Archives of Virology

, Volume 163, Issue 6, pp 1701–1703 | Cite as

Complete coding sequence of a novel picorna-like virus in a blackbird infected with Usutu virus

  • Steven Van Borm
  • Mieke Steensels
  • Elisabeth Mathijs
  • Claude Kwe Yinda
  • Jelle Matthijnssens
  • Bénédicte Lambrecht
Annotated Sequence Record


Using random high-throughput RNA sequencing, the complete coding sequence of a novel picorna-like virus (a 9,228-nt contig containing 212,202 reads) was determined from a blackbird (Turdus merula) infected with Usutu virus. This sequence shares only 36% amino acid sequence identity with its closest homolog, arivirus 1, (an unclassified member of the order Picornavirales), and shares its dicistronic genome arrangement. The new virus was therefore tentatively named “blackbird arilivirus” (ari-like virus). The nearly complete genome sequence consists of at least 9,228 nt and contains two open reading frames (ORFs) encoding the nonstructural polyprotein (2235 amino acids) and structural polyprotein (769 amino acids). Two TaqMan RT-qPCR assays specific for ORF1 confirmed the presence of high levels of this novel virus in the original sample. Nucleotide composition analysis suggests that blackbird arilivirus is of dietary (plant) origin.



DVM. F. Hénin kindly collected the bird and circumstantial information. The expert technical assistance of O. Ozhelvaci, S. H. Mahibullah and A. Ausloos is much appreciated. Raw sequence data were generated by the Biotechnology and Molecular Biology Platform of the Scientific Institute for Public Health (Brussels, Belgium).


The authors received no financial support for the research, authorship, and/or publication of this article.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2018_3761_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 14 kb)


  1. 1.
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230CrossRefPubMedGoogle Scholar
  3. 3.
    Garigliany M, Linden A, Gilliau G, Levy E, Sarlet M, Franssen M, Benzarti E, Derouaux A, Francis F, Desmecht D (2017) Usutu virus, Belgium, 2016. Infect Genet Evol 48:116–119CrossRefPubMedGoogle Scholar
  4. 4.
    Holtz LR, Cao S, Zhao G, Bauer IK, Denno DM, Klein EJ, Antonio M, Stine OC, Snelling TL, Kirkwood CD, Wang D (2014) Geographic variation in the eukaryotic virome of human diarrhea. Virology 468–470:556–564CrossRefPubMedGoogle Scholar
  5. 5.
    Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD (2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics 31:2374–2376CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Koonin EV, Wolf YI, Nagasaki K, Dolja VV (2008) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6:925–939CrossRefPubMedGoogle Scholar
  8. 8.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH (2015) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:D222–D226CrossRefPubMedGoogle Scholar
  10. 10.
    Rosseel T, Ozhelvaci O, Freimanis G, Van Borm S (2015) Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. J Virol Methods 222:72–80CrossRefPubMedGoogle Scholar
  11. 11.
    Van Borm S, Lambrecht B, Vandenbussche F, Steensels M (2017) Complete coding sequence of Usutu virus strain Gracula religiosa/U1609393/Belgium/2016 obtained from the brain tissue of an infected captive common hill myna (Gracula religiosa). Genome Announc 5(12):e00042-17CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Yinda CK, Zell R, Deboutte W, Zeller M, Conceicao-Neto N, Heylen E, Maes P, Knowles NJ, Ghogomu SM, Van Ranst M, Matthijnssens J (2017) Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats. BMC Genom 18:249CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Steven Van Borm
    • 1
  • Mieke Steensels
    • 1
  • Elisabeth Mathijs
    • 1
  • Claude Kwe Yinda
    • 2
  • Jelle Matthijnssens
    • 2
  • Bénédicte Lambrecht
    • 1
  1. 1.Directorate Viral DiseasesVeterinary and Agrochemical Research Center CODA-CERVABrusselsBelgium
  2. 2.Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega InstituteKU LeuvenLeuvenBelgium

Personalised recommendations