1. Microbiology and Infectious Disease
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Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

  1. Ci-Xiu Li
  2. Mang Shi
  3. Jun-Hua Tian
  4. Xian-Dan Lin
  5. Yan-Jun Kang
  6. Liang-Jun Chen
  7. Xin-Cheng Qin
  8. Jianguo Xu
  9. Edward C Holmes
  10. Yong-Zhen Zhang  Is a corresponding author
  1. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, China
  2. Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, China
  3. Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Australia
  4. Wuhan Center for Disease Control and Prevention, China
  5. Wenzhou Center for Disease Control and Prevention, China
Research Article
Cite this article as: eLife 2015;4:e05378 doi: 10.7554/eLife.05378
12 figures, 5 tables and 2 data sets

Figures

Host component of each pool used in the RNA-seq library construction and sequencing.

The taxonomic units in the tree correspond to the unit samples used in the RNA extraction. Species or genus information is marked to the left of the tree.

https://doi.org/10.7554/eLife.05378.004
Abundance level (transcripts per million—TPM) of the RdRp genes from the negative-sense RNA viruses detected in this study.

Abundance is calculated after the removal of ribosomal RNA reads. As a comparison, we show the abundance of the two well characterized (positive-sense) RNA viruses: Japanese encephalitis virus and Gill-associated virus found in the Mosquito-Hubei and Shrimp libraries, respectively, as well as the range of abundance of host mitochondrial COI genes in these same multi-host libraries.

https://doi.org/10.7554/eLife.05378.008
Figure 3 with 3 supplements
Evolutionary history of negative-sense RNA viruses based on RdRp.

This is initially displayed in an unrooted maximum likelihood (ML) tree including all major groups of negative-sense RNA viruses (A). Separate and more detailed ML phylogenies are then shown for the Orthomyxoviridae-like (B), Bunya-Arenaviridae-like (C), and Mononegavirales-like viruses (D). In all the phylogenies, the RdRp sequences described here from arthropods are either shaded purple or marked with solid gray circles. The names of previously defined genera/families are labeled to the right of the phylogenies. Based on their host types, the branches are shaded red (vertebrate-specific), yellow (vertebrate and arthropod), green (plant and arthropod), blue (non-arthropod invertebrates), or black (arthropod only). For clarity, statistical supports (i.e., approximate likelihood-ratio test (aLRT) with Shimodaira–Hasegawa-like procedure/posterior probabilities) are shown for key internal nodes only.

https://doi.org/10.7554/eLife.05378.009
Figure 3—figure supplement 1
A fully labeled ML phylogeny for Orthomyxoviridae-like viruses.

The phylogeny is reconstructed using RdRp alignments. Statistical support from the approximate likelihood-ratio test (aLRT) is shown on each node of the tree. The names of the viruses discovered in this study are shown in red. The names of reference sequences, which contain both the GenBank accession number and the virus species name, are shown in black. The names of previously defined genera/families are shown to the right of the phylogenies.

https://doi.org/10.7554/eLife.05378.010
Figure 3—figure supplement 2
A fully labeled ML phylogeny for Bunya-Arenaviridae-like viruses.

The phylogeny is reconstructed using RdRp alignments. Statistical support from the aLRT is shown on each node of the tree. The names of the viruses discovered in this study are shown in red. The names of reference sequences, which contain both the GenBank accession number and the virus species name, are shown in black. The names of previously defined genera/families are shown to the right of the phylogenies.

https://doi.org/10.7554/eLife.05378.011
Figure 3—figure supplement 3
A fully labeled ML phylogeny for Mononegavirales-like viruses.

The phylogeny is reconstructed using RdRp alignments. Statistical support from the aLRT is shown on each node of the tree. The names of the viruses discovered in this study are shown in red. The names of reference sequences, which contain both the GenBank accession number and the virus species name, are shown in black. The names of previously defined genera/families are shown to the right of the phylogenies.

https://doi.org/10.7554/eLife.05378.012
The unrooted ML phylogeny based on RdRp showing the topological position of segmented viruses within the genetic diversity of negative-sense RNA viruses.

The segmented viruses are labeled with segment numbers and shaded red. The unsegmented viruses are shaded green. The Chuviridae, which exhibit a wide variety of genome organizations, are shaded cyan. Three major types of putative chuvirus genomes (circular, circular and segmented, and linear) are shown in the right panel and are annotated with predicted ORFs: putative RdRp genes are shaded blue, putative glycoprotein genes are shaded orange, and the remaining ORFs are shaded gray.

https://doi.org/10.7554/eLife.05378.013
The unrooted ML phylogeny of negative-sense RNA viruses (RdRp) with the common names of the principle arthropod hosts analyzed in this study indicated.

Vertebrate-specific viruses are shaded red, those infecting both vertebrates and arthropods (or with unknown vectors) are shaded yellow, those infecting both plants and arthropods are shaded green, those infecting non-arthropod invertebrates are shaded blue, and the remainder (arthropod only) are shaded black.

https://doi.org/10.7554/eLife.05378.014
Phylogenetic congruence between viruses (M segments) and hosts.

The comparisons include (A) Wuhan Horsefly Virus, (B) Wuhan Fly Virus 1, (C) Wuhan Mosquito Virus 2, and (D) Wuhan Mosquito Virus 1. Different host species/genera are distinguished with different colors, which are then mapped onto virus phylogeny to assess the phylogenetic congruence. ML phylogenetic trees were inferred in all cases.

https://doi.org/10.7554/eLife.05378.015
The differing genome organizations in the Chuviridae.

(A) ML trees of three main putative proteins conserved among the chuviruses. Viruses with circular genomes (Type I) are shaded blue, while those with segmented genomes (Type II) are shaded red. (B) Structures of all complete chuvirus genomes. Circular genomes are indicated with the arrow (blue) situated at the 3′ end, and the genome is drawn in a linear form for ease of comparison only, being broken at the region of variable sequence (refer to the ‘Materials and methods’). (C) An example showing mapping of sequencing reads to the circular chuvirus genome. The template for mapping contains two genomes connected head-to-tail. The two boxes magnify the genomic region containing abundant sequence variation.

https://doi.org/10.7554/eLife.05378.016
Genome structures of segmented negative-sense RNA viruses.

Predicted viral proteins homologous to known viral proteins are shown and colored according to their putative functions. The numbers below each ORF box give the predicted molecular mass.

https://doi.org/10.7554/eLife.05378.017
Genome structures of unsegmented negative-sense RNA viruses.

Predicted ORFs encoding viral proteins with >10 kDa molecular mass are shown and colored according to their putative functions. The numbers below each ORF box give the predicted molecular mass.

https://doi.org/10.7554/eLife.05378.018
Comparison of the genome structure of a potential tenui-like virus from horsefly with a prototype tenuivirus (Rice grassy stunt virus) genome.
https://doi.org/10.7554/eLife.05378.019
ML phylogeny of EVEs.

The phylogeny is based on the glycoprotein of chuviruses in the context of exogenous members of this family (A), with subtrees magnified for (B) the Culicidae clade and (C) the Hymenoptera clade. The EVEs used in the phylogeny covered the complete or near complete length of the glycoprotein gene and are shown in red and labeled according to host taxonomy in the overall tree. For clarity, monophyletic groups are collapsed based on the host taxonomy. Only bootstrap values >70% are shown.

https://doi.org/10.7554/eLife.05378.021
Transmission of negative-sense RNA viruses in arthropods and non-arthropods.

Three types of transmission cycle are shown: (i) those between arthropods and plants are shaded green; (ii) those between arthropods and vertebrates are shaded yellow; and (iii) those that are vertebrate-only are shaded red. Viruses associated with each transmission type are also indicated.

https://doi.org/10.7554/eLife.05378.022

Tables

Table 1

Host and geographic information and data output for each pool of arthropod samples

https://doi.org/10.7554/eLife.05378.003
PoolNo of unitsOrderSpeciesLocationsData generated (bases)
Mosquitoes—Hubei24DipteraAedes sp, Armigeres subalbatus, Anopheles sinensis, Culex quinquefasciatus, Culex tritaeniorhynchusHubei26,606,799,000
Mosquitoes—Zhejiang26DipteraAedes albopictus, Armigeres subalbatus, Anopheles paraliae, Anopheles sinensis, Culex pipiens, Culex sp, Culex tritaeniorhynchusZhejiang7,233,954,480
True flies24DipteraAtherigona orientalis, Chrysomya megacephala, Lucilia sericata, Musca domestica, Sarcophaga dux, S. peregrina, S. spHubei6,574,954,320
Horseflies24DipteraUnidentified Tabanidae (5 species)Hubei8,721,642,060
Cockroaches24BlattodeaBlattella germanicaHubei6,182,028,000
Water striders12HemipteraUnidentified Gerridae (2 species)Hubei3,154,714,200
Insects mix 16Diptera, Coleoptera, Lepidoptera, NeuropteraAbraxas tenuisuffusa, Hermetia illucens, unidentified Chrysopidae, unidentified Coleoptera, Psychoda alternata, unidentified Diptera, unidentified StratiomyidaeZhejiang7,745,172,660
Insects mix 24Diptera, HemipteraUnidentified Hippoboscidae (2 species), Cimex hemipterusHubei5,916,431,520
Insects mix 3 (insect near water)10Odonata, Hemiptera, Hymenoptera, IsopodaPseudothemis zonata, unidentified Nepidae (2 species), Camponotus japonicus, Diplonychus sp, Asellus spHubei11,973,368,200
Insects mix 4 (insect in the mountain)12Diptera, Orthoptera, Odonata, Hymenoptera, HemipteraPsychoda alternata, Velarifictorus micado, Crocothemis servilia, unidentified Phoridae, unidentified Lampyridae, Aphelinus sp, Hyalopterus pruni, Aulacorthum magnoliaHubei6,882,491,800
Ticks16IxodidaDermacentor marginatus, Dermacentor sp, Haemaphysalis doenitzi, H. longicornis, H. sp, H. formosensis, Hyalomma asiaticum, Rhipicephalus microplus, Argas miniatusHubei, Zhejiang, Beijing, Xinjiang24,708,479,580
Ticks Hyalomma asiaticum1IxodidaHyalomma asiaticumXinjiang2,006,000,100
Spiders32AraneaeNeoscona nautica, Parasteatoda tepidariorum, Plexippus setipes, Pirata sp, unidentified AraneaeHubei11,361,912,300
Shrimps48DecapodaExopalaemon carinicauda, Metapenaeus sp, Solenocera crassicornis, Penaeus monodon, Litopenaeus vannameiZhejiang5,365,359,900
Crabs and barnacles35Decapoda, ScalpelliformesCapitulum mitella, Charybdis hellerii, C. japonica, Uca arcuataZhejiang5,833,269,360
Millipedes12PolydesmidaUnidentified Polydesmidae (2 species)Hubei, Beijing7,176,702,400
Table 2

Mononegavirales-related RdRp sequences discovered in this study

https://doi.org/10.7554/eLife.05378.005
Virus nameLength of RdRpClassificationPoolAbundancePutative arthropod hostClosest relative (aa identity)
Bole Tick Virus 32155ChuvirusTicks202.35Hyalomma asiaticumMidway virus (17.1%)
Changping Tick Virus 22156ChuvirusTicks185.73Dermacentor spMidway virus (17.6%)
Changping Tick Virus 32209ChuvirusTicks41.80Dermacentor spMidway virus (16.5%)
Lishi Spider Virus 12180ChuvirusSpiders5.82Parasteatoda tepidariorumMidway virus (16.9%)
Shayang Fly Virus 12459ChuvirusTrue flies8.99Atherigona orientalisMaize mosaic virus (16.8%)
Shuangao Fly Virus 12097ChuvirusInsect mix 123.63Unidentified DipteraLettuce big-vein associated virus (16.3%)
Shuangao Insect Virus 52291ChuvirusInsect mix 1209.31Unidentified Diptera, Abraxas tenuisuffusa, unidentified ChrysopidaePotato yellow dwarf virus (16.3%)
Shuangao Lacewing Virus2145ChuvirusInsect mix 144.48Unidentified ChrysopidaePotato yellow dwarf virus (16.8%)
Tacheng Tick Virus 42101ChuvirusTicks137.22Argas miniatusMidway virus (17.5%)
Tacheng Tick Virus 52201ChuvirusTicks276.32Dermacentor marginatusMidway virus (16.8%)
Wenzhou Crab Virus 22208ChuvirusCrabs and barnacles4054.25Charybdis japonica, Charybdis lucifera, Charybdis helleriiMidway virus (15.8%)
Wenzhou Crab Virus 32077ChuvirusCrabs and barnacles169.21Charybdis japonicaMidway virus (16.3%)
Wuchang Cockroach Virus 32203ChuvirusCockroaches440.14Blattella germanicaMidway virus (16.3%)
Wuhan Louse Fly Virus 62182ChuvirusInsect mix 24.12Unidentified HippoboscidaeMidway virus (16.4%)
Wuhan Louse Fly Virus 72174ChuvirusInsect mix 299.83Unidentified HippoboscidaeMidway virus (17.2%)
Wuhan Mosquito Virus 82159ChuvirusMosquito Hubei300.33Culex tritaeniorhynchus, C. quinquefasciatus, Anopheles sinensis, Armigeres subalbatusMidway virus (16.7%)
Wuhan Tick Virus 22189ChuvirusTicks154.46Rhipicephalus microplusMidway virus (16.7%)
Culex tritaeniorhynchus rhabdovirus2142Culex tritaeniorhynchus rhabdovirusMosquito Hubei3517.32Culex tritaeniorhynchus, C. quinquefasciatus, Anopheles sinensis, Armigeres subalbatus, Aedes spIsfahan virus (38.5%)
Wuhan Insect Virus 42105CytorhabdovirusInsect mix 494.92Hyalopterus pruni OR Aphelinus spLettuce necrotic yellows virus (40.6%)
Wuhan Insect Virus 52098CytorhabdovirusInsect mix 4622.97Hyalopterus pruni OR Aphelinus spPersimmon virus A (47.9%)
Wuhan Insect Virus 62079CytorhabdovirusInsect mix 4991.99Hyalopterus pruni OR Aphelinus spPersimmon virus A (45.2)
Wuhan Louse Fly Virus 52123Kolente virus likeInsect mix 298.92Unidentified HippoboscidaeKolente virus (54.5%)
Yongjia Tick Virus 22113Nishimuro virus likeTicks13.14Haemaphysalis hystricisNishimuro virus (54.2%)
Shayang Fly Virus 22170Sigmavirus likeTrue flies36.83Musca domestica, Chrysomya megacephalaIsfahan virus (44.1%)
Wuhan Fly Virus 22134Sigmavirus likeTrue flies18.37Musca domestica, Sarcophaga spVesicular stomatitis Indiana virus (43.4%)
Wuhan House Fly Virus 12098Sigmavirus likeTrue flies31.04Musca domesticaIsfahan virus (42.8%)
Wuhan Louse Fly Virus 102146Sigmavirus likeInsect mix 2235.94Unidentified HippoboscidaeDrosophila melanogaster sigmavirus (51.2%)
Wuhan Louse Fly Virus 82145Sigmavirus likeInsect mix 2292.11Unidentified HippoboscidaeDrosophila melanogaster sigmavirus (50.6%)
Wuhan Louse Fly Virus 92145Sigmavirus likeInsect mix 269.37Unidentified HippoboscidaeDrosophila melanogaster sigmavirus (51.4%)
Bole Tick Virus 22171Unclassified dimarhabdovirus 1Ticks38.19Hyalomma asiaticumIsfahan virus (38.1%)
Huangpi Tick Virus 32193Unclassified dimarhabdovirus 1Ticks15.81Haemaphysalis doenitziEel virus European X (40%)
Tacheng Tick Virus 32182Unclassified dimarhabdovirus 1Ticks96.30Dermacentor marginatusEel virus European X (39.8%)
Taishun Tick Virus2226Unclassified dimarhabdovirus 1Ticks24.56Haemaphysalis hystricisVesicular stomatitis Indiana virus (36.6%)
Wuhan Tick Virus 12191Unclassified dimarhabdovirus 1Ticks119.92Rhipicephalus microplusEel virus European X (38.3%)
Wuhan Insect Virus 72120Unclassified dimarhabdovirus 2Insect mix 4241.7Hyalopterus pruni OR Aphelinus spIsfahan virus (42.6%)
Lishi Spider Virus 22201Unclassified mononegavirus 1Spiders5.57Unidentified AraneaeMaize fine streak virus (19.6%)
Sanxia Water Strider Virus 42108Unclassified mononegavirus 1Water striders4767.82Unidentified GerridaeOrchid fleck virus (20.5%)
Tacheng Tick Virus 62068Unclassified mononegavirus 1Ticks17.92Argas miniatusMaize mosaic virus (20.6%)
Shuangao Fly Virus 21966Unclassified mononegavirus 2Insect mix 125.94Psychoda alternataMidway virus (21.3%)
Xincheng Mosquito Virus2026Unclassified mononegavirus 2Mosquito Hubei400.12Anopheles sinensisMidway virus (19.2%)
Wenzhou Crab Virus 11807Unclassified mononegavirus 3Crabs and barnacles382.29Capitulum mitella, Charybdis japonica, Charybdis luciferaMidway virus (22.2%)
Tacheng Tick Virus 72215Unclassified rhabdovirus 1Ticks35.86Argas miniatusOrchid fleck virus (24.5%)
Jingshan Fly Virus 21970Unclassified rhabdovirus 2True flies4.43Sarcophaga spMaize fine streak virus (23.4%)
Sanxia Water Strider Virus 52264Unclassified rhabdovirus 2Water striders4373.68Unidentified GerridaeNorthern cereal mosaic virus (22.6%)
Shayang Fly Virus 32231Unclassified rhabdovirus 2True flies27.73Chrysomya megacephala, Atherigona orientalisMaize fine streak virus (22.6%)
Shuangao Bedbug Virus 22207Unclassified rhabdovirus 2Insect mix 216.29Cimex hemipterusMaize fine streak virus (22.5%)
Shuangao Insect Virus 62088Unclassified rhabdovirus 2Insect mix 114.37Unidentified Diptera, Abraxas tenuisuffusaPotato yellow dwarf virus (21.2%)
Wuhan Ant Virus2118Unclassified rhabdovirus 2Insect mix 3169.79Camponotus japonicusLettuce necrotic yellows virus (21.4%)
Wuhan Fly Virus 32230Unclassified rhabdovirus 2True flies6.00Musca domestica, Sarcophaga spMaize fine streak virus (21.9%)
Wuhan House Fly Virus 22233Unclassified rhabdovirus 2True flies221.04Musca domesticaNorthern cereal mosaic virus (23.4%)
Wuhan Mosquito Virus 92260Unclassified rhabdovirus 2Mosquito Hubei56.19Culex tritaeniorhynchus, C. quinquefasciatus, Aedes spPersimmon virus A (23.2%)
Wuhan Louse Fly Virus 112110Vesiculovirus likeInsect mix 26.11Unidentified HippoboscidaeVesicular stomatitis Indiana virus (52.9%)
Table 3

Bunya-arenaviridae-related RdRp sequences discovered in this study

https://doi.org/10.7554/eLife.05378.006
Virus nameLength of RdRpClassificationPoolAbundancePutative arthropod hostClosest relative (aa identity)
Huangpi Tick Virus 13914Nairovirus likeTicks11.32Haemaphysalis doenitziHazara virus (39.5%)
Tacheng Tick Virus 13962Nairovirus likeTicks88.91Dermacentor marginatusHazara virus (39.6%)
Wenzhou Tick Virus3967Nairovirus likeTicks44.30Haemaphysalis hystricisCrimean-Congo hemorrhagic fever virus (39.1%)
Shayang Spider Virus 14403Nairovirus likeSpiders90.95Neoscona nautica, Parasteatoda tepidariorum, Plexippus setipesCrimean-Congo hemorrhagic fever virus (26.2%)
Xinzhou Spider Virus4037Nairovirus likeSpiders3.79Neoscona nautica, Parasteatoda tepidariorumErve virus (22.9%)
Sanxia Water Strider Virus 13936Nairovirus likeWater striders26,483.38Unidentified GerridaeHazara virus (23.4%)
Wuhan Louse Fly Virus 12250OrthobunyavirusInsect mix 267.06Unidentified HippoboscoideaLa Crosse virus (57.8%)
Shuangao Insect Virus 12335Orthobunyavirus likeInsect mix 17.97Unidentified Chrysopidae, Psychoda alternataKhurdun virus (29.1%)
Wuchang Cockroach Virus 12125Phasmavirus likeCockroaches11,283.22Blattella germanicaKigluaik phantom virus (35.9%)
GAQJ010071891554Phasmavirus likeDatabaseN/AOstrinia furnacalisKigluaik phantom virus (35.9%)
Shuangao Insect Virus 21765Phasmavirus likeInsect mix 136.32Abraxas tenuisuffusa, unidentified DipteraKigluaik phantom virus (31.9%)
Wuhan Mosquito Virus 12095Phasmavirus likeMosquito Hubei, Mosquito Zhejiang3523.08Culex tritaeniorhynchus, Anopheles sinensis, Culex quinquefasciatusKigluaik phantom virus (39.5%)
Wuhan Mosquito Virus 22111Phasmavirus likeMosquito Hubei, Mosquito Zhejiang39.66Culex tritaeniorhynchus, Anopheles sinensis, Culex quinquefasciatus, Aedes spKigluaik phantom virus (39.6%)
Huangpi Tick Virus 22121PhlebovirusN/AN/AHaemaphysalis spUukuniemi virus (49.3%)
Bole Tick Virus 12148PhlebovirusTicks67.86Hyalomma asiaticumUukuniemi virus (37.9%)
Changping Tick Virus 12194PhlebovirusTicks335.25Dermacentor spUukuniemi virus (39.7%)
Dabieshan Tick Virus2148PhlebovirusTicks250.62Haemaphysalis longicornisUukuniemi virus (39.2%)
Lihan Tick Virus2151PhlebovirusTicks60.40Rhipicephalus microplusUukuniemi virus (38.6%)
Tacheng Tick Virus 22189PhlebovirusTicks132.59Dermacentor marginatusUukuniemi virus (39.0%)
Yongjia Tick Virus 12138PhlebovirusTicks119.49Haemaphysalis hystricisUukuniemi virus (40.5%)
GAIX010000592151Phlebovirus likeDatabaseN/APararge aegeriaCumuto virus (24.1%)
GAKZ010482601583Phlebovirus likeDatabaseN/AProcotyla fluviatilisCumuto virus (22.8%)
GAQJ010086812261Phlebovirus likeDatabaseN/AOstrinia furnacalisGouleako virus (22.0%)
Shuangao Insect Virus 32050Phlebovirus likeInsect mix 1339.41Unidentified Chrysopidae, unidentified DipteraCumuto virus (23.7%)
Wuhan Louse Fly Virus 22327Phlebovirus likeInsect mix 23.57Unidentified HippoboscoideaUukuniemi virus (25.2%)
Wuhan Insect Virus 12099Phlebovirus likeInsect mix 3178.53Asellus sp, unidentified Nepidae, Camponotus japonicusCumuto virus (24.8%)
Huangshi Humpbacked Fly Virus2009Phlebovirus likeInsect mix 413.13Unidentified PhoridaeCumuto virus (18.1%)
Yichang Insect Virus2100Phlebovirus likeInsect mix 471.50Aulacorthum magnoliaeGouleako virus (45.3%)
Wuhan Millipede Virus 11854Phlebovirus likeMillipedes and insect mix 3825.66Unidentified PolydesmidaeCumuto virus (25.3%)
Qingnian Mosquito Virus2243Phlebovirus likeMosquito Hubei17.09Culex quinquefasciatusRazdan virus (21.0%)
Wutai Mosquito Virus2185Phlebovirus likeMosquito Hubei70.72Culex quinquefasciatusRice stripe virus (26.4%)
Xinzhou Mosquito Virus2022Phlebovirus likeMosquito Hubei98.95Anopheles sinensisCumuto virus (24.7%)
Zhee Mosquito Virus2443Phlebovirus likeMosquito Hubei, Mosquito Zhejiang308.98Anopheles sinensis, Armigeres subalbatusCumuto virus (22.6%)
Wenzhou Shrimp Virus 12051Phlebovirus likeShrimps5859.37Penaeus monodonUukuniemi virus (32.2%)
Wuhan Spider Virus2251Phlebovirus likeSpiders17.71Neoscona nautica, Parasteatoda tepidariorum, Plexippus setipesUukuniemi virus (21.7%)
Wuhan Fly Virus 12192Phlebovirus likeTrue flies68.58Atherigona orientalis, Chrysomya megacephala, Sarcophaga sp, Musca domesticaGrand Arbaud virus (27.8%)
Wuhan Horsefly Virus3117Tenuivirus likeHorseflies13.50Unidentified TabanidaeUukuniemi virus (28.2%)
Jiangxia Mosquito Virus 11889Unclassified segmented virus 1Mosquito Hubei11.55Culex tritaeniorhynchusGouleako virus (16.7%)
Shuangao Bedbug Virus 12015Unclassified segmented virus 2Insect mix 212.71Cimex hemipterusMurrumbidgee virus (16.3%)
Jiangxia Mosquito Virus 21860Unclassified segmented virus 2Mosquito Hubei2.81Culex tritaeniorhynchusHantavirus (18.9%)
Shuangao Mosquito Virus1996Unclassified segmented virus 2Mosquito Zhejiang11.67Armigeres subalbatusHantavirus (18.7%)
Wenzhou Shrimp Virus 22241Unclassified segmented virus 3Shrimps3824.55Penaeus monodon, Exopalaemon carinicaudaLa Crosse virus (19.0%)
Shayang Spider Virus 22165Unclassified segmented virus 4Spiders12.75Neoscona nautica, Pirata sp, Parasteatoda tepidariorum, unidentified AraneaeAkabane virus (16.6%)
Wuhan Insect Virus 22377Unclassified segmented virus 5Insect mix 4223.06Hyalopterus pruni OR Aphelinus spKigluaik phantom virus (19.2%)
Sanxia Water Strider Virus 22349Unclassified segmented virus 5Water striders707.09Unidentified GerridaeKigluaik phantom virus (19.8%)
Wuhan Millipede Virus 23709Unclassified segmented virus 6Millipedes1513.41Unidentified PolydesmidaeDugbe virus (17.2%)
Wuhan Insect Virus 32231Unclassified segmented virus 7Insect mix 33.50Asellus spHerbert virus (17.2%)
Table 4

Orthomyxoviridae-related RdRp sequences discovered in this study

https://doi.org/10.7554/eLife.05378.007
Virus nameLength of RdRpClassificationPoolAbundancePutative arthropod hostClosest relative (aa identity)
Jingshan Fly Virus 1795QuaranjavirusTrue flies21.93Atherigona orientalis, Chrysomya megacephala, Sarcophaga sp, Musca domesticaJohnston Atoll virus (36.9%)
Jiujie Fly Virus653QuaranjavirusHorseflies10.30Unidentified TabanidaeJohnston Atoll virus (39.7%)
Sanxia Water Strider Virus 3789QuaranjavirusWater striders1101.03Unidentified GerridaeJohnston Atoll virus (36.7%)
Shayang Spider Virus 3768QuaranjavirusSpiders1.95Neoscona nauticaJohnston Atoll virus (38.5%)
Shuangao Insect Virus 4793QuaranjavirusInsect mix 159.90Unidentified Diptera, unidentified StratiomyidaeJohnston Atoll virus (36.9%)
Wuhan Louse Fly Virus 3784QuaranjavirusInsect mix 2500.77Unidentified HippoboscoideaJohnston Atoll virus (37.7%)
Wuhan Louse Fly Virus 4783QuaranjavirusInsect mix 296.80Unidentified HippoboscoideaJohnston Atoll virus (38.2%)
Wuhan Mosquito Virus 3801QuaranjavirusMosquito Hubei40.07Culex tritaeniorhynchus, Culex quinquefasciatus, Armigeres subalbatusJohnston Atoll virus (35.6%)
Wuhan Mosquito Virus 4792QuaranjavirusMosquito Hubei86.21Culex tritaeniorhynchus, Culex quinquefasciatus, Armigeres subalbatusJohnston Atoll virus (34.8%)
Wuhan Mosquito Virus 5806QuaranjavirusMosquito Hubei75.05Culex tritaeniorhynchus, Culex quinquefasciatus, Armigeres subalbatusJohnston Atoll virus (35.5%)
Wuhan Mosquito Virus 6800QuaranjavirusMosquito Hubei56.30Culex quinquefasciatusJohnston Atoll virus (34.2%)
Wuhan Mosquito Virus 7779QuaranjavirusMosquito Hubei20.74Anopheles sinensis, Culex quinquefasciatusJohnston Atoll virus (34.1%)
Wuhan Mothfly Virus710QuaranjavirusInsect mix 414.47Psychoda alternataJohnston Atoll virus (39.7%)
Wuchang Cockroach Virus 2671Unclassified orthomyxovirus 1Cockroaches4.01Blattella germanicaInfluenza C virus (27.0%)
Table 5

Summary of Endogenous Virus Elements (EVEs) determined here

https://doi.org/10.7554/eLife.05378.020
Host classificationHost nameVirus classificationGene(s) present
ChelicerataIxodes scapularisChuvirusG, N
DimarhabdovirusRdRp, N
Nairovirus likeN
PhlebovirusRdRp, N
QuaranjavirusRdRp
Tetranychus urticaeDimarhabdovirusN
CrustaceaDaphnia pulexPhlebovirus likeRdRp
Eurytemora affinisChuvirusG
DimarhabdovirusRdRp, N
Hyalella aztecaChuvirusG, N
Unclassified mononegavirus 3RdRp, N
Lepeophtheirus salmonisPhlebovirus likeN, G
Insecta: ColeopteraDendroctonus ponderosaeChuvirusG
PhasmavirusG, N
Tribolium castaneumChuvirusG
Insecta: DipteraAedes aegyptiChuvirusRdRp
DimarhabdovirusRdRp, N
PhasmavirusG
Phlebovirus likeN
QuaranjavirusRdRp
Anopheles spp.ChuvirusG
DimarhabdovirusRdRp, N
PhasmavirusG, N
Phlebovirus likeN
QuaranjavirusRdRp
Culex quinquefasciatusChuvirusG, N
DimarhabdovirusN
Drosophila spp.DimarhabdovirusRdRp, N
PhasmavirusN
Unclassified rhabdovirus 2RdRp, N
Insecta: IsopteraZootermopsis nevadensisChuvirusN
Insecta: HemipteraAcyrthosiphon pisumChuvirusG, N
DimarhabdovirusN
Phlebovirus likeN
QuaranjavirusRdRp
Unclassified mononegavirus 1RdRp, N
Rhodnius prolixusChuvirusG
PhasmavirusG
Insecta: HymenopteraAtta cephalotesUnclassified mononegavirus 2RdRp
Acromyrmex echinatiorChuvirusG
Unclassified mononegavirus 2RdRp
Camponotus floridanusChuvirusG
Unclassified mononegavirus 1N
Unclassified mononegavirus 3RdRp
Unclassified rhabdovirus 2RdRp
Harpegnathos saltatorChuvirusG
Linepithema humileChuvirusG
Nasonia spp.ChuvirusG
Pogonomyrmex barbatusChuvirusG
Solenopsis invictaChuvirusG
Unclassified mononegavirus 1N
Unclassified mononegavirus 3RdRp, N
Insecta: LepidopteraBombyx moriChuvirusRdRp, G
QuaranjavirusRdRp
Unclassified rhabdovirus 2RdRp
Melitaea cinxiaDimarhabdovirusN
QuaranjavirusRdRp
Plutella xylostellaDimarhabdovirusN, G
Spodoptera frugiperdaPhlebovirus likeG
MyriapodaStrigamia maritimaChuvirusN
Phlebovirus likeG

Data availability

The following data sets were generated
  1. 1
  2. 2

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