Complete coding sequence of a novel picorna-like virus in a blackbird infected with Usutu virus
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).
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Conflict of interest
The authors declare no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- 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
- 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
- 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