotinia gemycircularvirus 1 KF268028 Sclerotinia gemycircularvirus 1 KF268026 Sclerotinia gemycircularvirus 1 KF268027 Sclerotinia gemycircularvirus 1

JQ412056 Cassava associated gemycircularvirus 1 JQ412057 Cassava associated gemycircularvirus 1

KT862253 Bovine associated gemycircularvirus 1 JX185429 Dragonfly associated gemycircularvirus 1

KM598385 Odonata associated gemycircularvirus 1 KM598386 Odonata associated gemycircularvirus 1

KT732814 Pteropus associated gemycircularvirus 4 KT732792 Pteropus associated gemycircularvirus 2 KT732793 Pteropus associated gemycircularvirus 2

KP263547 Mongoose associated gemycircularvirus 1 KF371636 Gerygone associated gemycircularvirus 1

KT862249 Sheep associated gemycircularvirus 1 KT862251 Sheep associated gemycircularvirus 1

KR912221 Rat associated gemycircularvirus 1 KM598387 Odonata associated gemycircularvirus 2 KM598388 Odonata associated gemycircularvirus 2


KT732807 Pteropus associated gemycircularvirus 7 KT732809 Pteropus associated gemycircularvirus 7 KT732810 Pteropus associated gemycircularvirus 7 KT732808 Pteropus associated gemycircularvirus 7 KT732811 Pteropus associated gemycircularvirus 7 KT732812 Pteropus associated gemycircularvirus 7

KT732806 Pteropus associated gemycircularvirus 8 HQ335086 Mosquito associated gemycircularvirus 1 KF371635 Mallard associated gemycircularvirus 1

KT309029 Chickadee associated gemycircularvirus 1 KT732804 Pteropus associated gemycircularvirus 1 KT732805 Pteropus associated gemycircularvirus 1 KF371637 Gerygone associated gemycircularvirus 2

KT862242 Chicken associated gemycircularvirus 2 KT598248 Soybean associated gemycircularvirus 1

KF371641 Blackbird associated gemycircularvirus 1 KF371642 Blackbird associated gemycircularvirus 1

KF371643 Blackbird associated gemycircularvirus 1 KF371639 Gerygone associated gemycircularvirus 3

KF371640 Porcine associated gemycircularvirus 2 KF371638 Fur seal associated gemycircularvirus 1 KT862241 Fur seal associated gemycircularvirus 1

KT862248 Equine associated gemycircularvirus 1 KT862250 Porcine associated gemycircularvirus 1


KT253579 Poaceae associated gemycircularvirus 1 KT253578 Poaceae associated gemycircularvirus 1 KT253577 Poaceae associated gemycircularvirus 1

KJ641719 Miniopterus associated gemycircularvirus 1 KT732800 Pteropus associated gemykolovirus 2 KT732798 Pteropus associated gemykolovirus 1 KT732799 Pteropus associated gemykolovirus 1

KF371632 Starling associated gemygorvirus 1 KT862254 Canine associated gemygorvirus 1

KT862238 Mallard associated gemygorvirus 1 KT862239 Mallard associated gemygorvirus 1

JN704610 Mallard associated gemygorvirus 1 KT732790 Pteropus associated gemygorvirus 1 KT732791 Pteropus associated gemygorvirus 1

KJ413144 Sewage derived gemygorvirus 1 KJ547635 Sewage derived gemygorvirus 1

JX185430 Dragonfly associated gemykibivirus 1 KU343137 Human associated gemykibivirus 5

KF371634 Black robin associated gemykibivirus 1 KJ547643 Sewage derived gemykibivirus 1 KT862255 Sewage derived gemykibivirus 1 KT862240 Sewage derived gemykibivirus 1 KT862252 Sewage derived gemykibivirus 1 KJ641726 Rhinolophus associated gemykibivirus 2

KJ547645 Human associated gemykibivirus 1 LK931485 Human associated gemykibivirus 1

KP974694 Human associated gemykibivirus 1 KJ547644 Human associated gemykibivirus 1

KT732813 Pteropus associated gemykibivirus 1 KF371633 Blackbird associated gemykibivirus 1

KT363839 Human associated gemykibivirus 4 KJ547642 Sewage derived gemykibivirus 2

KP263546 Human associated gemykibivirus 3 KP987887 Human associated gemykibivirus 3

KP263545 Mongoose associated gemykibivirus 1 LK931483 Bovine associated gemykibivirus 1

KP263543 Badger associated gemykibivirus 1 KJ641737 Rhinolophus associated gemykibivirus 1 KP263544 Rhinolophus associated gemykibivirus 1

KP133079 Human associated gemykibivirus 1 KP133080 Human associated gemykibivirus 1 KP133078 Human associated gemykibivirus 1 KP133077 Human associated gemykibivirus 1 KP133075 Human associated gemykibivirus 1 KP133076 Human associated gemykibivirus 1

JX185428 Dragonfly associated gemyduguivirus 1 KP974693 Human associated gemyvongvirus 1

KJ547634 Sewage derived gemykrogvirus 1 KJ938717 Caribou associated gemykrogvirus 1

LK931484 Bovine associated gemykrogvirus 1 KF371631 Rabbit associated gemykroznavirus 1

KF371630 Ostrich associated gemytondvirus 198

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Gemyvongvirus

Gemykolovirus


Figure 3 Maximum likelihood phylogenetic tree of the genomes of viruses in the Genomoviridae family The tree was inferred using FastTree (Price Dehal and Arkin

2010) (GTRthornCAT) The numbers at the branches indicate SH-like support values The topology of tree supports the proposed genera demarcation at the genome level

despite there being evidence of recombination within the genomes Branches withlt75 SH-like branch support have been collapsed


35 Gemyvongvirus

The name of the genus is an acronym of words geminivirus-likeand myco-like vong virus (vong means circular in Lao) The sin-gle species Human associated gemyvongvirus 1 (Table 1) within thegenus shares between 56 and 62 genome-wide sequence simi-larity with viruses in other genera and is a divergent taxon inthe phylogenetic trees constructed from either Rep or full ge-nome sequences (Figs 2 and 3)

36 Gemytondvirus

The name of the genus is an acronym of words geminivirus-likeand myco-like tond virus (tond means round in Maltese) Thesingle species Ostrich associated gemytondvirus 1 (Table 1) withinthe genus shares between 53 and 61 genome-wide sequencesimilarity with viruses in other genera and is a divergent taxonin the phylogenetic trees constructed from either Rep or full ge-nome sequences (Figs 2 and 3)

37 Gemykroznavirus

The name of the genus is an acronym of words geminivirus-likeand myco-like krozna virus (krozna means circular in Slovenian)The single species Rabbit associated gemykroznavirus 1 (Table 1)

KM598384 Sclerotinia gemycircularvirus 1 KF268026 Sclerotinia gemycircularvirus 1 KM598382 Sclerotinia gemycircularvirus 1 KF268028 Sclerotinia gemycircularvirus 1 KF268027 Sclerotinia gemycircularvirus 1 KM598383 Sclerotinia gemycircularvirus 1

GQ365709 Sclerotinia gemycircularvirus 1 KF268025 Sclerotinia gemycircularvirus 1

KF371643 Blackbird associated gemycircularvirus 1 KF371641 Blackbird associated gemycircularvirus 1 KF371642 Blackbird associated gemycircularvirus 1

JX185429 Dragonfly associated gemycircularvirus 1 KF371637 Gerygone associated gemycircularvirus 2

KF371639 Gerygone associated gemycircularvirus 3 KM598387 Odonata associated gemycircularvirus 2 KM598388 Odonata associated gemycircularvirus 2


KT732792 Pteropus associated gemycircularvirus 2 KT732793 Pteropus associated gemycircularvirus 2

KF371640 Porcine associated gemycircularvirus 2 KR912221 Rat associated gemycircularvirus 1

KT862253 Bovine associated gemycircularvirus 1 KT862251 Sheep associated gemycircularvirus 1

KF371636 Gerygone associated gemycircularvirus 1 KT862248 Equine associated gemycircularvirus 1

KT862250 Porcine associated gemycircularvirus 1 KJ547641 Sewage derived gemycircularvirus 2

KJ547636 Sewage derived gemycircularvirus 3 KT253579 Poaceae associated gemycircularvirus 1 KT253578 Poaceae associated gemycircularvirus 1 KT253577 Poaceae associated gemycircularvirus 1 KT732794 Pteropus associated gemycircularvirus 10

KJ641719 Miniopterus associated gemycircularvirus 1 KT732800 Pteropus associated gemykolovirus 2

KT732798 Pteropus associated gemykolovirus 1 KT732799 Pteropus associated gemykolovirus 1

KT732806 Pteropus associated gemycircularvirus 8 KT309029 Chickadee associated gemycircularvirus 1



KF371638 Fur seal associated gemycircularvirus 1 KT862241 Fur seal associated gemycircularvirus 1

HQ335086 Mosquito associated gemycircularvirus 1 KT598248 Soybean associated gemycircularvirus 1 KF371632 Starling associated gemygorvirus 1


KT862242 Chicken associated gemycircularvirus 2 KT862249 Sheep associated gemycircularvirus 1

KF413620 Hypericum associated gemycircularvirus 1 KT732803 Pteropus associated gemycircularvirus 6



KT732809 Pteropus associated gemycircularvirus 7 KT732807 Pteropus associated gemycircularvirus 7 KT732811 Pteropus associated gemycircularvirus 7 KT732810 Pteropus associated gemycircularvirus 7 KT732808 Pteropus associated gemycircularvirus 7

KU343137 Human associated gemykibivirus 5 KF371634 Black robin associated gemykibivirus 1

KJ547643 Sewage derived gemykibivirus 1 KT862240 Sewage derived gemykibivirus 1 KT862255 Sewage derived gemykibivirus 1 KT862252 Sewage derived gemykibivirus 1 KF371635 Mallard associated gemycircularvirus 1

KF371633 Blackbird associated gemykibivirus 1 KT862243 Chicken associated gemycircularvirus 1 KT862246 Chicken associated gemycircularvirus 1 KT862244 Chicken associated gemycircularvirus 1

KT363839 Human associated gemykibivirus 4 JX185428 Dragonfly associated gemyduguivirus 1

JX185430 Dragonfly associated gemykibivirus 1 KT862245 Lama associated gemycircularvirus 1 KT862247 Lama associated gemycircularvirus 1

KM510192 Bromus associated gemycircularvirus 1 KT732814 Pteropus associated gemycircularvirus 4


KM821747 Sewage derived gemycircularvirus 1 KJ547637 Sewage derived gemycircularvirus 4

KJ547640 Sewage derived gemycircularvirus 4 KJ547634 Sewage derived gemykrogvirus 1

KJ938717 Caribou associated gemykrogvirus 1 LK931484 Bovine associated gemykrogvirus 1

KP974693 Human associated gemyvongvirus 1 KF371631 Rabbit associated gemykroznavirus 1


KJ641737 Rhinolophus associated gemykibivirus 1 KP263544 Rhinolophus associated gemykibivirus 1 KP263543 Badger associated gemykibivirus 1



KP263547 Mongoose associated gemycircularvirus 1 KJ641726 Rhinolophus associated gemykibivirus 2

KJ547645 Human associated gemykibivirus 1 LK931485 Human associated gemykibivirus 1 KP974694 Human associated gemykibivirus 1

KT732813 Pteropus associated gemykibivirus 1 KJ547644 Human associated gemykibivirus 1

KJ547642 Sewage derived gemykibivirus 2 KT862238 Mallard associated gemygorvirus 1 KT862239 Mallard associated gemygorvirus 1

JN704610 Mallard associated gemygorvirus 1 KT862254 Canine associated gemygorvirus 1

KT732790 Pteropus associated gemygorvirus 1 KT732791 Pteropus associated gemygorvirus 1

KJ413144 Human associated gemygorvirus 1 KJ547635 Sewage derived gemygorvirus 1

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Gemyvongvirus

Gemykolovirus


Figure 4 Maximum likelihood phylogenetic tree of the CP amino acid sequences

inferred using PHYML (Guindon et al 2010) with LGthornGthornI substitution models

and rooted with geminivirus sequences Branches withlt75 SH-like branch sup-

port have been collapsed

0 10 20 30 40 50 60 70 80

Percentage diversity

Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

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Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus

Figure 5 Summary of genera and the associated species and their diversity

(within genera) within the Genomoviridae family


within the genus shares between 56 and 61 genome-widesequence similarity with other sequences in other genera and isa divergent taxon in the phylogenetic trees constructed fromeither Rep or full genome sequences (Figs 2 and 3)

38 Gemyduguivirus

The name of the genus is an acronym of words geminivirus-likeand myco-like dugui virus (dugui means circular in Mongolian)The single species Dragonfly associated gemyduguivirus 1 (Table 1)within the genus shares between 57 and 62 genome-wide se-quence similarity with viruses in other genera and is a divergenttaxon in the phylogenetic trees constructed from either Rep orfull genome sequences (Figs 2 and 3)

4 Conserved sequence motifs in theGenomoviridae

CRESS DNA viruses replicate through the rolling circle replica-tion (RCR) mechanism which is similar to that used by bacterialplasmids (Khan 1997 Chandler et al 2013 Ruiz-Maso et al2015) RCR is initiated by the Rep encoded by CRESS DNAviruses cleaving the dsDNA between positions 7 and 8 of anonanucleotide sequence located at a putative stem-loopstructure at the origin of replication (Heyraud-Nitschke et al1995 Laufs et al 1995b Timchenko et al 1999 RosarioDuffy and Breitbart 2012) In the case of genomoviruses this

nonanucleotide is variable (lsquoTAWWDWRNrsquo) with lsquoTAATWYATrsquobeing the consensus nonanucleotide for gemycircularviruseswhereas gemykibiruses display the greatest variation inthis motifmdashlsquoWATAWWHANrsquo (Fig 6 Supplementary Data S1)In contrast we note that within the Geminiviridae familyincluding all recently described geminiviruses (Varsani et al2009 Briddon et al 2010 Krenz et al 2012 Loconsole et al 2012Bernardo et al 2013 Heydarnejad et al 2013 Ma et al 2015Bernardo et al 2016) the consensus nonanucleotide motif islsquoTRAKATTRCrsquo

The N terminus of the Rep contains motifs that are impor-tant for initiating RCR and it is not surprising that some of thesemotifs are well conserved across many ssDNA viruses phagesand plasmids that replicate using the RCR mechanism (Ilyinaand Koonin 1992 Vega-Rocha et al 2007a Rosario Duffy andBreitbart 2012 Krupovic 2013) The presence of a single cata-lytic tyrosine residue in the RCR motif III classifies genomovi-rus geminivirus bacilladnavirus circovirus and nanovirus Repsas members of superfamily II (Ilyina and Koonin 1992Krupovic 2013)

In genomoviruses the conserved sequence of the RCRmotif I which is thought to be involved in the recognition ofiterative sequences associated with the origin of replicationis predominantly lsquouuTYxQrsquo (u denotes hydrophobic residuesand x any residue) (Fig 6 Supplementary Data S1) with theexception of the Reps of currently known gemykolovirusesand gemykrogviruses The genomovirus RCR motif II lsquoxHxHxrsquo

Figure 6 Summary of conserved motifs that is nonanucleotide and Rep motifs illustrated using WebLogo3 (Crooks et al 2004) identified in the family Genomoviridae as

a whole and its nine genera separately Note the highly derived Walker A motif (GPHRRRRT) in the sole member of the genus Gemytondvirus


(Fig 6 Supplementary Data S1) resembles that found in gemini-viruses and early work has shown that histidines in this motifcoordinate divalent metal ions Mg2thornor Mn2thorn which areimportant cofactors for endonuclease activity at the origin ofreplication (Koonin and Ilyina 1992 Laufs et al 1995b)Genomoviruses have an RCR motif III of lsquoYxxKrsquo and based onother Rep studies this motif is involved in the dsDNA cleavageand subsequent covalent attachment of Rep through thecatalytic tyrosine residue to the 50 end of the cleaved product(Laufs et al 1995a b Orozco and Hanley-Bowdoin 1998Timchenko et al 1999 Steinfeldt Finsterbusch and Mankertz2006 Rosario Duffy and Breitbart 2012) The conserved lysineresidue in the RCR motif III (Fig 6 Supplementary Data S1) isproposed to mediate binding and positioning during catalysis(Vega-Rocha et al 2007a b) A fourth conserved motif the gemi-nivirus Rep sequence (GRS) is only found in geminiviruses andgenomoviruses (Fig 6) In geminiviruses it enables appropriatespatial arrangements of RCR motifs II and III (Nash et al 2011)Site-directed mutagenesis of the GRS domain in tomato goldenmosaic virus yielded non-infectious clones demonstrating thatthe GRS is essential for geminivirus replication (Nash et al 2011)and it is likely this is also the case for genomoviruses

Rep is a multifunctional protein with both endonucleaseand helicase activities Rep helicase activity is mediated by con-served motifs known as Walker A Walker B and motif C locatedin a C-terminal NTP-binding domain (Fig 6 SupplementaryData S1) (Gorbalenya Koonin and Wolf 1990 Koonin 1993Choudhury et al 2006 Clerot and Bernardi 2006) The helicasedomain found in Rep proteins of eukaryotic ssDNA viruses be-longs to the helicase superfamily 3 (Gorbalenya Koonin andWolf 1990 Koonin 1993) The conserved Walker A motif ofgenomoviruses is lsquoGxxxxGKTrsquo with the exception of gemytond-virus which contains a highly derived variant of this motif(GPHRRRRT Fig 6) Previous studies have shown that duringsynthesis of progeny strands Rep helicase activity unwinds thedsDNA intermediate in the 30ndash50 direction using nucleotide tri-phosphates as an energy source (Choudhury et al 2006 Clerotand Bernardi 2006) Walker A motif forms part of the lsquoP-looprsquostructure in the NTP-binding domain that facilitates ATP recog-nition and binding with a conserved lysine residue (Desbiez et al1995 Timchenko et al 1999 Choudhury et al 2006 Clerot andBernardi 2006 Rosario Duffy and Breitbart 2012 George et al2014) The Walker B of genomoviruses is predominantly lsquouuDDursquo(Fig 6 Supplementary Data S1) whereas the motif C is lsquouxxNrsquo(u denotes hydrophobic residues and x any residue Fig 6Supplementary Data S1) The hydrophobic residues in Walker Bmotif contribute to ATP binding and are essential for ATP hydro-lysis whereas the one in motif C (Fig 6 Supplementary Data S1)interacts with the gamma phosphate of ATP and the nucleo-philic water molecule via a conserved asparagine residue(Choudhury et al 2006 George et al 2014)

Genomoviruses from different genera display distinct signa-tures within the nonanucleotide as well as conserved nucleaseand helicase motifs which are generally consistent with theproposed taxa (Fig 6 Supplementary Data S1)

5 Concluding remarks

The Reps of genomoviruses are most closely related to those ofgeminiviruses and hence here we used a geminivirustaxonomy-informed approach to classify 121 genomovirusesinto Rep sequence-based genera Within the Genomoviridae fam-ily we establish eight new genera in addition to the one createdpreviously (Krupovic et al 2016) Detailed analysis of sequence

motifs conserved within the genomoviral genomes further sup-ports the validity of the proposed genera We also define a spe-cies demarcation criterion of 78 genome-wide identity that issequences that sharegt78 pairwise identity with othergenomovirus sequences belong to the same species and thosethat sharelt78 can be considered as new species It is worthnoting that despite the fact that geminiviruses have been stud-ied for over two decades the sequence diversity of all knowngeminiviruses is similar to that of the recently discoveredgenomoviruses (46 vs 47 respectively) This observationstrongly suggests that the extent of sequence diversity withinthis expansive virus group remains largely unexplored

Although the guidelines presented here are tailored for theclassification of viral genomes in the family Genomoviridae asimilar sequence-based framework can be easily adapted forother virus clusters identified though metagenomics studiesand lacking a pre-existing taxonomic framework in particularfor novel CRESS DNA viruses We do acknowledge that this ap-proach deviates from a previous norm that used a set of criteriaincluding biological properties such as host range pathologyvectors etc coupled with sequence data However given thatthe rate at which genome sequences of uncultivated viruses arebeing identified from various sources we need to establishmore robust classification approaches that can easily be imple-mented on the bases of sequence data alone Indeed this neces-sity is acknowledged by the ICTV which encouragessubmissions of taxonomic proposals for classification of virusesthat are known exclusively from their genome sequences(Simmonds et al 2017) This new tide in virus taxonomy is ex-pected to catalyze the comprehension of the diversity ecologyand evolution of the global virome

Supplementary data

Supplementary data are available at Virus Evolution online

Disclaimer

This article is based on the taxonomic proposal 2016001a-agFUv5Genomoviridae which has been considered and ap-proved by the Executive Committee (EC) of the ICTV AV and MKare elected members of the ICTV EC

Conflict of interest None declared

ReferencesAdams M J et al (2016) lsquoRatification Vote on Taxonomic

Proposals to the International Committee on Taxonomy ofVirusesrsquo Archives of Virology 161 2921ndash49

Bernardo P et al (2013) lsquoIdentification and Characterisation of aHighly Divergent Geminivirus Evolutionary and TaxonomicImplicationsrsquo Virus Research 177 35ndash45

et al (2016) lsquoMolecular Characterization and Prevalence ofTwo Capulaviruses Alfalfa Leaf Curl Virus From France andEuphorbia Caput-Medusae Latent Virus From South AfricarsquoVirology 493 142ndash53

Briddon R W et al (2010) lsquoTurnip Curly Top Virus a HighlyDivergent Geminivirus Infecting Turnip in Iranrsquo Virus Research152 169ndash75

Brown J K et al (2015) lsquoRevision of Begomovirus TaxonomyBased on Pairwise Sequence Comparisonsrsquo Archives of Virology160 1593ndash619


Cadar D et al (2013) lsquoPhylogeny Spatio-TemporalPhylodynamics and Evolutionary Scenario of Torque teno susvirus 1 (TTSuV1) and 2 (TTSuV2) in Wild Boars Fast Dispersaland High Genetic Diversityrsquo Veterinary Microbiology 166 200ndash13

Chandler M et al (2013) lsquoBreaking and Joining Single-StrandedDNA the HUH Endonuclease Superfamilyrsquo Nature ReviewsMicrobiology 11 525ndash38

Choudhury N R et al (2006) lsquoThe Oligomeric Rep Protein ofMungbean Yellow Mosaic India Virus (MYMIV) Is a LikelyReplicative Helicasersquo Nucleic Acids Research 34 6362ndash77

Clerot D and Bernardi F (2006) lsquoDNA Helicase Activity IsAssociated with the Replication Initiator Protein Rep ofTomato Yellow Leaf Curl Geminivirusrsquo Journal of Virology 8011322ndash30

Conceicao-Neto N et al (2015) lsquoFecal Virome Analysis of ThreeCarnivores Reveals a Novel Nodavirus and MultipleGemycircularvirusesrsquo Virology Journal 12 79

Crooks G E et al (2004) lsquoWebLogo a Sequence Logo GeneratorrsquoGenome Research 14 1188ndash90

Dayaram A et al (2012) lsquoMolecular Characterisation of a NovelCassava Associated Circular ssDNA Virusrsquo Virus Research 166130ndash5

et al (2015) lsquoIdentification of Diverse Circular Single-Stranded DNA Viruses in Adult Dragonflies and Damselflies(Insecta Odonata) of Arizona and Oklahoma USArsquo InfectionGenetics and Evolution 30 278ndash87

et al (2016) lsquoDiverse Circular Replication-AssociatedProtein Encoding Viruses Circulating in InvertebratesWithin a Lake Ecosystemrsquo Infection Genetics and Evolution 39304ndash16

Desbiez C et al (1995) lsquoRep Protein of Tomato Yellow Leaf CurlGeminivirus Has an ATPase Activity Required for Viral DNAReplicationrsquo Proceedings of the National Academy of Sciences of theUnited States of America 92 5640ndash4

Du Z et al (2014) lsquoIdentification and MolecularCharacterization of a Single-Stranded Circular DNA Virus withSimilarities to Sclerotinia sclerotiorum Hypovirulence-Associated DNA Virus 1rsquo Archives of Virology 159 1527ndash31

Duffy S and Holmes E C (2008) lsquoPhylogenetic Evidence forRapid Rates of Molecular Evolution in the Single-StrandedDNA Begomovirus Tomato Yellow Leaf Curl Virusrsquo Journal ofVirology 82 957ndash65

and (2009) lsquoValidation of High Rates of NucleotideSubstitution in Geminiviruses Phylogenetic Evidence FromEast African Cassava Mosaic Virusesrsquo Journal of GeneralVirology 90 1539ndash47

Dutilh B E et al (2014) lsquoA Highly Abundant BacteriophageDiscovered in the Unknown Sequences of Human FaecalMetagenomesrsquo Nature Communications 5 4498

Firth C et al (2009) lsquoInsights into the Evolutionary History of anEmerging Livestock Pathogen Porcine Circovirus 2rsquo Journal ofVirology 83 12813ndash21

George B et al (2014) lsquoMutational Analysis of the HelicaseDomain of a Replication Initiator Protein Reveals Critical Rolesof Lys 272 of the Brsquo Motif and Lys 289 of the Beta-Hairpin Loopin Geminivirus Replicationrsquo Journal of General Virology 951591ndash602

Gorbalenya A E Koonin E V and Wolf Y I (1990) lsquoA NewSuperfamily of Putative NTP-Binding Domains Encoded byGenomes of Small DNA and RNA Virusesrsquo FEBS Letters 262145ndash8

Grigoras I et al (2010) lsquoHigh Variability and Rapid Evolution of aNanovirusrsquo Journal of Virology 84 9105ndash17

Guindon S et al (2010) lsquoNew Algorithms and Methods toEstimate Maximum-Likelihood Phylogenies Assessing thePerformance of PhyML 30rsquo Systems Biology 59 307ndash21

Halary S et al (2016) lsquoNovel Single-Stranded DNA CircularViruses in Pericardial Fluid of Patient with RecurrentPericarditisrsquo Emerging infectious diseases 22 1839ndash41

Hanna Z R et al (2015) lsquoIsolation of a Complete Circular VirusGenome Sequence from an Alaskan Black-Capped Chickadee(Poecile atricapillus) Gastrointestinal Tract Samplersquo GenomeAnnouncements 3 e01081_15

Harkins G W et al (2009) lsquoExperimental Evidence Indicatingthat Mastreviruses Probably Did Not Co-Diverge with TheirHostsrsquo Virology Journal 6 104

et al (2014) lsquoTowards Inferring the Global Movement ofBeak and Feather Disease Virusrsquo Virology 450ndash451 24ndash33

Heydarnejad J et al (2013) lsquoFulfilling Kochrsquos Postulates for BeetCurly Top Iran Virus and Proposal for Consideration of NewGenus in the Family Geminiviridaersquo Archives of Virology 158435ndash43

Heyraud-Nitschke F et al (1995) lsquoDetermination of the OriginCleavage and Joining Domain of Geminivirus Rep ProteinsrsquoNucleic Acids Research 23 910ndash6

Ilyina T V and Koonin E V (1992) lsquoConserved SequenceMotifs in the Initiator Proteins for Rolling Circle DNAReplication Encoded by Diverse Replicons from EubacteriaEucaryotes and Archaebacteriarsquo Nucleic Acids Research 203279ndash85

Khan S A (1997) lsquoRolling-Circle Replication of Bacterial PlasmidsrsquoMicrobiology and Molecular Biology Reviews 61 442ndash55

Kolawole A O et al (2014) lsquoFlexibility in Surface-Exposed Loopsin a Virus Capsid Mediates Escape From AntibodyNeutralizationrsquo Journal of Virology 88 4543ndash57

Koonin E V (1993) lsquoA Common Set of Conserved Motifs in a VastVariety of Putative Nucleic Acid-Dependent ATPases IncludingMCM Proteins Involved in the Initiation of Eukaryotic DNAReplicationrsquo Nucleic Acids Research 21 2541ndash7

and Ilyina T V (1992) lsquoGeminivirus Replication ProteinsAre Related to Prokaryotic Plasmid Rolling Circle DNAReplication Initiator Proteinsrsquo Journal of General Virology 732763ndash6

Kraberger S et al (2013) lsquoDiscovery of Sclerotinia sclerotiorumHypovirulence-Associated Virus-1 in Urban River Sedimentsof Heathcote and Styx Rivers in Christchurch City NewZealandrsquo Genome Announcements 1 e00559_13

et al (2015a) lsquoCharacterisation of a Diverse Range ofCircular Replication-Associated Protein Encoding DNA VirusesRecovered From a Sewage Treatment Oxidation PondrsquoInfection Genetics and Evolution 31 73ndash86

et al (2015b) lsquoIdentification of Novel Bromus- andTrifolium-Associated Circular DNA Virusesrsquo Archives ofVirology 160 1303ndash11

Krenz B et al (2012) lsquoComplete Genome Sequence of aNew Circular DNA Virus From Grapevinersquo Journal of Virology86 7715

Krupovic M (2013) lsquoNetworks of Evolutionary InteractionsUnderlying the Polyphyletic Origin of ssDNA Virusesrsquo CurrentOpinion in Virology 3 578ndash86

et al (2016) lsquoGenomoviridae a New Family of WidespreadSingle-Stranded DNA Virusesrsquo Archives of Virology 1612633ndash43

Labonte J M and Suttle C A (2013) lsquoPreviously Unknown andHighly Divergent ssDNA Viruses Populate the Oceansrsquo ISMEJournal 7 2169ndash77


Lamberto I et al (2014) lsquoMycovirus-Like DNA Virus SequencesFrom Cattle Serum and Human Brain and Serum SamplesFrom Multiple Sclerosis Patientsrsquo Genome Announcements 2e00848_14

Laufs J et al (1995a) lsquoIdentification of the Nicking Tyrosine ofGeminivirus Rep Proteinrsquo FEBS Letters 377 258ndash62

et al (1995b) lsquoIn Vitro Cleavage and Joining at the ViralOrigin of Replication by the Replication Initiator Protein ofTomato Yellow Leaf Curl Virusrsquo Proceedings of the NationalAcademy of Sciences of the United States of America 923879ndash83

Li W et al (2015) lsquoA Novel Gemycircularvirus From ExperimentalRatsrsquo Virus Genes 51 302ndash5

Liu S et al (2016) lsquoFungal DNA Virus Infects a MycophagousInsect and Utilizes It as a Transmission Vectorrsquo Proceedings ofthe National Academy of Sciences of the United States of AmericaDOI 101073pnas1608013113

Loconsole G et al (2012) lsquoIdentification of a Single-StrandedDNA Virus Associated with Citrus Chlorotic Dwarf Disease aNew Member in the Family Geminiviridaersquo Virology 432162ndash72

Ma Y et al (2015) lsquoIdentification and MolecularCharacterization of a Novel Monopartite GeminivirusAssociated with Mulberry Mosaic Dwarf Diseasersquo Journal ofGeneral Virology 96 2421ndash34

Male M F et al (2015) lsquoGenome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island ofTongarsquo Genome Announcements 3 e01144_15

et al (2016) lsquoCycloviruses Gemycircularviruses and OtherNovel Replication-Associated Protein Encoding CircularViruses in Pacific flying fox (Pteropus tonganus) Faecesrsquo InfectionGenetics and Evolution 39 279ndash92

Martin D P et al (2011) lsquoRecombination in Eukaryotic SingleStranded DNA Virusesrsquo Viruses 3 1699ndash738

Marzano S Y and Domier L L (2016) lsquoNovel MycovirusesDiscovered from Metatranscriptomics Survey of SoybeanPhyllosphere Phytobiomesrsquo Virus Research 213 332ndash42

Muhire B et al (2013) lsquoA Genome-Wide Pairwise-Identity-BasedProposal for the Classification of Viruses in the GenusMastrevirus (family Geminiviridae)rsquo Archives of Virology 1581411ndash24

Muhire B M Varsani A and Martin D P (2014) lsquoSDT a VirusClassification Tool Based on Pairwise Sequence Alignment andIdentity Calculationrsquo PLoS One 9 e108277

Nash T E et al (2011) lsquoFunctional Analysis of a Novel MotifConserved Across Geminivirus Rep Proteinsrsquo Journal ofVirology 85 1182ndash92

Ng T F et al (2011) lsquoBroad Surveys of DNA Viral DiversityObtained Through Viral Metagenomics of Mosquitoesrsquo PLoSOne 6 e20579

et al (2014) lsquoPreservation of Viral Genomes in 700-y-oldCaribou Feces from a Subarctic Ice Patchrsquo Proceedings of theNational Academy of Sciences of the United States of America 11116842ndash7

Nguyen V G et al (2012) lsquoPopulation Dynamics and ORF3 GeneEvolution of Porcine Circovirus Type 2 Circulating in KorearsquoArchives of Virology 157 799ndash810

Orozco B M and Hanley-Bowdoin L (1998) lsquoConservedSequence and Structural Motifs Contribute to the DNA Bindingand Cleavage Activities of a Geminivirus Replication ProteinrsquoJournal of Biological Chemistry 273 24448ndash56

Phan T G et al (2015) lsquoSmall Circular Single Stranded DNAViral Genomes in Unexplained Cases of Human EncephalitisDiarrhea and in Untreated Sewagersquo Virology 482 98ndash104

Price M N Dehal P S and Arkin A P (2010) lsquoFastTree 2mdashApproximately Maximum-Likelihood Trees for LargeAlignmentsrsquo PLoS One 5 e9490

Rosario K et al (2012) lsquoDiverse Circular ssDNA VirusesDiscovered in Dragonflies (Odonata Epiprocta)rsquo Journal ofGeneral Virology 93 2668ndash81

Duffy S and Breitbart M (2012) lsquoA Field Guide toEukaryotic Circular Single-Stranded DNA Viruses InsightsGained From Metagenomicsrsquo Archives of Virology 157 1851ndash71

Roux S et al (2012) lsquoEvolution and Diversity of the MicroviridaeViral Family Through a Collection of 81 New CompleteGenomes Assembled from Virome Readsrsquo PLoS One 7 e40418

et al (2013) lsquoChimeric Viruses Blur the Borders Betweenthe Major Groups of Eukaryotic Single-Stranded DNA VirusesrsquoNature Communications 4 2700

Ruiz-Maso J A et al (2015) lsquoPlasmid Rolling-Circle ReplicationrsquoMicrobiology Spectrum 3 PLAS-0035-2014

Shangjin C Cortey M and Segales J (2009) lsquoPhylogeny andEvolution of the NS1 and VP1VP2 Gene Sequences fromPorcine Parvovirusrsquo Virus Research 140 209ndash15

Sikorski A et al (2013) lsquoNovel Myco-Like DNA VirusesDiscovered in the Faecal Matter of Various Animalsrsquo VirusResearch 177 209ndash16

Simmonds P et al (2017) lsquoVirus Taxonomy in the Age ofMetagenomicsrsquo Nature Reviews Microbiology (in press) DOI101038nrmicro2016177

Steel O et al (2016) lsquoCircular Replication-Associated ProteinEncoding DNA Viruses Identified in the Faecal Matter ofVarious Animals in New Zealandrsquo Infection Genetics andEvolution 43 151ndash64

Steinfeldt T Finsterbusch T and Mankertz A (2006)lsquoDemonstration of NickingJoining Activity at the Origin ofDNA Replication Associated with the Rep and Reprsquo Proteins ofPorcine Circovirus Type 1rsquo Journal of Virology 80 6225ndash34

Streck A F et al (2011) lsquoHigh Rate of Viral Evolution in theCapsid Protein of Porcine Parvovirusrsquo Journal of GeneralVirology 92 2628ndash36

Timchenko T et al (1999) lsquoA Single Rep Protein InitiatesReplication of Multiple Genome Components of Faba BeanNecrotic Yellows Virus a Single-Stranded DNA Virus ofPlantsrsquo Journal of Virology 73 10173ndash82

Uch R et al (2015) lsquoDivergent Gemycircularvirus in HIV-PositiveBlood Francersquo Emerging Infectious Diseases 21 2096ndash8

van den Brand J M et al (2012) lsquoMetagenomic Analysis of theViral Flora of Pine Marten and European Badger Fecesrsquo Journalof Virology 86 2360ndash5

Varsani A et al (2009) lsquoA Highly Divergent South AfricanGeminivirus Species Illuminates the Ancient EvolutionaryHistory of This Familyrsquo Virology Journal 6 36

et al (2014a) lsquoRevisiting the Classification of CurtovirusesBased on Genome-Wide Pairwise Identityrsquo Archives of Virology159 1873ndash82

et al (2014b) lsquoEstablishment of Three New Genera in theFamily Geminiviridae Becurtovirus Eragrovirus andTurncurtovirusrsquo Archives of Virology 159 2193ndash203

Vega-Rocha S et al (2007a) lsquoSolution Structure Divalent Metaland DNA Binding of the Endonuclease Domain from theReplication Initiation Protein from Porcine Circovirus 2rsquoJournal of Molecular Biology 367 473ndash87

et al (2007b) lsquoSolution Structure of the EndonucleaseDomain from the Master Replication Initiator Protein of theNanovirus Faba Bean Necrotic Yellows Virus and Comparisonwith the Corresponding Geminivirus and CircovirusStructuresrsquo Biochemistry 46 6201ndash12


Wu Z et al (2016) lsquoDeciphering the Bat Virome Catalog to BetterUnderstand the Ecological Diversity of Bat Viruses and the BatOrigin of Emerging Infectious Diseasesrsquo ISME Journal 10609ndash20

Yau S et al (2011) lsquoVirophage Control of Antarctic Algal Host-Virus Dynamicsrsquo Proceedings of the National Academy of Sciencesof the United States of America 108 6163ndash8

Yu X et al (2010) lsquoA Geminivirus-Related DNA Mycovirus thatConfers Hypovirulence to a Plant Pathogenic FungusrsquoProceedings of the National Academy of Sciences of the United Statesof America 107 8387ndash92

et al (2013) lsquoExtracellular Transmission of a DNAMycovirus and Its Use as a Natural Fungicidersquo Proceedings of theNational Academy of Sciences of the United States of America 1101452ndash7

Yutin N et al (2015) lsquoA Novel Group of Diverse Polinton-LikeViruses Discovered by Metagenome Analysisrsquo BMC Biology 13 95

Zhang W et al (2016) lsquoViral Nucleic Acids in Human PlasmaPoolsrsquo Transfusion 56 2248ndash55

Zhou C et al (2015) lsquoA Novel Gemycircularvirus in anUnexplained Case of Child Encephalitisrsquo Virology Journal12 197


when the new viruses fall into existing taxa with well-defined de-marcation criteria However in the absence of isolated representa-tives and established taxonomic framework rational definition ofappropriate taxonomic ranks such as families genera and spe-cies for novel groups of uncultured viruses might be considerablymore complex Solutions to this problem are perhaps most ur-gently needed in the case of single-stranded (ss) DNA viruseswhich are extremely widespread in nature Due to their small ge-nomes sizes high mutation and recombination rates (Duffy andHolmes 2008 Duffy and Holmes 2009 Firth et al 2009 Harkinset al 2009 2014 Grigoras et al 2010 Martin et al 2011 Streck et al2011 Nguyen et al 2012 Cadar et al 2013 Roux et al 2013) andrelative ease of genome amplification an incredible diversity ofthese viruses has been discovered through metagenomics studiesin all conceivable habitats ssDNA viruses infect cells from allthree domains of life and are currently classified by theInternational Committee on Taxonomy of Viruses (ICTV) intoeleven families and one unassigned genus Members of the fami-lies Microviridae and Inoviridae infect bacteria viruses of the fami-lies Spiraviridae and Pleolipoviridae prey on archaea whereaseukaryotes host viruses classified into the families AnelloviridaeBidnaviridae Circoviridae Geminiviridae Genomoviridae Nanoviridaeand Parvoviridae and the unassigned genus Bacilladnavirus In addi-tion several widespread groups of uncultured viruses discoveredby viral metagenomics remain unclassified predominantly thosethat are circular replication-associated protein encoding single-stranded (CRESS) DNA viruses (Simmonds et al 2017)

The Genomoviridae family is one of the most recently establishedfamilies of ssDNA viruses (Adams et al 2016 Krupovic et al 2016)The family currently includes a single genus Gemycircularviruswhich contains a single species Sclerotinia gemycircularvirus 1 en-compassing a single isolate Sclerotinia sclerotiorumhypovirulence-associated DNA virus 1 (SsHADV-1) SsHADV-1 wasisolated from a plantndashpathogenic fungus Sclerotinia sclerotiorum andis the only ssDNA virus known to infect fungi (Yu et al 2010 2013)Recently Liu et al (2016) have shown that SsHADV-1 is able to in-fect a mycophagous insect (Lycoriella ingenua) which acts as a trans-mission vector SsHADV-1 virions are non-enveloped isometric20ndash22 nm in diameter and assembled from a single capsid protein(CP) (Yu et al 2010) The genome is a circular ssDNA molecule of2166 nucleotides and contains two genesmdashfor CP and rolling-circlereplication initiation protein (Rep) Like in many other ssDNA vi-ruses with circular genomes the large intergenic region ofSsHADV-1 contains a potential stem-loop structure with a nonanu-cleotide (TAATATTAT) motif at its apex which is likely to be im-portant for rolling-circle replication initiation The CP of SsHADV-1is not recognizably similar to the corresponding proteins from vi-ruses in other taxa Although SsHADV-1 remains the only isolatedand classified member of the Genomoviridae 121 viral genomeswith varying degree of similarity to that of SsHADV-1 have been re-covered and sequenced from various environmental plant- andanimal-associated samples indicating that these viruses are wide-spread and abundant in the environment (Table 1) However aproper taxonomic framework and demarcation criteria necessaryto accommodate these viruses within the family Genomoviridae arelacking Here we explore the diversity and evolution of unculturedSsHADV-1-like viruses and attempt to establish a framework fortheir classification based on sequence data alone

2 Genomoviridae diversity and speciesclassification

At the time of the analysis (August 2016) there were 121SsHADV-1-like genome sequences in the GenBank database

Each of these genomes encodes two putative proteins homolo-gous to the CP and Rep of SsHADV-1 highlighting strongcoherence of this virus assemblage Nevertheless there is a con-siderable sequence divergence within the group (SupplementaryFig S1) To investigate the extent of genomoviral sequence diver-sity we analyzed the distribution of genome-wide pairwiseidentities (one minus Hamming distances of pairwise alignedsequences with pairwise deletion of gaps) across all 121 availablegenomes (Fig 1A) using SDT v12 (Muhire Varsani and Martin2014) Most of the virus genomes in our dataset share 56ndash66genome-wide pairwise identities and only a handful containednearly identical relatives (98 identity) indicating that se-quence diversity among SsHADV-1-like viruses remains largelyunexplored

Pairwise comparison of the Rep and CP protein sequencesrevealed a broader distribution of identity values (Fig 1B and C)Notably the CPs were considerably more divergent that theReps with the highest proportion of pairwise identities being33 (versus 48 for the Rep) This observation is in line withfunctional differences of the two proteins and the fact that viralCPs often encompass host recognition determinants which areunder constant pressure to co-evolve with the cellular receptors(Kolawole et al 2014 Shangjin Cortey and Segales 2009) Basedon the analysis of distribution of the pairwise identities acrossgenomes CPs and Reps we consider a threshold of 78 to be aconservative value for species demarcation Thus all viral ge-nomes showing identities higher than this value should be con-sidered as variants of the existing species Nonetheless theremay be situations where it is difficult to assign species becausea particular new sequence is

1 gt78 similar to sequences from a particular species butislt 78 similar to other variants of that same species

2 gt78 similar to sequences from two or more differentspecies

To resolve the above conflicts we suggest adopting a similarapproach proposed for geminiviruses (Muhire et al 2013Varsani et al 2014a b Brown et al 2015) To resolve conflict 1we suggest that the new sequence be classified within any spe-cies in which it sharesgt78 identity to any one variant for-merly classified as belonging to that species even if it islt78identical to other viruses within that species To resolve conflict2 we suggest that the new sequence be considered as belongingto the species with sequences with which it shares the highestdegree of similarity

3 Rep-based approach for creation of genera

Maximum likelihood phylogenetic analyses based on the Rep of121 genomoviruses revealed several well-supported clades thatcould be considered as genera within the family (Fig 2) Wenote that the clades obtained in the Rep-based phylogeny arenot fully consistent with those obtained in the phylogeneticanalysis of the full genome or the more diverse CP sequences(Figs 3 and 4) This is most explicit in the case of the newly pro-posed genus Gemykolovirus (see below) In the Rep-based treecorresponding sequences form a sister clade to the single repre-sentative of the genus Gemyduguivirus (Fig 2) In contrast in thewhole-genome-based phylogeny gemykoloviruses form a sistergroup to members of the genus Gemycircularvirus (Fig 3) Thereason for this incongruence is likely to be intra-familial recom-bination between different genomovirus genomes resulting inchimeric entities encoding Rep and CP with different evolution-ary histories (Kraberger et al 2015a) Indeed in the CP-based


Tab

le1

Det

ails

of

allm

embe

rso

fth

eG

enom

ovir

idae

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Gem

ycir

cula

rvir

us

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

1P9

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

2P2

2T

urdu

sm

erul

aB

lack

bird

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

3as

41O

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Bovi

neas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5352

Fec7

8023

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Brom

us

asso

ciat

edge

myc

ircu

larv

irus

1K

M51

0192

Bas

CV

-3N

Z-N

ZG

01Se

f-20

12Br

omus

hord

eace

usSo

ftbr

om

eB

ull

gras

sLe

afN

ewZ

eala

nd

Kra

berg

eret

al(

2015

b)

Cas

sava

asso

ciat

edge

myc

ircu

larv

irus

1JQ

4120

56G

14M

anih

otes

cule

nta

Cas

sava

Leaf

Gh

ana

Day

aram

etal

(20

12)

Cas

sava

asso

ciat

edge

myc

ircu

larv

irus

1JQ

4120

57G

5M

anih

otes

cule

nta

Cas

sava

Leaf

Gh

ana

Day

aram

etal

(20

12)

Chi

ckad

eeas

soci

ated

gem

ycir

cula

rvir

us1

KT

3090

2925

4065

908

Poec

ileat

rica

pillu

sB

lack

-cap

ped

chic

kad

eeB

ucc

alan

d

clo

acal

swab

USA

Han

na

etal

(20

15)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4327

Fec7

9971

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4429

Fec7

9971

Ilam

aLa

ma

glam

aLl

ama

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4630

Fec7

9971

ho

rse

Equu

sfe

rus

caba

llus

Ho

rse

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s2

KT

8622

4227

Fec1

6497

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Dra

gonfl

yas

soci

ated

gem

ycir

cula

rvir

us1

JX18

5429

FL2-

5X-2

010

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAR

osa

rio

etal

(20

12)

Equi

neas

soci

ated

gem

ycir

cula

rvir

us

1K

T86

2248

30Fe

c800

61h

ors

eEq

uus

feru

sca

ballu

sH

ors

eFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Fur

seal

asso

ciat

edge

myc

ircu

larv

irus

1K

F371

638

as50

Arc

toce

phal

usfo

rste

riN

ewZ

eala

nd

fur

seal

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Fur

seal

asso

ciat

edge

myc

ircu

larv

irus

1K

T86

2241

27Fe

c1ch

icke

nG

allu

sga

llus

dom

esti

cus

Ch

icke

nFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us1

KF3

7163

6P2

4aG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us2

KF3

7163

7P2

4bG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us3

KF3

7163

9P2

4cG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Hyp

eric

um

asso

ciat

edge

myc

ircu

larv

irus

1K

F413

620

VN

HJ1

WH

yper

icum

japo

nicu

mH

yper

icu

mLe

afV

ietn

amD

uet

al(

2014

)

Lam

aas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4529

Fec8

0018

llam

aLa

ma

glam

aLl

ama

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Lam

aas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4730

Fec8

0018

ho

rse

Equu

sfe

rus

caba

llus

Ho

rse

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Mal

lard

asso

ciat

edge

myc

ircu

larv

iru

s1

KF3

7163

5as

24A

nas

plat

yrhy

ncho

sM

alla

rdd

uck

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Min

iopt

erus

asso

ciat

edge

myc

ircu

larv

irus

1K

J641

719

BtM

f-C

V-2

3G

D20

12M

inio

pter

usfu

ligin

osus

Bat

Phar

ynge

alamp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ycir

cula

rvir

us1

KP2

6354

747

8dH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Mos

quit

oas

soci

ated

gem

ycir

cula

rvir

us1

HQ

3350

86SD

BV

LG

Cul

exer

ythr

otho

rax

Mo

squ

ito

Mo

squ

ito

sam

ple

sU

SAN

get

al(

2011

)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s1

KM

5983

85O

daG

mV

-1-U

S-26

0BC

-12

Isch

nura

posi

taD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s1

KM

5983

86O

daG

mV

-1-U

S-26

0SR

1-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s2

KM

5983

87O

daG

mV

-2-U

S-16

42K

W-1

2A

eshn

am

ulti

colo

rD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s2

KM

5983

88O

daG

mV

-2-U

S-16

34LM

2-12

Libe

llula

satu

rata

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3577

PaG

mV

-1T

OST

O14

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3578

PaG

mV

-1T

OST

O15

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3579

PaG

mV

-1T

OST

O18

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Porc

ine

asso

ciat

edge

myc

ircu

larv

irus

1K

T86

2250

49Fe

c800

61p

igSu

ssc

rofa

dom

esti

caPi

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Porc

ine

asso

ciat

edge

myc

ircu

larv

irus

2K

F371

640

as5

Sus

scro

faD

om

esti

cp

igFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

1K

T73

2804

Tba

t45

285

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

1K

T73

2805

Tba

t47

364

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

2K

T73

2792

Tba

t10

3791

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

2K

T73

2793

Tba

tA

1037

91Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

3K

T73

2797

Tba

tA

1038

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

4K

T73

2814

Tba

tH

1038

06Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

5K

T73

2801

Tba

t12

377

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

5K

T73

2802

Tba

tH

1237

7Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

6K

T73

2796

Tba

tH

1036

39Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

6K

T73

2803

Tba

t10

3951

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

7K

T73

2807

Tba

tA

1037

46Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

7K

T73

2808

Tba

tA

1039

09Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

) (co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

09T

bat

H10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

10T

bat

H10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

11T

bat

L10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

12T

bat

L10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us8

KT

7328

06T

bat

3157

9Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us9

KT

7327

95T

bat

2138

3Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us10

KT

7327

94T

bat

H10

3958

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rat

asso

ciat

edge

myc

ircu

larv

irus

1K

R91

2221

Ch

-zjr

at-0

1R

attu

sno

rveg

icus

Rat

Blo

od

Ch

ina

Liet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

GQ

3657

09Ss

HA

DV

-1C

NSc

lero

tini

asc

lero

tior

umSc

lero

tin

iaM

ycel

ials

amp

les

Ch

ina

Yu

etal

(20

10)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

5Ss

HA

DV

-1N

ZH

620

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

6Ss

HA

DV

-1N

ZSR

120

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

7Ss

HA

DV

-1N

ZSR

320

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

8Ss

HA

DV

-1N

ZSR

520

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

82Ss

HA

DV

-1-U

S-54

9LB

-12

Isch

nura

ram

buri

iD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

83Ss

HA

DV

-1-U

S-54

9DFS

-12

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

84Ss

HA

DV

-1-U

S-54

9SR

-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KJ5

4763

8B

S391

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KM

8217

47Sa

Gm

V-1

NZ

-BS3

970-

2012

Sew

age

oxid

atio

npo

ndndash

Sew

age

New

Zea

lan

dK

rabe

rger

etal

(20

15a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us2

KJ5

4764

1B

S411

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us3

KJ5

4763

6B

S401

4Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4763

7B

S393

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4764

0B

S397

2Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us5

KJ5

4763

9B

S397

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4947

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5151

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Soyb

ean

asso

ciat

edge

myc

ircu

larv

irus

1K

T59

8248

SlaG

emV

1-1

Gly

cine

max

Soyb

ean

Leaf

USA

Mar

zan

oan

dD

om

ier

(201

6)

Gem

ydug

uiv

irus

Dra

gonfl

yas

soci

ated

gem

ydug

uivi

rus

1JX

1854

28T

O-D

FS3B

2-20

10Pa

ntal

afla

vesc

ens

Dra

gon

fly

Abd

om

enT

on

gaR

osa

rio

etal

(20

12)

Gem

ygor

viru

sC

anin

eas

soci

ated

gem

ygor

viru

s1

KT

8622

5453

Fec7

do

gC

anis

lupu

sfa

mili

aris

Do

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1JN

7046

10V

S470

0006

Mel

esm

eles

Euro

pea

nba

dge

rR

ecta

lsw

abN

eth

erla

nd

sva

nd

enB

ran

det

al(

2012

)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2238

4Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2239

24Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2790

Tba

tA

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2791

Tba

tH

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Sew

age

deri

ved

gem

ygor

viru

s1

KJ4

1314

434

9H

omo

sapi

ens

Hu

man

Cer

vica

lsam

ple

Sou

thA

fric

a

Sew

age

deri

ved

gem

ygor

viru

s1

KJ5

4763

5B

S396

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Star

ling

asso

ciat

edge

myg

orvi

rus

1K

F371

632

P14

Stur

nus

vulg

aris

Euro

pea

nst

arli

ng

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Gem

ykib

ivir

usBa

dger

asso

ciat

edge

myk

ibiv

irus

1K

P263

543

588t

Mel

esm

eles

Euro

pea

nba

dge

rFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Blac

kro

bin

asso

ciat

edge

myk

ibiv

irus

1K

F371

634

P21

Petr

oica

trav

ersi

Ch

ath

amIs

lan

d

blac

kro

bin

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ykib

ivir

us

1K

F371

633

P22

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Bovi

neas

soci

ated

gem

ykib

ivir

us1

LK93

1483

HC

BI8

215

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Dra

gonfl

yas

soci

ated

gem

ykib

ivir

us1

JX18

5430

FL1-

2X-2

010

Mia

thyr

iam

arce

llaD

rago

nfl

yA

bdo

men

USA

Ro

sari

oet

al(

2012

)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

4B

S398

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

5B

S384

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KP9

7469

4D

B2

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)

Hum

anas

soci

ated

gem

ykib

ivir

us1

LK93

1485

MSS

I22

25H

omo

sapi

ens

Hu

man

Blo

od

Ger

man

yLa

mbe

rto

etal

(20

14)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

5SL

1H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

6SL

2H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

7SL

3H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

(co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

8B

Z1

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

9B

Z2

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3308

0N

PU

ntre

ated

sew

age

ndashSe

wag

eN

epal

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP2

6354

654

1cH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP9

8788

7G

emyC

1cH

omo

sapi

ens

Hu

man

Plas

ma

Fran

ceU

chet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us4

KT

3638

39G

eTz1

Hom

osa

pien

sH

um

anC

ereb

rosp

inal

flu

idC

hin

aZ

ho

uet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us5

KU

3431

37H

V-G

cV2

Hom

osa

pien

sH

um

anPe

rica

rdia

lflu

idFr

ance

Hal

ary

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ykib

ivir

us1

KP2

6354

516

0bH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Pter

opu

sas

soci

ated

gem

ykib

ivir

us1

KT

7328

13T

bat

A64

418

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

J641

737

BtR

h-C

V-6

Tib

et20

13R

hino

loph

ushi

ppos

ider

osB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

P263

544

181a

Her

pest

esic

hneu

mon

Egyp

tian

mo

ngo

ose

Faec

esPo

rtu

gal

Co

nce

icao

-Net

oet

al(

2015

)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

2K

J641

726

BtR

f-C

V-8

NM

2013

Rhi

nolo

phus

ferr

umeq

uinu

mB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Sew

age

deri

ved

gem

ykib

ivir

us1

KJ5

4764

3B

S414

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

4027

BS1

4149

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5252

BS1

4149

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5556

BS1

4149

har

eLe

pus

euro

paeu

sH

are

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us2

KJ5

4764

2B

S391

1Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykol

ovir

us

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

98T

bat

A10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

99T

bat

H10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myk

olov

irus

2K

T73

2800

Tba

tH

1039

21Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Gem

ykro

gvir

usB

ovin

eas

soci

ated

gem

ykro

gvir

us1

LK93

1484

HC

BI9

212

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Car

ibou

asso

ciat

edge

myk

rogv

irus

1K

J938

717

FaG

mC

V-1

3R

angi

fer

tara

ndus

Car

ibou

Faec

esC

anad

aN

get

al(

2014

)

Sew

age

deri

ved

gem

ykro

gvir

us1

KJ5

4763

4B

S391

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykro

znav

iru

sR

abbi

tas

soci

ated

gem

ykro

znav

irus

1K

F371

631

as35

Ory

ctol

agus

cuni

culu

sR

abbi

tFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yton

dvir

usO

stri

chas

soci

ated

gem

yton

dvir

us1

KF3

7163

0as

3St

ruth

ioca

mel

usO

stri

chFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yvon

gvir

usH

um

anas

soci

ated

gem

yvon

gvir

us1

KP9

7469

3D

B1

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)





000

005

010

015

020

025A

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Genome

Rep

CP

B

C


2014)





32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer
































































































Tab

le1

Det

ails

of

allm

embe

rso

fth

eG

enom

ovir

idae

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Gem

ycir

cula

rvir

us

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

1P9

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

2P2

2T

urdu

sm

erul

aB

lack

bird

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ycir

cula

rvir

us1

KF3

7164

3as

41O

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Bovi

neas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5352

Fec7

8023

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Brom

us

asso

ciat

edge

myc

ircu

larv

irus

1K

M51

0192

Bas

CV

-3N

Z-N

ZG

01Se

f-20

12Br

omus

hord

eace

usSo

ftbr

om

eB

ull

gras

sLe

afN

ewZ

eala

nd

Kra

berg

eret

al(

2015

b)

Cas

sava

asso

ciat

edge

myc

ircu

larv

irus

1JQ

4120

56G

14M

anih

otes

cule

nta

Cas

sava

Leaf

Gh

ana

Day

aram

etal

(20

12)

Cas

sava

asso

ciat

edge

myc

ircu

larv

irus

1JQ

4120

57G

5M

anih

otes

cule

nta

Cas

sava

Leaf

Gh

ana

Day

aram

etal

(20

12)

Chi

ckad

eeas

soci

ated

gem

ycir

cula

rvir

us1

KT

3090

2925

4065

908

Poec

ileat

rica

pillu

sB

lack

-cap

ped

chic

kad

eeB

ucc

alan

d

clo

acal

swab

USA

Han

na

etal

(20

15)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4327

Fec7

9971

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4429

Fec7

9971

Ilam

aLa

ma

glam

aLl

ama

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s1

KT

8622

4630

Fec7

9971

ho

rse

Equu

sfe

rus

caba

llus

Ho

rse

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Chi

cken

asso

ciat

edge

myc

ircu

larv

iru

s2

KT

8622

4227

Fec1

6497

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Dra

gonfl

yas

soci

ated

gem

ycir

cula

rvir

us1

JX18

5429

FL2-

5X-2

010

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAR

osa

rio

etal

(20

12)

Equi

neas

soci

ated

gem

ycir

cula

rvir

us

1K

T86

2248

30Fe

c800

61h

ors

eEq

uus

feru

sca

ballu

sH

ors

eFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Fur

seal

asso

ciat

edge

myc

ircu

larv

irus

1K

F371

638

as50

Arc

toce

phal

usfo

rste

riN

ewZ

eala

nd

fur

seal

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Fur

seal

asso

ciat

edge

myc

ircu

larv

irus

1K

T86

2241

27Fe

c1ch

icke

nG

allu

sga

llus

dom

esti

cus

Ch

icke

nFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us1

KF3

7163

6P2

4aG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us2

KF3

7163

7P2

4bG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Ger

ygon

eas

soci

ated

gem

ycir

cula

rvir

us3

KF3

7163

9P2

4cG

eryg

one

albo

fron

tata

Ch

ath

amIs

lan

dw

arbl

erFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Hyp

eric

um

asso

ciat

edge

myc

ircu

larv

irus

1K

F413

620

VN

HJ1

WH

yper

icum

japo

nicu

mH

yper

icu

mLe

afV

ietn

amD

uet

al(

2014

)

Lam

aas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4529

Fec8

0018

llam

aLa

ma

glam

aLl

ama

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Lam

aas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4730

Fec8

0018

ho

rse

Equu

sfe

rus

caba

llus

Ho

rse

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Mal

lard

asso

ciat

edge

myc

ircu

larv

iru

s1

KF3

7163

5as

24A

nas

plat

yrhy

ncho

sM

alla

rdd

uck

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Min

iopt

erus

asso

ciat

edge

myc

ircu

larv

irus

1K

J641

719

BtM

f-C

V-2

3G

D20

12M

inio

pter

usfu

ligin

osus

Bat

Phar

ynge

alamp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ycir

cula

rvir

us1

KP2

6354

747

8dH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Mos

quit

oas

soci

ated

gem

ycir

cula

rvir

us1

HQ

3350

86SD

BV

LG

Cul

exer

ythr

otho

rax

Mo

squ

ito

Mo

squ

ito

sam

ple

sU

SAN

get

al(

2011

)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s1

KM

5983

85O

daG

mV

-1-U

S-26

0BC

-12

Isch

nura

posi

taD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s1

KM

5983

86O

daG

mV

-1-U

S-26

0SR

1-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s2

KM

5983

87O

daG

mV

-2-U

S-16

42K

W-1

2A

eshn

am

ulti

colo

rD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Odo

nata

asso

ciat

edge

myc

ircu

larv

iru

s2

KM

5983

88O

daG

mV

-2-U

S-16

34LM

2-12

Libe

llula

satu

rata

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3577

PaG

mV

-1T

OST

O14

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3578

PaG

mV

-1T

OST

O15

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Poac

eae

asso

ciat

edge

myc

ircu

larv

irus

1K

T25

3579

PaG

mV

-1T

OST

O18

-292

0420

14Br

achi

aria

defle

xaSi

gnal

gras

sLe

afT

on

gaM

ale

etal

(20

15)

Porc

ine

asso

ciat

edge

myc

ircu

larv

irus

1K

T86

2250

49Fe

c800

61p

igSu

ssc

rofa

dom

esti

caPi

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Porc

ine

asso

ciat

edge

myc

ircu

larv

irus

2K

F371

640

as5

Sus

scro

faD

om

esti

cp

igFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

1K

T73

2804

Tba

t45

285

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

1K

T73

2805

Tba

t47

364

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

2K

T73

2792

Tba

t10

3791

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

2K

T73

2793

Tba

tA

1037

91Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

3K

T73

2797

Tba

tA

1038

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

4K

T73

2814

Tba

tH

1038

06Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

5K

T73

2801

Tba

t12

377

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

5K

T73

2802

Tba

tH

1237

7Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

6K

T73

2796

Tba

tH

1036

39Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

6K

T73

2803

Tba

t10

3951

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

7K

T73

2807

Tba

tA

1037

46Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myc

ircu

larv

irus

7K

T73

2808

Tba

tA

1039

09Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

) (co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

09T

bat

H10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

10T

bat

H10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

11T

bat

L10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

12T

bat

L10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us8

KT

7328

06T

bat

3157

9Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us9

KT

7327

95T

bat

2138

3Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us10

KT

7327

94T

bat

H10

3958

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rat

asso

ciat

edge

myc

ircu

larv

irus

1K

R91

2221

Ch

-zjr

at-0

1R

attu

sno

rveg

icus

Rat

Blo

od

Ch

ina

Liet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

GQ

3657

09Ss

HA

DV

-1C

NSc

lero

tini

asc

lero

tior

umSc

lero

tin

iaM

ycel

ials

amp

les

Ch

ina

Yu

etal

(20

10)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

5Ss

HA

DV

-1N

ZH

620

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

6Ss

HA

DV

-1N

ZSR

120

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

7Ss

HA

DV

-1N

ZSR

320

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

8Ss

HA

DV

-1N

ZSR

520

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

82Ss

HA

DV

-1-U

S-54

9LB

-12

Isch

nura

ram

buri

iD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

83Ss

HA

DV

-1-U

S-54

9DFS

-12

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

84Ss

HA

DV

-1-U

S-54

9SR

-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KJ5

4763

8B

S391

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KM

8217

47Sa

Gm

V-1

NZ

-BS3

970-

2012

Sew

age

oxid

atio

npo

ndndash

Sew

age

New

Zea

lan

dK

rabe

rger

etal

(20

15a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us2

KJ5

4764

1B

S411

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us3

KJ5

4763

6B

S401

4Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4763

7B

S393

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4764

0B

S397

2Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us5

KJ5

4763

9B

S397

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4947

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5151

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Soyb

ean

asso

ciat

edge

myc

ircu

larv

irus

1K

T59

8248

SlaG

emV

1-1

Gly

cine

max

Soyb

ean

Leaf

USA

Mar

zan

oan

dD

om

ier

(201

6)

Gem

ydug

uiv

irus

Dra

gonfl

yas

soci

ated

gem

ydug

uivi

rus

1JX

1854

28T

O-D

FS3B

2-20

10Pa

ntal

afla

vesc

ens

Dra

gon

fly

Abd

om

enT

on

gaR

osa

rio

etal

(20

12)

Gem

ygor

viru

sC

anin

eas

soci

ated

gem

ygor

viru

s1

KT

8622

5453

Fec7

do

gC

anis

lupu

sfa

mili

aris

Do

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1JN

7046

10V

S470

0006

Mel

esm

eles

Euro

pea

nba

dge

rR

ecta

lsw

abN

eth

erla

nd

sva

nd

enB

ran

det

al(

2012

)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2238

4Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2239

24Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2790

Tba

tA

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2791

Tba

tH

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Sew

age

deri

ved

gem

ygor

viru

s1

KJ4

1314

434

9H

omo

sapi

ens

Hu

man

Cer

vica

lsam

ple

Sou

thA

fric

a

Sew

age

deri

ved

gem

ygor

viru

s1

KJ5

4763

5B

S396

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Star

ling

asso

ciat

edge

myg

orvi

rus

1K

F371

632

P14

Stur

nus

vulg

aris

Euro

pea

nst

arli

ng

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Gem

ykib

ivir

usBa

dger

asso

ciat

edge

myk

ibiv

irus

1K

P263

543

588t

Mel

esm

eles

Euro

pea

nba

dge

rFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Blac

kro

bin

asso

ciat

edge

myk

ibiv

irus

1K

F371

634

P21

Petr

oica

trav

ersi

Ch

ath

amIs

lan

d

blac

kro

bin

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ykib

ivir

us

1K

F371

633

P22

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Bovi

neas

soci

ated

gem

ykib

ivir

us1

LK93

1483

HC

BI8

215

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Dra

gonfl

yas

soci

ated

gem

ykib

ivir

us1

JX18

5430

FL1-

2X-2

010

Mia

thyr

iam

arce

llaD

rago

nfl

yA

bdo

men

USA

Ro

sari

oet

al(

2012

)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

4B

S398

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

5B

S384

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KP9

7469

4D

B2

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)

Hum

anas

soci

ated

gem

ykib

ivir

us1

LK93

1485

MSS

I22

25H

omo

sapi

ens

Hu

man

Blo

od

Ger

man

yLa

mbe

rto

etal

(20

14)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

5SL

1H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

6SL

2H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

7SL

3H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

(co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

8B

Z1

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

9B

Z2

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3308

0N

PU

ntre

ated

sew

age

ndashSe

wag

eN

epal

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP2

6354

654

1cH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP9

8788

7G

emyC

1cH

omo

sapi

ens

Hu

man

Plas

ma

Fran

ceU

chet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us4

KT

3638

39G

eTz1

Hom

osa

pien

sH

um

anC

ereb

rosp

inal

flu

idC

hin

aZ

ho

uet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us5

KU

3431

37H

V-G

cV2

Hom

osa

pien

sH

um

anPe

rica

rdia

lflu

idFr

ance

Hal

ary

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ykib

ivir

us1

KP2

6354

516

0bH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Pter

opu

sas

soci

ated

gem

ykib

ivir

us1

KT

7328

13T

bat

A64

418

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

J641

737

BtR

h-C

V-6

Tib

et20

13R

hino

loph

ushi

ppos

ider

osB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

P263

544

181a

Her

pest

esic

hneu

mon

Egyp

tian

mo

ngo

ose

Faec

esPo

rtu

gal

Co

nce

icao

-Net

oet

al(

2015

)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

2K

J641

726

BtR

f-C

V-8

NM

2013

Rhi

nolo

phus

ferr

umeq

uinu

mB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Sew

age

deri

ved

gem

ykib

ivir

us1

KJ5

4764

3B

S414

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

4027

BS1

4149

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5252

BS1

4149

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5556

BS1

4149

har

eLe

pus

euro

paeu

sH

are

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us2

KJ5

4764

2B

S391

1Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykol

ovir

us

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

98T

bat

A10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

99T

bat

H10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myk

olov

irus

2K

T73

2800

Tba

tH

1039

21Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Gem

ykro

gvir

usB

ovin

eas

soci

ated

gem

ykro

gvir

us1

LK93

1484

HC

BI9

212

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Car

ibou

asso

ciat

edge

myk

rogv

irus

1K

J938

717

FaG

mC

V-1

3R

angi

fer

tara

ndus

Car

ibou

Faec

esC

anad

aN

get

al(

2014

)

Sew

age

deri

ved

gem

ykro

gvir

us1

KJ5

4763

4B

S391

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykro

znav

iru

sR

abbi

tas

soci

ated

gem

ykro

znav

irus

1K

F371

631

as35

Ory

ctol

agus

cuni

culu

sR

abbi

tFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yton

dvir

usO

stri

chas

soci

ated

gem

yton

dvir

us1

KF3

7163

0as

3St

ruth

ioca

mel

usO

stri

chFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yvon

gvir

usH

um

anas

soci

ated

gem

yvon

gvir

us1

KP9

7469

3D

B1

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)





000

005

010

015

020

025A

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Genome

Rep

CP

B

C


2014)





32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer
































































































Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

09T

bat

H10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

10T

bat

H10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

11T

bat

L10

3746

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us7

KT

7328

12T

bat

L10

3909

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us8

KT

7328

06T

bat

3157

9Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us9

KT

7327

95T

bat

2138

3Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opu

sas

soci

ated

gem

ycir

cula

rvir

us10

KT

7327

94T

bat

H10

3958

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rat

asso

ciat

edge

myc

ircu

larv

irus

1K

R91

2221

Ch

-zjr

at-0

1R

attu

sno

rveg

icus

Rat

Blo

od

Ch

ina

Liet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

GQ

3657

09Ss

HA

DV

-1C

NSc

lero

tini

asc

lero

tior

umSc

lero

tin

iaM

ycel

ials

amp

les

Ch

ina

Yu

etal

(20

10)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

5Ss

HA

DV

-1N

ZH

620

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

6Ss

HA

DV

-1N

ZSR

120

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

7Ss

HA

DV

-1N

ZSR

320

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KF2

6802

8Ss

HA

DV

-1N

ZSR

520

12R

iver

Sedi

men

tsndash

Riv

erSe

dim

ents

New

Zea

lan

dK

rabe

rger

etal

(20

13)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

82Ss

HA

DV

-1-U

S-54

9LB

-12

Isch

nura

ram

buri

iD

amse

lfly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

83Ss

HA

DV

-1-U

S-54

9DFS

-12

Eryt

hem

issi

mpl

icic

ollis

Dra

gon

fly

Abd

om

enU

SAD

ayar

amet

al(

2015

)

Scle

roti

nia

gem

ycir

cula

rvir

us1

KM

5983

84Ss

HA

DV

-1-U

S-54

9SR

-12

Pant

ala

hym

enae

aD

rago

nfl

yA

bdo

men

USA

Day

aram

etal

(20

15)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KJ5

4763

8B

S391

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us1

KM

8217

47Sa

Gm

V-1

NZ

-BS3

970-

2012

Sew

age

oxid

atio

npo

ndndash

Sew

age

New

Zea

lan

dK

rabe

rger

etal

(20

15a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us2

KJ5

4764

1B

S411

7Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us3

KJ5

4763

6B

S401

4Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4763

7B

S393

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us4

KJ5

4764

0B

S397

2Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ycir

cula

rvir

us5

KJ5

4763

9B

S397

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

4947

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Shee

pas

soci

ated

gem

ycir

cula

rvir

us1

KT

8622

5151

Fec8

0064

shee

pO

vis

arie

sSh

eep

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Soyb

ean

asso

ciat

edge

myc

ircu

larv

irus

1K

T59

8248

SlaG

emV

1-1

Gly

cine

max

Soyb

ean

Leaf

USA

Mar

zan

oan

dD

om

ier

(201

6)

Gem

ydug

uiv

irus

Dra

gonfl

yas

soci

ated

gem

ydug

uivi

rus

1JX

1854

28T

O-D

FS3B

2-20

10Pa

ntal

afla

vesc

ens

Dra

gon

fly

Abd

om

enT

on

gaR

osa

rio

etal

(20

12)

Gem

ygor

viru

sC

anin

eas

soci

ated

gem

ygor

viru

s1

KT

8622

5453

Fec7

do

gC

anis

lupu

sfa

mili

aris

Do

gFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1JN

7046

10V

S470

0006

Mel

esm

eles

Euro

pea

nba

dge

rR

ecta

lsw

abN

eth

erla

nd

sva

nd

enB

ran

det

al(

2012

)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2238

4Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Mal

lard

asso

ciat

edge

myg

orvi

rus

1K

T86

2239

24Fe

c7d

uck

Ana

spl

atyr

hync

hos

Du

ckFa

eces

New

Zea

lan

dSt

eele

tal

(20

16)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2790

Tba

tA

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Pter

opus

asso

ciat

edge

myg

orvi

rus

1K

T73

2791

Tba

tH

1039

52Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Sew

age

deri

ved

gem

ygor

viru

s1

KJ4

1314

434

9H

omo

sapi

ens

Hu

man

Cer

vica

lsam

ple

Sou

thA

fric

a

Sew

age

deri

ved

gem

ygor

viru

s1

KJ5

4763

5B

S396

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Star

ling

asso

ciat

edge

myg

orvi

rus

1K

F371

632

P14

Stur

nus

vulg

aris

Euro

pea

nst

arli

ng

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Gem

ykib

ivir

usBa

dger

asso

ciat

edge

myk

ibiv

irus

1K

P263

543

588t

Mel

esm

eles

Euro

pea

nba

dge

rFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Blac

kro

bin

asso

ciat

edge

myk

ibiv

irus

1K

F371

634

P21

Petr

oica

trav

ersi

Ch

ath

amIs

lan

d

blac

kro

bin

Faec

esN

ewZ

eala

nd

Siko

rski

etal

(20

13)

Blac

kbir

das

soci

ated

gem

ykib

ivir

us

1K

F371

633

P22

Tur

dus

mer

ula

Bla

ckbi

rdFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Bovi

neas

soci

ated

gem

ykib

ivir

us1

LK93

1483

HC

BI8

215

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Dra

gonfl

yas

soci

ated

gem

ykib

ivir

us1

JX18

5430

FL1-

2X-2

010

Mia

thyr

iam

arce

llaD

rago

nfl

yA

bdo

men

USA

Ro

sari

oet

al(

2012

)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

4B

S398

0Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KJ5

4764

5B

S384

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Hum

anas

soci

ated

gem

ykib

ivir

us1

KP9

7469

4D

B2

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)

Hum

anas

soci

ated

gem

ykib

ivir

us1

LK93

1485

MSS

I22

25H

omo

sapi

ens

Hu

man

Blo

od

Ger

man

yLa

mbe

rto

etal

(20

14)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

5SL

1H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

6SL

2H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

7SL

3H

omo

sapi

ens

Hu

man

Cer

ebro

spin

alfl

uid

SriL

anka

Phan

etal

(20

15)

(co

nti

nu

ed)


Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

8B

Z1

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

9B

Z2

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3308

0N

PU

ntre

ated

sew

age

ndashSe

wag

eN

epal

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP2

6354

654

1cH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP9

8788

7G

emyC

1cH

omo

sapi

ens

Hu

man

Plas

ma

Fran

ceU

chet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us4

KT

3638

39G

eTz1

Hom

osa

pien

sH

um

anC

ereb

rosp

inal

flu

idC

hin

aZ

ho

uet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us5

KU

3431

37H

V-G

cV2

Hom

osa

pien

sH

um

anPe

rica

rdia

lflu

idFr

ance

Hal

ary

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ykib

ivir

us1

KP2

6354

516

0bH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Pter

opu

sas

soci

ated

gem

ykib

ivir

us1

KT

7328

13T

bat

A64

418

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

J641

737

BtR

h-C

V-6

Tib

et20

13R

hino

loph

ushi

ppos

ider

osB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

P263

544

181a

Her

pest

esic

hneu

mon

Egyp

tian

mo

ngo

ose

Faec

esPo

rtu

gal

Co

nce

icao

-Net

oet

al(

2015

)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

2K

J641

726

BtR

f-C

V-8

NM

2013

Rhi

nolo

phus

ferr

umeq

uinu

mB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Sew

age

deri

ved

gem

ykib

ivir

us1

KJ5

4764

3B

S414

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

4027

BS1

4149

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5252

BS1

4149

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5556

BS1

4149

har

eLe

pus

euro

paeu

sH

are

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us2

KJ5

4764

2B

S391

1Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykol

ovir

us

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

98T

bat

A10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

99T

bat

H10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myk

olov

irus

2K

T73

2800

Tba

tH

1039

21Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Gem

ykro

gvir

usB

ovin

eas

soci

ated

gem

ykro

gvir

us1

LK93

1484

HC

BI9

212

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Car

ibou

asso

ciat

edge

myk

rogv

irus

1K

J938

717

FaG

mC

V-1

3R

angi

fer

tara

ndus

Car

ibou

Faec

esC

anad

aN

get

al(

2014

)

Sew

age

deri

ved

gem

ykro

gvir

us1

KJ5

4763

4B

S391

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykro

znav

iru

sR

abbi

tas

soci

ated

gem

ykro

znav

irus

1K

F371

631

as35

Ory

ctol

agus

cuni

culu

sR

abbi

tFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yton

dvir

usO

stri

chas

soci

ated

gem

yton

dvir

us1

KF3

7163

0as

3St

ruth

ioca

mel

usO

stri

chFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yvon

gvir

usH

um

anas

soci

ated

gem

yvon

gvir

us1

KP9

7469

3D

B1

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)





000

005

010

015

020

025A

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Genome

Rep

CP

B

C


2014)





32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer
































































































Tab

le1

Co

nti

nu

ed

Gen

us

Spec

ies

Acc

essi

on

Se

qu

ence

IDIs

ola

tio

nso

urc

eC

om

mo

nn

ame

Sam

ple

typ

eC

ou

ntr

yR

efer

ence

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

8B

Z1

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3307

9B

Z2

Hom

osa

pien

sH

um

anFa

eces

Bra

zil

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us2

KP1

3308

0N

PU

ntre

ated

sew

age

ndashSe

wag

eN

epal

Phan

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP2

6354

654

1cH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Hum

anas

soci

ated

gem

ykib

ivir

us3

KP9

8788

7G

emyC

1cH

omo

sapi

ens

Hu

man

Plas

ma

Fran

ceU

chet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us4

KT

3638

39G

eTz1

Hom

osa

pien

sH

um

anC

ereb

rosp

inal

flu

idC

hin

aZ

ho

uet

al(

2015

)

Hum

anas

soci

ated

gem

ykib

ivir

us5

KU

3431

37H

V-G

cV2

Hom

osa

pien

sH

um

anPe

rica

rdia

lflu

idFr

ance

Hal

ary

etal

(20

16)

Mon

goos

eas

soci

ated

gem

ykib

ivir

us1

KP2

6354

516

0bH

erpe

stes

ichn

eum

onEg

ypti

anm

on

goo

seFa

eces

Port

uga

lC

on

ceic

ao-N

eto

etal

(20

15)

Pter

opu

sas

soci

ated

gem

ykib

ivir

us1

KT

7328

13T

bat

A64

418

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

J641

737

BtR

h-C

V-6

Tib

et20

13R

hino

loph

ushi

ppos

ider

osB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

1K

P263

544

181a

Her

pest

esic

hneu

mon

Egyp

tian

mo

ngo

ose

Faec

esPo

rtu

gal

Co

nce

icao

-Net

oet

al(

2015

)

Rhi

nolo

phus

asso

ciat

edge

myk

ibiv

irus

2K

J641

726

BtR

f-C

V-8

NM

2013

Rhi

nolo

phus

ferr

umeq

uinu

mB

atPh

aryn

geal

amp

rect

alsw

abs

Ch

ina

Wu

etal

(20

16)

Sew

age

deri

ved

gem

ykib

ivir

us1

KJ5

4764

3B

S414

9Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

4027

BS1

4149

chic

ken

Gal

lus

gallu

sdo

mes

ticu

sC

hic

ken

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5252

BS1

4149

cow

Bos

taur

usC

ow

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us1

KT

8622

5556

BS1

4149

har

eLe

pus

euro

paeu

sH

are

Faec

esN

ewZ

eala

nd

Stee

let

al(

2016

)

Sew

age

deri

ved

gem

ykib

ivir

us2

KJ5

4764

2B

S391

1Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykol

ovir

us

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

98T

bat

A10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opu

sas

soci

ated

gem

ykol

ovir

us1

KT

7327

99T

bat

H10

3779

Pter

opus

tong

anus

Bat

Faec

esT

on

gaM

ale

etal

(20

16)

Pter

opus

asso

ciat

edge

myk

olov

irus

2K

T73

2800

Tba

tH

1039

21Pt

erop

usto

ngan

usB

atFa

eces

To

nga

Mal

eet

al(

2016

)

Gem

ykro

gvir

usB

ovin

eas

soci

ated

gem

ykro

gvir

us1

LK93

1484

HC

BI9

212

Bos

taur

usC

ow

Seru

mG

erm

any

Lam

bert

oet

al(

2014

)

Car

ibou

asso

ciat

edge

myk

rogv

irus

1K

J938

717

FaG

mC

V-1

3R

angi

fer

tara

ndus

Car

ibou

Faec

esC

anad

aN

get

al(

2014

)

Sew

age

deri

ved

gem

ykro

gvir

us1

KJ5

4763

4B

S391

3Se

wag

eox

idat

ion

pond

ndashSe

wag

eN

ewZ

eala

nd

Kra

berg

eret

al(

2015

a)

Gem

ykro

znav

iru

sR

abbi

tas

soci

ated

gem

ykro

znav

irus

1K

F371

631

as35

Ory

ctol

agus

cuni

culu

sR

abbi

tFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yton

dvir

usO

stri

chas

soci

ated

gem

yton

dvir

us1

KF3

7163

0as

3St

ruth

ioca

mel

usO

stri

chFa

eces

New

Zea

lan

dSi

kors

kiet

al(

2013

)

Gem

yvon

gvir

usH

um

anas

soci

ated

gem

yvon

gvir

us1

KP9

7469

3D

B1

Hom

osa

pien

sH

um

anPl

asm

aG

erm

any

Zh

ang

etal

(20

16)





000

005

010

015

020

025A

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Genome

Rep

CP

B

C


2014)





32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer



































































































000

005

010

015

020

025A

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

000

001

002

003

004

005

006

007

008

1009896949290888684828078767472706866646260585654525048464442403836343230282624222018161412

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Percentage identity

Prop

ortio

n of

per

cent

age

pairw

ise

iden

titie

s

Genome

Rep

CP

B

C


2014)





32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer



































































































32 Gemykibivirus


33 Gemygorvirus


34 Gemykolovirus


35 Gemykrogvirus



96

8899

100

99

98

10098

9899

9699

99

99

100

100

8391

100

99100

98100

93

97

99

9798

93

9999

9999

95100

100

10096

100

96

10086

89

100

10092

99

100

9998

89

91

99

100

9497

99

93100

87

100

96

10094

83

92

99100

99

9599

100

97

82

95

99

99

94

90

93

99

88100

93

9698

8896

99

98

92

99

100

99

95

96100

9086

93

95

90

97

100

100

99

0005101520



Gemyvongvirus

Gemykolovirus























































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer













































































































































99100

97

75

9499

100

100

100

100100

100

99

9999

99100

96

91

96

93

97100

99100

100

10089

95

93

9797

97100

100

100

95

100100

97

10091

100

100100

7799

100

100

10087

83

100

98

100

100

100100

10099

10099

100100

100100

99

100

99

99

100100

97

92100

92

91

91

100

100

100

100

93

81

97

10075

96

94

89

96

97

100

10098

99100

100

99




Gemyvongvirus

Gemykolovirus






35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer
































































































35 Gemyvongvirus


36 Gemytondvirus


37 Gemykroznavirus

















































100

100

100

80

94

86

100

100100

10099

97

9986

8688

95

99

10091

89

100

100

80

96

84

100100

100

87

10083

79

89 95

100

91

9391

100

93

92

94

88

93100

10094

77

10096

90

94

9284

100

10089

9696

99

80

96

95

100

100

94

100

10099

89

94100

100

93100

93

100

9895

100

100

87




Gemyvongvirus

Gemykolovirus






0 10 20 30 40 50 60 70 80


Number of isolates

Number of species

Gemyvongvirus

Gemytondvirus

Gemykroznavirus

Gemykrogvirus

Gemykolovirus

Gemykibivirus

Gemygorvirus

Gemyduguivirus

Gemycircularvirus





38 Gemyduguivirus

















Supplementary data


Disclaimer

































































































38 Gemyduguivirus

















Supplementary data


Disclaimer







































































































Supplementary data


Disclaimer
































































































Sequence-based taxonomic framework for the classification ... taxonomic...Sequence-based taxonomic...

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