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A novel circular Rep-encoding single-stranded DNA virus detected in Agrotis ipsilon (Lepidoptera: Noctuidae) in China

Abstract

Long-distance migratory insects carry microorganisms that can potentially play a crucial role in the life cycles of their hosts. Here, we used Illumina and Sanger sequencing to determine the complete genome sequence of a novel circular Rep-encoding single-stranded (ss) DNA virus from an important migratory pest, Agrotis ipsilon (Hufnagel). The full genome of this new virus is about 2, 242 nt in length and shares 55-75% genome-wide pairwise sequence identity with members of the family Genomoviridae but 91% nucleotide sequence identity with finch-associated genomovirus 3 isolate S30P_D, which is tentatively abbreviated “FaGmV-3”. Viral infection rates in A. ipsilon from Yantai, Langfang and Xinxiang were 4.5% (n = 88), 11.8% (n = 85) and 0% (n = 35), respectively. Phylogenetic analysis based on the deduced amino acid sequence of Rep indicated that the Agrotis ipsilon-associated virus is closely related to members of the genus Gemykibivirus, and we propose it to be a new member of this genus. Hence, it is tentatively named “Agrotis ipsilon-associated genomovirus” (AiGmV).

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References

  1. 1.

    Liu YQ, Fu XW, Feng HQ, Liu ZF, Wu KM (2015) Trans-regional Migration of Agrotis ipsilon (Lepidoptera: Noctuidae) in North-East Asia. Ann Entomol Soc Am 108:519–527

  2. 2.

    Swiatoniowska M, Ogorzalek A, Golas A, Michalik A, Szklarzewicz T (2012) Ultrastructure, distribution, and transovarial transmission of symbiotic microorganisms in Nysius ericae and Nithecus jacobaeae (Heteroptera: Lygaeidae: Orsillinae). Protoplasma 250:325–332

  3. 3.

    Xu PJ, Liu YQ, Graham RI, Wilson K, Wu KM (2014) Densovirus is a mutualistic symbiont of a global crop pest (Helicoverpa armigera) and protects against a baculovirus and Bt biopesticide. PLoS Pathog 10:e1004490

  4. 4.

    Lewis LC, Adams JR (1979) Pathogenicity of a nuclear polyhedrosis virus from Rachiplusia ou to Agrotis ipsilon. J Invertebr Pathol 33:253–256

  5. 5.

    Kraberger S, Argüello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A (2015) Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. Infect Genet Evol 31:73–86

  6. 6.

    Halary S, Duraisamy R, Fancello L, Monteil-Bouchard S, Jardot P, Biagini P, Gouriet F, Raoult D, Desnus C (2016) Novel single-stranded DNA circular viruses in pericardial fluid of patient with recurrent pericarditis. Emerg Infect Dis 22:1839–1841

  7. 7.

    Kraberger S, Cook CN, Schmidlin K, Fontenele RS, Bautista J, Smith B, Varsani A (2019) Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera). Infect Genet Evol 71:179–188

  8. 8.

    Ge X, Li Y, Yang X, Zhang H, Zhou P, Zhang Y, Shi Z (2012) Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J Virol 86:4620–4630

  9. 9.

    Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY (2014) A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 24:1180–1192

  10. 10.

    Schalk HJ, Matzeit V, Schiller B, Schell J, Gronenborn B (1989) Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO J 8:359–364

  11. 11.

    Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9(9):e108277

  12. 12.

    Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165

  13. 13.

    Schmidlin K, Sepp T, Khalifeh A, Smith K, Fontenele RS, McGraw KJ, Varsani A (2019) Diverse genomoviruses representing eight new and one known species identified in feces and nests of house finches (Haemorhous mexicanus). Arch Virol 164:2345–2350

  14. 14.

    Varsani A, Krupovic M (2017) Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol 3:vew037

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Funding

This work was supported by the National Natural Science Funds of China (Grant no. 31621064) and China Agriculture Research System (Grant no. CARS-15-19).

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Correspondence to Kongming Wu.

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Yang, F., Yang, X. & Wu, K. A novel circular Rep-encoding single-stranded DNA virus detected in Agrotis ipsilon (Lepidoptera: Noctuidae) in China. Arch Virol 165, 771–774 (2020). https://doi.org/10.1007/s00705-019-04521-5

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