Skip to main content
SpringerLink
Log in

Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Valles SM, Chen Y, Firth AE, Guérin DMA, Hashimoto Y, Herrero S, de Miranda JR, Ryabov E, ICTV Report Consortium (2017) ICTV Virus Taxonomy Profiles: Iflaviridae. J Gen Virol 98:527–528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Geng P, Li W, de Miranda JR, Qian Z, An L, Terenius O (2017) Studies on the transmission and tissue distribution of Antheraea pernyi iflavirus in the Chinese oak silkmoth Antheraea pernyi. Virol 502:171–175

    Article  CAS  Google Scholar 

  3. Geng P, Li W, Lin L, de Miranda JR, Emrich S, An L, Terenius O (2014) Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi. PLoS One 9:e92107

    Article  PubMed  PubMed Central  Google Scholar 

  4. Kalynych S, Fuzik T, Pridal A, de Miranda J, Plevka P (2017) Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism. Proc Natl Acad Sci U S A 114:598–603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kalynych S, Pridal A, Palkova L, Levdansky Y, de Miranda JR, Plevka P (2016) Virion structure of iIflavirus slow bee paralysis virus at 2.6-angstrom resolution. J Virol 90:7444–7455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ryabov EV, Wood GR, Fannon JM, Moore JD, Bull JC, Chandler D, Mead A, Burroughs N, Evans DJ (2014) A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission. PLoS Pathog 10:e1004230

    Article  PubMed  PubMed Central  Google Scholar 

  7. Silva LA, Ardisson-Araujo DM, Tinoco RS, Fernandes OA, Melo FL, Ribeiro BM (2015) Complete genome sequence and structural characterization of a novel iflavirus isolated from Opsiphanes invirae (Lepidoptera: Nymphalidae). J Invertebr Pathol 130:136–140

    Article  CAS  PubMed  Google Scholar 

  8. Carrillo-Tripp J, Krueger EN, Harrison RL, Toth AL, Miller WA, Bonning BC (2014) Lymantria dispar iflavirus 1 (LdIV1), a new model to study iflaviral persistence in lepidopterans. J Gen Virol 95:2285–2296

    Article  PubMed  Google Scholar 

  9. Liu S, Chen Y, Sappington TW, Bonning BC (2017) Genome sequence of the first coleopteran iflavirus isolated from western corn rootworm. Diabrotica virgifera virgifera LeConte, Genome Announc, p 5

    Google Scholar 

  10. Murakami R, Suetsugu Y, Kobayashi T, Nakashima N (2013) The genome sequence and transmission of an iflavirus from the brown planthopper, Nilaparvata lugens. Virus Res 176:179–187

    Article  CAS  PubMed  Google Scholar 

  11. Murakami R, Suetsugu Y, Nakashima N (2014) Complete genome sequences of two iflaviruses from the brown planthopper, Nilaparvata lugens. Arch Virol 159:585–588

    Article  CAS  PubMed  Google Scholar 

  12. Yuan H, Xu P, Yang X, Graham RI, Wilson K, Wu K (2017) Characterization of a .novel member of genus Iflavirus in Helicoverpa armigera. J Invertebr Pathol 144:65–73

    Article  CAS  PubMed  Google Scholar 

  13. Arno J, Castane C, Riudavets J, Gabarra R (2010) Risk of damage to tomato crops by the generalist zoophytophagous predator Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae). Bull Entomol Res 100:105–115

    Article  CAS  PubMed  Google Scholar 

  14. Nakaishi K, Arakawa R (2011) Effects of spiracle-blocking insecticides and microbial insecticides on the predator mirid bug, Nesidiocoris tenuis (reuter) (heteroptera: miridae). Pak J Biol Sci 14:991–995

    Article  CAS  PubMed  Google Scholar 

  15. Sanchez JA, Lacasa A (2008) Impact of the zoophytophagous plant bug Nesidiocoris tenuis (Heteroptera: Miridae) on tomato yield. J Econ Entomol 101:1864–1870

    Article  CAS  PubMed  Google Scholar 

  16. Xu P, Song X, Yang X, Tang Z, Ren G, Lu Y (2017) A novel single-stranded RNA virus in Nesidiocoris tenuis. Arch Virol 162:1125–1128

    Article  CAS  PubMed  Google Scholar 

  17. Wang J, Zhang J, Jiang H, Liu C, Yi F, Hu Y (2005) Nucleotide sequence and genomic organization of a newly isolated densovirus infecting Dendrolimus punctatus. J Gen Virol 86:2169–2173

    Article  CAS  PubMed  Google Scholar 

  18. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  Google Scholar 

  20. Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ (2014) The family Parvoviridae. Arch Virol 159:1239–1247

    Article  CAS  PubMed  Google Scholar 

  21. Luria N, Reingold V, Lachman O, Sela N, Dombrovsky A (2016) Extended phylogenetic analysis of a new Israeli isolate of Brevicoryne brassicae virus (BrBV-IL) suggests taxonomic revision of the genus Iflavirus. Virol J 13:50

    Article  PubMed  PubMed Central  Google Scholar 

  22. Xu P, Graham RI, Wilson K, Wu K (2017) Structure and transcription of the Helicoverpa armigera densovirus (HaDV2) genome and its expression strategy in LD652 cells. Virol J 14:23

    Article  PubMed  PubMed Central  Google Scholar 

  23. Xu P, Liu Y, Graham RI, Wilson K, Wu K (2014) Densovirus is a mutualistic symbiont of a gGlobal crop pest (Helicoverpa armigera) and protects against a baculovirus and Bt Biopesticide. PLoS Pathog 10:e1004490

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This study was funded by the National Natural Science Foundation of China (Grant No. 31401752) and the Agricultural Science and Technology Innovation Program (Grant No. ASTIP-TRIC04).

Author information

Author notes

  1. Yonghao Dong and Jiangtao Chao contribute equally to this work.

Authors and Affiliations

  1. Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China

    Yonghao Dong, Jiangtao Chao, Jinyan Liu & Pengjun Xu

  2. College of Plant Protection, Shandong Agricultural University, Taian, P.R. China

    Yonghao Dong & Yongjie Liu

  3. Lancaster Environment Centre, Lancaster University, Lancaster, UK

    Annabel Rice, Robert Holdbrook & Pengjun Xu

Authors
  1. Yonghao Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiangtao Chao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jinyan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Annabel Rice
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Robert Holdbrook
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yongjie Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Pengjun Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pengjun Xu.

Ethics declarations

Conflicts of interest

The authors declare that they have no competing interests.

Ethical approval

No permits were required for the described insect collection and experimentation.

Additional information

Handling Editor: T. K. Frey.

Nucleotide sequence accession number. The complete genome sequence of NtV-1 was submitted to GenBank with the accession number KY969634.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 2860 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dong, Y., Chao, J., Liu, J. et al. Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus . Arch Virol 163, 571–574 (2018). https://doi.org/10.1007/s00705-017-3622-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-017-3622-8

Search

Navigation