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An umbra-related virus found in babaco (Vasconcellea × heilbornii)

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Abstract

The complete sequence of a new viral RNA from babaco (Vasconcellea × heilbornii) was determined. The genome consisted of 4,584 nucleotides, containing two open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus, and an unusually long (1,843 nt) NCR at the 3’ terminus. The presence of a potential heptameric slippery signal located 12 nt upstream the stop codon of ORF 1 suggests a -1 ribosomal frameshift mechanism for the translation of ORF 2. Sequence comparisons of ORF 2 revealed similarity to the RNA-dependent RNA polymerase (RdRp) of several umbra- and umbra-like viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported in papaya, citrus, opuntia, maize, and sugarcane hosts. Viruses of this clade share a most recent ancestor with the umbraviruses but have different genomic features. The creation of a new genus within the family Tombusviridae is proposed for the classification of these novel viruses.

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Availability of data

The complete genome sequence of the virus reported here has been deposited in the GenBank database under accession number MT113181.

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Acknowledgements

The authors acknowledge the Rumiñahui high performance cluster at Universidad de las Fuerzas Armadas-ESPE for allowing the analysis of high-throughput sequencing data.

Funding

Partial funding for this work came from red ecuatoriana de universidades y escuelas politécnicas del Ecuador (REDU), under research grant PREDU-2016-001.

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Authors and Affiliations

Authors

Contributions

Conceptualization: DQA. Methodology: JCF, FF, DM. Formal analysis and investigation: DQA, FF. Writing (original draft): DQA. Writing review and editing: DQA, FF, DM. Funding acquisition: DQA. Supervision: DQA.

Corresponding author

Correspondence to Diego F. Quito-Avila.

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The authors declare no conflict of interest.

Ethics approval

Plant samples were collected under Genetic Resource Access Permit # MAE–DNB–CM–2018–0098 granted by the Department of Biodiversity of the Ecuadorean Ministry of the Environment.

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Handling Editor: Massimo Turina.

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Cornejo-Franco, J.F., Flores, F., Mollov, D. et al. An umbra-related virus found in babaco (Vasconcellea × heilbornii). Arch Virol 166, 2321–2324 (2021). https://doi.org/10.1007/s00705-021-05117-8

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  • DOI: https://doi.org/10.1007/s00705-021-05117-8

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