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ACCEPTED MANUSCRIPT
Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of
negative-sense RNA viruses
Ci-Xiu Li, Mang Shi, Jun-Hua Tian, Xian-Dan Lin, Yan-Jun Kang, Liang-Jun Chen, Xin-Cheng Qin,
Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang
DOI: http://dx.doi.org/10.7554/eLife.05378
Cite as: eLife 2015;10.7554/eLife.05378
Received: 29 October 2014
Accepted: 27 January 2015
Published: 29 January 2015
This PDF is the version of the article that was accepted for publication after peer review. Fully
formatted HTML, PDF, and XML versions will be made available after technical processing, editing,
and proofing.
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Mononegavirales
Ophioviridae
Arenaviridae
Orthomyxoviridae
Bunyaviridae
Arenaviridae Bunyaviridae
Orthomyxoviridae
Emaravirus
Mononegavirales
Tenuivirus
Varicosavirus
Arenaviridae
Bunyaviridae
Nairovirus
Tenuivirus
Emaravirus
Orthobunyavirus
Tospovirus
Heterodera glycines
Procotyla fluviatilis
Bunyaviridae
Mononegavirales
Orthomyxoviridae
Mononegavirales
Phlebovirus
de novo
Γ
Journal of virology
Bioinformatics
PloS one
Virology
Annual review of phytopathology
Molecular
marine biology and biotechnology
Nature biotechnology
Systematic biology
Current opinion in microbiology
Molecular biology and evolution
PLoS genetics
Nature methods
Bioinformatics
PloS one
Journal of virology
Journal of virology
Proceedings of the National
Academy of Sciences of the United States of America
Nucleic acids research
Bioinformatics
Science
Virology
journal
Journal of virology
Journal of virology
Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi
Aedes sp, Armigeres subalbatus, Anopheles
sinensis, Culex quinquefasciatus, Culex
tritaeniorhynchus
Aedes albopictus, Armigeres subalbatus,
Anopheles paraliae, Anopheles sinensis, Culex
pipiens, Culex sp, Culex tritaeniorhynchus,
Atherigona orientalis, Chrysomya megacephala,
Lucilia sericata, Musca domestica, Sarcophaga
dux, S. peregrina, S. sp
Tabanidae
Blattella germanica
Gerridae
Abraxas tenuisuffusa, Hermetia illucens,
Chrysopidae,
Coleoptera, Psychoda alternata,
Diptera,
Stratiomyidae
Hippoboscidae
Cimex
hemipterus
Pseudothemis zonata
Nepidae
Camponotus japonicus, Diplonychus
sp, Asellus sp
Psychoda alternata, Velarifictorus micado,
Crocothemis servilia,
Phoridae,
Lampyridae Aphelinus sp
Hyalopterus pruni, Aulacorthum magnolia,
Dermacentor marginatus, Dermacentor sp,
Haemaphysalis doenitzi, H. longicornis, H. sp,
H. formosensis, Hyalomma asiaticum,
Rhipicephalus microplus, Argas miniatus
Hyalomma asiaticum
Neoscona nautica, Parasteatoda tepidariorum,
Plexippus setipes, Pirata sp,
Araneae
Exopalaemon carinicauda, Metapenaeus sp,
Solenocera crassicornis, Penaeus monodon,
Litopenaeus vannamei
Capitulum mitella, Charybdis hellerii, C.
japonica, Uca arcuata
Polydesmidae
Hyalomma asiaticum
Dermacentor sp
Dermacentor sp
Parasteatoda tepidariorum
Atherigona orientalis
Diptera
Diptera, Abraxas tenuisuffusa,
Chrysopidae
Chrysopidae
Argas miniatus
Dermacentor marginatus
Charybdis japonica, Charybdis lucifera,
Charybdis hellerii
Charybdis japonica
Blattella germanica
unidentified Hippoboscidae
unidentified Hippoboscidae
Culex tritaeniorhynchus, C.
quinquefasciatus, Anopheles sinensis,
Armigeres subalbatus
Rhipicephalus microplus
Culex tritaeniorhynchus, C.
quinquefasciatus, Anopheles sinensis,
Armigeres subalbatus, Aedes sp
Hyalopterus pruni OR Aphelinus sp
Hyalopterus pruni OR Aphelinus sp
Hyalopterus pruni OR Aphelinus sp
unidentified Hippoboscidae
Haemaphysalis hystricis
Musca domestica, Chrysomya megacephala
Musca domestica, Sarcophaga sp
Musca domestica
Hippoboscidae
Hippoboscidae
Hippoboscidae
Hyalomma asiaticum
Haemaphysalis doenitzi
Dermacentor marginatus
Haemaphysalis hystricis
Rhipicephalus microplus
Hyalopterus pruni OR Aphelinus sp
unidentified Araneae
unidentified Gerridae
Argas miniatus
Psychoda alternata
Anopheles sinensis
Capitulum mitella, Charybdis japonica,
Charybdis lucifera
Argas miniatus
Sarcophaga sp
Gerridae
Chrysomya megacephala, Atherigona
orientalis
Cimex hemipterus
Diptera, Abraxas tenuisuffusa
Camponotus japonicus
Musca domestica, Sarcophaga sp
Musca domestica
Culex tritaeniorhynchus, C.
quinquefasciatus, Aedes sp
Hippoboscidae
Haemaphysalis doenitzi
Dermacentor marginatus
Haemaphysalis hystricis
Neoscona nautica, Parasteatoda
tepidariorum, Plexippus setipes
Neoscona nautica, Parasteatoda
tepidariorum
Gerridae
Hippoboscoidea
Chrysopidae, Psychoda
alternata
Blattella germanica
Ostrinia furnacalis
Abraxas tenuisuffusa, unidentified diptera
Culex tritaeniorhynchus, Anopheles
sinensis, Culex quinquefasciatus
Culex tritaeniorhynchus, Anopheles
sinensis, Culex quinquefasciatus, Aedes sp
Haemaphysalis sp
Hyalomma asiaticum
Dermacentor sp
Haemaphysalis longicornis
Rhipicephalus microplus
Dermacentor marginatus
Haemaphysalis hystricis
Pararge aegeria
Procotyla fluviatilis
Ostrinia furnacalis
unidentified Chrysopidae, unidentified
Diptera
unidentified Hippoboscoidea
Asellus sp, unidentified Nepidae,
Camponotus japonicus
Phoridae
Aulacorthum magnoliae
unidentified Polydesmidae
Culex quinquefasciatus
Culex quinquefasciatus
Anopheles sinensis
Anopheles sinensis, Armigeres subalbatus
Penaeus monodon
Neoscona nautica, Parasteatoda
tepidariorum, Plexippus setipes
Atherigona orientalis, Chrysomya
megacephala, Sarcophaga sp, Musca
domestica
Tabanidae
Culex tritaeniorhynchus
Cimex hemipterus
Culex tritaeniorhynchus
Armigeres subalbatus
Penaeus monodon, Exopalaemon
carinicauda
Neoscona nautica, Pirata sp, Parasteatoda
tepidariorum,
Araneae
Hyalopterus pruni OR Aphelinus sp
Gerridae
Polydesmidae
Asellus sp
Atherigona orientalis, Chrysomya
megacephala, Sarcophaga sp, Musca domestica
Tabanidae
Gerridae
Neoscona nautica
Diptera,
Stratiomyidae
Hippoboscoidea
Hippoboscoidea
Culex tritaeniorhynchus, Culex
quinquefasciatus, Armigeres subalbatus
Culex tritaeniorhynchus, Culex
quinquefasciatus, Armigeres subalbatus
Culex tritaeniorhynchus, Culex
quinquefasciatus, Armigeres subalbatus
Culex quinquefasciatus
Anopheles sinensis, Culex quinquefasciatus
Psychoda alternata
Blattella germanica
Ixodes scapularis
Tetranychus urticae
Daphnia pulex
Eurytemora affinis
Hyalella azteca
Lepeophtheirus salmonis
Dendroctonus ponderosae
Tribolium castaneum
Aedes aegypti
Anopheles spp.
Culex quinquefasciatus
Drosophila spp.
Zootermopsis nevadensis
Acyrthosiphon pisum
Rhodnius prolixus
Atta cephalotes
Acromyrmex echinatior
Camponotus floridanus
Harpegnathos saltator
Linepithema humile
Nasonia spp.
Pogonomyrmex barbatus
Solenopsis invicta
Bombyx mori
Melitaea cinxia
Plutella xylostella
Spodoptera frugiperda
Strigamia maritima
MosHB
(mosquitos)
77
74
99
Culex
quinquefasciatus
MosZJ
(mosquitos)
Horseflies
(unidentified
Tabanidae)
84
75
98
C. tritaeniorhynchus
0.1
0.1
C. tritaeniorhynchus
94
91
75
0.1
99
83
96
Aedes sp.
Anopheles sinensis
74
76
100
100
unknown Chrysopidae
Spiders
0.1
Camponotus japonicus
92
81
97
96
100
100
Psychoda alternata
unknown Stratiomyidae
unknown Stratiomyidae
85
0.1
Insect mix 2
(louseflies and bed bugs)
100
Cimex
hemipterus
0.1
91
Insect mix 4 (moth flies, crickets
aphids, dragonflies, etc)
83
92
D. marginatus
Velarifictorus ornatus
Crocothemis servilia
Unknown Phoridae
25
100
Rhipicephalus microplus
H. longicornis
59
99
88
H. doenitzi
100
99
99
Parasteatoda
tepidariorum
Plexippus setipes
77
Pirata sp
85
77
0.1
Shrimps
94
99
Crabs and barnacles
Penaeus monodon (X12)
68
85
Litopenaeus vannamei (X12)
Capitulum mitella (X12)
Exopalaemon carinicauda (X12)
0.05
Charybdis lucifera (X1)
Uca arcuata (X11)
Solenocera crassicornis (X6)
Aphelinus sp
Charybdis japonica (X9)
Charybdis hellerii (X2)
Metapenaeus sp (X6)
52
unknown
Araneae
99
Argas miniatus
Psychoda alternata
Unknown Lampyridae
100
Aulacorthum magnoliae
100
Hyalopterus pruni
96
Neoscona
nautica
91
Haemaphysalis formosensis
Haemaphysalis sp
H. hystricis
Velarifictorus micado
96
0.1
99
unknown
Hippoboscidae
Asellus sp
98
93
100
Pseudothemis zonata
72
98
93
Dermacentor sp
Millipedes
(two species:
unknown
Polydesmidae)
55
unknown Phalangiidae
40
5
Atherigona
orientalis
Hyalomma asiaticum
Abraxas tenuisuffusa
36
Lucilia sericata
47
Diplonychus sp
93
cockroaches
(single species:
Blattella germanica)
89
unknown Nepidae
100
unknown Diptera
sp4
sp5
99
Coleoptera sp.
0.05
Chrysomya
megacephala
Ticks
90
0.1
99
sp3
Insect mix 3 (dragonflies, ants,
beettles, waterscorpion, etc)
Insect mix 1 (lacewings, moths,
beetles, moth flies, soldier flies)
sp1
sp2
98
Anopheles sinensis
97
100
sp2
Sarcophaga
sp
99
Armigeres
86
Aedes sp.
54
Musca
domestica
78
97
7
100
sp1
49
99
71
97
Water striders
(unidentified
Gerridae)
C. sp
Armigeres
subalbatus
100
0.05
C. quinquefasciatus
C. sp
100
95
91
79
88
Common
flies
92
0.1
60
Frequency
50
40
30
20
10
Abundance
(TPM)
0
0 ~ 10
10 ~ 100
100 ~ 1000
Host mtDNA COI gene
Japanese
encephalitis
virus
(TPM = 4.19)
Gill-associated
virus
(TPM = 20.05)
> 1000
A
C
Mononega-like
D
Vesiculovirus,
Ephemerovirus,
etc
Phlebovirus
Chuviridae
Ophioviridae
Sigmavirus
Tenuivirus
0.5
100/100
Gouleako virus
Orthomyxolike
Lyssavirus
96/100
98/100
Varicosavirus
Arenavirus
97/100
98/100
Bunya-arena-like
98/100
B
Nucleorhabdovirus
91/100
Nairovirus
Cytorhabdovirus
Novirhabdovirus
Phasmavirus
99/100
0.5
Hantavirus
75/85
96/100
88/99
98/100
85/57
Quaranjavirus
97/100
Thogotovirus
Paramyxovirus
and
Filovirus
Tospovirus
Nyamiviridae
Emaravirus
99/99
92/100
Bornaviridae
89/99
100/100
Influenza A-D
0.5
ISAV
Orthobunyavirus
Chuviridae
100/100
Arenavirus
(N=2)
Unsegmented
Nairovirus
(N=3)
Type I
Tacheng
Tick Virus 5
10,017bp
Varicosavirus (N=2)
Phasmavirus
(N=3)
Bole
Tick Virus 3
11,183kb
Orchid fleck
virus (N=2)
Phlebovirus
(N=3)
Type II
Tenuivirus
(N>4)
Wuchang Cockroach Virus 3
L seg
7152bp
Phlebo-like
viruses
(N=3)
Wuhan Louse Fly Virus 7
Emaravirus (N>4)
Chuviridae
Tospovirus (N=3)
Orthobunyavirus
(N=3)
Hantavirus (N=3)
Segmented
S seg
4788bp
Ophiovirus
(N>3)
Orthomyxovirus
(N=6-8)
Various
Genome
Organizations
L seg
6808bp
S seg
2343bp
Type III
Wenzhou Crab Virus 3 12,860bp
3’
5’
millipede
(Arenavirus)
(Phlebovirus)
tick
aphis,moths
mosquito
cockroach
water strider
mosquito
tick, crab
fly, spier, lousefly
unknown diptera
mosquito
cockroach
(Ophiovirus)
(Pneumovirus)
spider
water strider
(Nairovirus)
(Paramyxovirus
and filovirus)
spider
tick
moth, crab
mosquito
tick
(Tenuivirus)
fly
lousefly
spider
aphid
moth
mosquito
waterscorpion
butterfly
Asellus sp
millipede
shrimp
humbleback- (Emaravirus)
fly
(Tospovirus)
midges
(orthobunyvirus)
mosquito
bed bug
(Nucleorhabdovirus)
tick
fly, lousefly, bed bug,
ant, mosquito,
water strider
(Cytorhabdovirus), aphid
(Lyssavirus)
spider
water strider
shrimp
cockroach
(Hantavirus)
tick, lousefly
coleoptera
mosquito
spider
moth fly
horsefly
dragonfly
water strider
(Influenza virus)
(Vesiculovirus,
Ephemerovirus,
etc)
fly, lousefly
mosquito
tick
(A)
Wuhan
Horsefly
Virus
DG3-4
DG3-2
JJ3-9
JJ3-6
DG3-4
DG2-3
DG3-1
DG2-4
DG1-1
DG2-5
0.01
horseflies
(host)
(B)
Wuhan
Fly
Virus 1
0.05
DG3-9
DG3-10
SYY4-2
SYY2-2
SYY4-8
SYY2-4
DG3-1
SYY4-1
DG3-2
JJ3-1
DG3-9
DG2-6
JJ2-5
DG2-5
JJ2-1
JJ2-5
SYY4-5
SYY3-1
SYY2-6
DG3-10
SYY2-1
JJ2-6
DG2-2
flies
(host)
SYY2-1
SYY2-2
SYY2-4
SYY2-6
SYY4-5
SYY4-2
SYY4-8
SYY3-1
SYY4-1
JJ2-8
JJ2-6
DG2-6
JJ2-1
JJ3-6
JJ3-9
DG2-3
JJ3-1
JJ2-8
DG1-1
(D)
(C)
Wuhan
Mosquito
Virus 2
XC1-5
WT3-14
XC1-6
XC1-9
WT3-15
WT3-13
QN3-6
QN2-7
JX1-13
WT3-14
WT3-13
JX1-14
WT3-15
XZ1-6
QN3-5
XC1-9
XC2-6
JX1-12
WT3-13
QN3-6
QN3-5
JX1-14
JX1-12
JX1-13
QN3-6
XC1-5
XC1-8
QN3-5
JX1-14
XC1-7
WT3-13
XC1-6
WT3-15
XZ3-11
XC1-5
XC1-6
QN2-6
XC2-6
XZ3-11
XC1-9
JX1-14
JX1-13
XC1-8
XC1-7
WT3-14
XC1-6
XC1-5
XZ1-6
QN2-6
XZ3-11
XC1-9
mosquitos
(host)
WT3-14
WT3-15
JX1-12
QN2-7
QN3-5
QN3-6
0.01
mosquitos
(host)
Wuhan
Mosquito
Virus 1
JX1-12
JX1-13
XZ3-11
0.05
0.005
DG2-4
DG2-2
0.05
0.01
0.05
A
RdRP
Putative Glycoprotein
Bole Tick Virus 3
Changping Tick Virus 2
97
0
Bole Tick Virus 3
Changping Tick Virus 2
Wuhan Tick Virus 2
Wuchang Cockraoch Virus 3
Lishi Spider Virus 1
99
Tacheng Tick Virus 5
100
Changping Tick Virus 3
99
Wuhan Tick Virus 2
Wuhan Louse Fly Virus 7
94
Wuhan Louse Fly Virus 6
100
0.2
92
86
100
97
12
Putative Nucleoprotein
33
41
Wuhan Mosquito Virus 8
Wenzhou Crab Virus 2
Tacheng Tick Virus 4
70
Wenzhou Crab Virus 2
Wuchang Cockraoch Virus 3
Lishi Spider Virus 1
Wuhan Mosquito Virus 8
Tacheng Tick Virus 4
Shayang Fly Virus 1
79
90
0.5
Wuhan Mosquito Virus 8
12004 nts
3’
5’
L 247.3kDa
N?
47.6kDa
Tacheng Tick Virus 5
10017 nts
L 251.3kDa
Wuhan Tick Virus 2
11395 nts
10877 nts
3’
Lishi Spider Virus 1
7051 nts
5’
G 73.8kDa
L 244.0kDa
Bole Tick Virus 3
3’
11183 nts
L 244.7kDa
5’
G 72.3kDa
N? VP4
51.3kDa 12.2kDa
6777 nts
5’
14X
G
5’
G 121.6kDa VP2 N?
69.5kDa
11.7kDa
5’
L 238.1kDa
VP5
19.6kDa
5’
L 281.4kDa
TTTTATTT------GAATACAAGGG
TTTTATTCAAA---GAATACAAGGG
TTTTATTCGG----GAATACAAGGG
TTTTATTCAATTTTGAATACAAGGG
TTTTATTTTT----GAATACAAGGG
TTTTATTCAATT--GAATACAAGGG
TTTTATTCTTT---GAATACAAGGG
N?
L
5’
G 75.7kDa N? VP4
47.0kDa 20.2kDa
0-899X
L
5’
4788 nts
3’
12860 nts
3’
N? VP3
G1 96.8kDa N? G2 61.3kDa
47.0kDa 15.1kDa
Shayang Fly Virus 1
13732 nts
3’
2343 nts 5’
3’
N?
47.5kDa
4426 nts
3’
L 247.2kDa
3’
L 247.7kDa
C
5’
N?
54.7kDa
Wenzhou Crab Virus 3
G 72.9kDa
5’
L 249.1kDa
Wuhan Louse Fly Virus 7
6808 nts
3’
2291 nts
N? VP4
67.9kDa 17.6kDa
10815 nts
3’
Wuhan Louse Fly Virus 6
3’
5’
L 254.2kDa
N?
51.6kDa
5’
G 75.1kDa
N? VP4
46.3kDa 14.5kDa
Tacheng Tick Virus 4
3’
4698 nts
3’
L 252.1kDa
Wuchang Cockroach Virus 3
7152 nts
5’
VP4
N?
70.6kDa 11.2kDa
G 72.4kDa
5’
3’
G 75.7kDa N? VP4
45.0kDa 13.8kDa
Changping Tick Virus 2
5’
3’
N? VP3
47.2kDa 12.5kDa
5’
G 73.4kDa
Wenzhou Crab Virus 2
6959 nts
5’
L 252.5kDa
L 250.6kDa
Wuchang Cockraoch Virus 3
Lishi Spider Virus 1
Wenzhou Crab Virus 2
Tacheng Tick Virus 4
L 252.7kDa
3’
Wuhan Louse Fly Virus 6
Wuhan Louse Fly Virus 7
Wuhan Mosquito Virus 8
100
38
0.5
9527 nts
3’
83
90
Changping Tick Virus 3
3’
Tacheng Tick Virus 5
Changping Tick Virus 3
Wuhan Tick Virus 2
64
Wenzhou Crab Virus 3
B
Bole Tick Virus 3
Changping Tick Virus 2
97
G
N?
L segment
Phlebovirus 3’
Huangpi Tick Virus 2
6441 nts
3568 nts
3’
Yongjia Tick Virus 1
6527 nts
3’
N/A
3’
6549 nts
3’
N/A
L 245.6kDa
3’
Tacheng Tick Virus 2
6660 nts
3’
N/A
3’
Changping Tick Virus 1
6637 nts
Bole Tick Virus 1
6483 nts
6517 nts
5’
Whenzhou Shrimp Virus 1
3’
Wutai Mosquito Virus
6284 nts
L 233.3kDa
6754 nts
3’
6779 nts
3’
L 252.6kDa
7082 nts
3’
L 267.2kDa
7046 nts
Wuhan Fly Virus 1
Wuhan Louse Fly Virus 2
Qingnian Mosquito Virus
3’
Wuhan Insect Virus 1
L 252.7kDa
6520 nts
5’ 3’
5’ 3’
3648 nts
Gn 63.8 kDa
3’
7604 nts
L 276.5kDa
5’
3’
6362 nts
L 230.6kDa
5’
3’
6870 nts
L 256.6kDa
5’
3’
Huangshi
Humpbacked Fly Virus
6055 nts
L 230.2kDa
5’
Tenuivirus_like 3’
9525 nts
L 363.0kDa
5’ 3’
5’
N 30.4kDa
1285 nts
N partial
5’
5’
N/A
1211 nts
N partial
5’
5’
5’ 3’
1480 nts
5’
Gc 54.6 kDa
N/A
N/A
Gn 43.4 kDa
Gc 50.5 kDa
5’ 3’
1889 nts
N 51.6kDa
5’ 3’
2171 nts
N 53.9kDa
5’
5’ 3’
1940 nts
5’
5’ 3’
N 64.2kDa
1969 nts
5’
5’ 3’
N 53.9kDa
1785 nts
5’
5’ 3’
N 54.7kDa
1840 nts
5’
5’ 3’
N 54.6kDa
2208 nts
5’
Gc 53.2 kDa
2636 nts
Gn 35.1 kDa
Gc 53.7 kDa
2255 nts
Gn
Gc 51.7 kDa
23.1 kDa
2939 nts
Gc partial
Gn NSm
partial15.9kDa
4753 nts
Gn NSm
27.4kDa
NSs (?) N 42.9kDa
5’
2111 nts
5’ 3’ 13.1kDa
NSs(?) N 38.2kDa
VP3(?)
5’ 3’ 14.1kDa 1808 nts 12.3kDa 5’
NSs (?)
13.9kDa
5’ 3’
NSs N 27.1kDa
5’ 3’ 9.6kDa 1233 nts
Gc 111.4 kDa
2957 nts
6085 nts
3’
L 229.7kDa
6553 nts
L partial
3302 nts
5’
5’ 3’
Gn 49.0 kDa Gc 67.7 kDa
Wuhan Insect Virus 2
Sanxia Water Strider Virus 2
Unclassified segmented virus 6 3’
Wuhan Millipede Virus 2
Unclassified segmented virus 7 3’
Gn
6646 nts
L 249.4kDa
5’
7243 nts
L 272.2kDa
7151 nts
L 271.6kDa
5’ 3’
N/A
2466 nts
Gn
5’
N/A
Gc 56.3 kDa
partial
N/A
N/A
2852 nts
5’ 3’
1820 nts
5’
N 53.9kDa
Gc partial
Gn partial
5’
N/A
5’
N/A
3’
1960 nts
N 53.8kDa
5’
3’
1867 nts
N 53.8kDa
5’
N/A
L 417.0kDa
6743 nts
N/A
N/A
5’ 3’
L 249.0kDa
N/A
5’
6873 nts
L 258.0kDa
11332 nts
N/A
5’
Gc partial
partial
5’
5’
Gc partial
2312 nts
5’ 3’
5’
N 30.0kDa
3’
Gn partial
N 48.3kDa
1959 nts
NSs (?) N 54.7kDa
VP3 (?)
3’ 15.4kDa 1148 nts 18.4kDa 5’
N partial
NSs (?)
5’
5’ 3’ partial 959 nts
5’ 3’
Shayang Spider Virus 2
Wuhan Insect Virus 3
partial
5’ 3’
5754 nts
L partial
5956 nts
L 217.0kDa
Unclassified segmented virus 5 3’
5’
2217 nts
Gn
L 264.8kDa
Unclassified segmented virus 1 3’
Gc 52.8 kDa
5’ 3’
Shuangao Insect Virus 1
3’
2804 nts
Gn
5’ 3’
Whenzhou Shrimp Virus 2
N/A
N/A
Gn 72.0 kDa Gc 73.7 kDa
5147 nts
5’ 3’
Gn 73.2 kDa Gc 76.1 kDa
5’ 3’
2073 nts
7325 nts
Unclassified segmented virus 4 3’
N/A
4675 nts
5’ 3’
Gn 66.1 kDa Gc 77.9 kDa
4428 nts
5’ 3’
partial
5’
Gc 100.9 kDa
60.2 kDa
Orthobunyavirus_like 3’
Shuangao Mosquito Virus
N/A
4805 nts
Gn
5’ 3’
Unclassified segmented virus 3 3’
N/A
6574 nts
L 242.4kDa
6474 nts
L 238.4kDa
6493 nts
L 246.1kDa
52.2 kDa
5’ 3’
2241 nts
N 56.6kDa
Gc 74.9 kDa
Gn
6787 nts
L 262.4kDa
Orthobunyavirus 3’
Shuangao Bedbug Virus 1
N 45.9kDa
4193 nts
5’ 3’
5’ 3’
Gc partial
Gn 66.3 kDa
Wuhan Louse Fly Virus 1
Shuangao Insect Virus 2
Jiangxia Mosquito Virus 2
1030 nts
N 28.1kDa
3322 nts
5’ 3’
Unclassified segmented virus 2 3’
5’ 3’
L 441.4kDa
12184 nts
L 446.9kDa
S segment
M segment
5’ 3’
4899 nts
L partial
Jiangxia Mosquito Virus 1
N/A
N/A
Wuchang Cockraoch Virus 1
3’
3’
Gc 54.6 kDa
3357 nts
1454 nts
Wuhan Mosquito Virus 1
3’
5’
Gc 57.8 kDa
3278 nts
Gn 62.3 kDa
3’
5’
1116 nts
N/A
Gn 55.9 kDa
Phasmavirus_like 3’
5’ 3’
N/A
5’ 3’
898 nts
3’
L 444.7kDa
12073 nts
3’
N 31.8kDa
3’
6276 nts
L 234.3kDa
Wuhan horsefly Virus
4454 nts
5’
3’
Wuhan Spider Virus
5’ 3’
Gc 55.9 kDa
N/A
5’ 3’
Xinzhou Mosquito Virus
Wuhan Mosquito Virus 2
154.5 kDa
6421 nts
L 238.8kDa
ZheE Mosquito Virus
5’
5’ 3’
5’
3’
Shuangao Insect Virus 3
Tacheng Tick Virus 1
N 27.2kDa
3357 nts
Gn 81.1 kDa
5’
Yichang Insect Virus
5’
partial
5662 nts
L partial
Wuhan Millipede Virus 1
1659 nts
N 50.0kDa
2969 nts
L 240.7kDa
3’
3’
1925 nts
3’
Huangpi Tick Virus 1
Wenzhou Tick Virus
3’
5’ 3’
5’
L 464.6kDa
12229 nts
13486 nts
L 506.5kDa
11823 nts
3’
15.1kDa
12336 nts
L 450.0kDa
Shayang Spider Virus 1
5’
N/A
L 251.3kDa
2185 nts
NSs
N 34.1kDa
5’
5’ 3’
5’
3’
Sanxia Water Strider virus 1
1227 nts
N partial
N/A
L 247.4kDa
Phlebovirus_like 3’
11.3kDa
1795 nts
Xinzhou Spider Virus
3’
N/A
L 244.9kDa
3’
Lihan Tick Virus
NSs
Nairovirus_like 3’
N 46.9kDa
5’
L 250.3kDa
3’
5’
1830 nts
N 30.2kDa
5’
L 247.1kDa
NSs 30.9kDa
N 29.8kDa
5’
5’
1709 nts
N 27.4kDa
5’
L 243.6kDa
Dabieshan Tick Virus
5’ 3’
Gn 57.9 kDa Gc 55.0 kDa
L 243.0kDa
L segment
S segment
M segment
5’ 3’
5’
N/A
Unclassified Rhabdovirus 2
Nishimuro virus like
Yongjia Tick Virus 2
Sanxia Water Strider Virus 5
10833 nts
3’
N
47.9
P(?) M
29.8 23.7
5’
G
L
N
VP2 VP3
G
L
239.6
48.4
38.3 28.6
71.0
259.2
Shuangao Bedbug Virus 2
3’
Wuhan Louse Fly Virus 5
11103 nts
3’
N
P
5’
60.5
Kolente virus like
48.2
12978 nts
3’
M
33.1 24.8
5’
G
L
63.5
245.7
10925 nts
5’
VP1
G
VP3
L
31.3
72.8
16.7
254.2
Wuhan Mosquito Virus 9
3’
13706 nts
5’
Sigmavirus_like
VP1
ORF1 VP2
ORF2 VP3
ORF3
Wuhan Fly Virus 2
12247 nts
3’
31.0
5’
58.2
G
G 69.5kDa
29.9
L
L 196.7kDa
256.0
69.5
Wuhan House Fly Virus 2
N P(?) X
50.1
M
27.3 38.7 27.8
G
L
62.5
244.5
Shayang Fly Virus 2
12291 nts
3’
14731 nts
3’
5’
VP1 VP2 VP3VP4
G VP6
L
54.3
73.2 11.4
254.1
42.4 18.2 31.3
Shayang Fly Virus 3
3’
N P(?) X
50.0 27.3
M
37.9 26.0
G
L
61.4
247.9
53.7
12651 nts
3’
5’
45.5
35.8
G
L
74.2
255.5
Unclassified Rhabdovirus 1
Tacheng Tick Virus 7
13408 nts
3’
N
51.7
P(?) X(?) M
35.2
42.0
25.5
G
L
60.4
299.3
VP1
51.3
Wuhan Louse Fly Virus 10
11541 nts
3’
N
50.2
P(?) M
35.4 26.5
5’
L
61.7
246.4
49.0 23.6
50.6
P(?) M
5’
29.1
25.1
L
60.4
245.7
Unclassified Dimarhabdovirus 2
Wuhan Insect virus 7
11165 nts
3’
N
48.5
P(?) M
30.9 24.3
5’
N
P
4b M(?)
G
L
33.4
37.9 19.5
64.1
243.5
Wuhan Insect virus 5
G
L
240.6
Unclassified Mononegavirus 1
Tacheng Tick Virus 6
5’
51.1
29.4
5’
12930 nts
3’
VP1
L
17.0
46.1
253.1
VP2 VP3
49.6
15.8
5’
G
VP5
L
61.7
20.5
243.2
Unclassified Mononegavirus 2
Xincheng Mosquito Virus
5’
12774 nts
3’
5’
G
L
VP1 VP2 VP3
G
L
57.0
246.3
52.3 18.4 48.1
72.0
231.1
P(?) M
Wuhan Tick Virus 1
Unclassified Mononegavirus 3
10306 nts
3’
5’
Wenzhou Crab Virus 1
9591 nts
3’
VP2 VP3
23.2
L
237.4
24.1 14.3 17.6
Sanxia Water Strider Virus 4
11843 nts
39.0
5’
VP1 VP2 VP3VP4 VP5
247.3
VP2 VP3
28.0 32.3
10787 nts
3’
L
G
59.1
29.3
3’
N
5’
60.9
Bole Tick Virus 2
55.1
12734 nts
3’
P 4b M
11280 nts
N
L
238.3
32.3 25.5 20.2
3’
54.5
G
63.4
N
P(?) M(?)
52.0
4b M
49.6
Taishun Tick Virus
52.2
P
33.4 26.2 19.6
L
13169 nts
N
N
51.4
242.9
3’
43.2
5’
G
Huangpi Tick Virus 3
N
14191 nts
58.6
Unclassified Dimarhabdovirus 1
54.1
5’
54.4
3’
G
249.5
13490 nts
Wuhan Insect virus 6
N
L
G
82.6
3’
11370 nts
5’
Cytorhabdovirus_like
Wuhan Louse Fly Virus 9
3’
VP4
VP2 VP3 38.3
Wuhan Insect virus 4
G
5’
15462 nts
VP1 VP2 VP3
Wuhan House Fly Virus 1
5’
L
248.9
N
40.7
VP2
20.3VP3
16.3
5’
G
L
57.5
202.2
RNA1
(9760bp)
Rice grassy stunt virus
P1
RdRp
RNA2
(4056bp)
P2
RNA3
(3123bp)
P3
RNA4
(2915bp)
P4
RNA5
(2704bp)
RNA6
(2584bp)
Wuhan horsefly Virus
RNA1
(9549bp)
RdRp
Putative Gn-Gc
RNA2
(2804bp)
PC3
RNA3
(1889bp)
N
RNA4
(1698bp)
NS4
PC4
P5
N
NCP
NS4
Putative Gn-Gc
A
97
Changping Tick Virus 2
Bole Tick Virus 3
Wuhan Tick Virus 2
99
97
70
EVE Anopheles maculatus
EVE Acyrthosiphon pisum (N = 9)
40
100
EVE Tribolium castaneum (N = 3)
61
98
EVE Hyalella azteca
Wenzhou Crab Virus 2
Lishi Spider Virus 1
Wuchang Cockroach Virus 3
89
70
94
100
93
EVE Culicidae
Wuhan Mosquito Virus 8
EVE Hymenoptera
97
Tacheng Tick Virus 4
0.5
98
93
B
Pogonomyrmex barbatus (N=13)
Solenopsis invicta
Camponotus floridanus
86
Linepithema humile
100
Linepithema humile
0.5
Acromyrmex echinatior (N=4)
100
100
Harpegnathos saltator (N=4)
100
93
Solenopsis invicta
Acromyrmex echinatior
Pogonomyrmex barbatus
98
Nasonia vitripennis
99
Nasonia vitripennis
100
Nasonia giraulti
100
99 Nasonia longicornis
Nasonia vitripennis
100
Nasonia vitripennis
Nasonia vitripennis
100
Nasonia giraulti
Nasonia
longicornis
92
Nasonia vitripennis
98
95 Nasonia longicornis
98
Nasonia vitripennis
Nasonia vitripennis
100
Nasonia longicornis
83
Nasonia vitripennis
100
Nasonia vitripennis (N=5)
Nasonia vitripennis
99
Nasonia vitripennis
100
Nasonia vitripennis
Nasonia giraulti
97 Nasonia longicornis
Nasonia giraulti
Nasonia vitripennis
Nasonia vitripennis
93
Nasonia vitripennis
98
Solenopsis invicta
Linepithema humile
Camponotus floridanus
99
Camponotus floridanus
Harpegnathos saltator
100
100 Harpegnathos saltator
Camponotus floridanus
100
Linepithema humile (N=5)
100
Acromyrmex echinatior (N=3)
100
86 93
C
Solenopsis invicta
Harpegnathos saltator
Solenopsis invicta
Pogonomyrmex barbatus
Anopheles funestus
Anopheles funestus
97
Anopheles funestus
Anopheles minimus
96
0.1
88
94
100
88
Anopheles stephensi
Anopheles stephensi
Anopheles stephensi
Anopheles stephensi
Anopheles minimus
Anopheles dirus
Anopheles dirus
100 Anopheles arabiensis
Anopheles gambiae
99
Anopheles minimus
99
A. quadriannulatus
95
91
Anopheles albimanus
Anopheles albimanus
71
100
94 99
Anopheles sinensis
Anopheles sinensis
Anopheles epiroticus
Anopheles atroparvus
86 Anopheles gambiae
100
100
80
Anopheles gambiae
Anopheles quadriannulatus
Anopheles dirus
99
85
Anopheles nili
Anopheles farauti
81
Anopheles farauti
Anopheles albimanus
84 100 Aedes aegypti
Aedes aegypti
98
Aedes aegypti
Aedes aegypti
Aedes aegypti
100 Aedes aegypti
Culex quinquefasciatus
C. quinquefasciatus
100
80
99
Solenopsis invicta
Linepithema humile (N=4)
83 87
Solenopsis invicta (N=7)
86
98
Pogonomyrmex barbatus (N=8)
98
Solenopsis invicta
100
90
100
95
Aedes aegypti
100 Aedes aegypti
Aedes aegypti
Aedes aegypti
Aedes aegypti
Aedes aegypti
Culex
quinquefasciatus
100
Culex quinquefasciatus
100
70
Culex quinquefasciatus
Arthropods
Phytophagous
vectors
Blood-feeding
vectors
Plants
Vertebrates
Vertebrates
Tospovirus
Cytorhabdovirus
Nucleorhabdovirus
Emaravirus
Tenuivirus
Nairovirus
Phlebovirus
Orthobunyavirus
Ephemerovirus
Vesiculovirus
Filovirus
Arenavirus
Bornavirus
Influenza virus
Paramyxovirus
Lyssavirus
Hantavirus