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Complete genome sequence and phylogenetic analysis of a newly discovered fusagra-like virus infecting Carica papaya in Ecuador

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Abstract

A new fusagra-like virus infecting papaya (Carica papaya L.) was genetically characterized. The genome of the virus, provisionally named "papaya sticky fruit-associated virus" (PSFaV), is a single molecule of double-stranded RNA, 9,199 nucleotides (nt) in length, containing two discontinuous open reading frames. Pairwise sequence comparisons based on complete RNA-dependent-RNA-polymerase (RdRp) sequences revealed identity of 79.4% and 83.3% at the nt and amino acid (aa) level, respectively, to babaco meleira-like virus (BabMelV), an uncharacterized virus sequence discovered in babaco (Vasconcellea x heilbornii) in Ecuador. Additional plant-associated viruses with sequence identity in the 50% range included papaya meleira virus (PMeV) isolates from Brazil. Phylogenetic analysis based on the amino acid sequences of the capsid protein (CP), RdRp, and CP-RdRp fusion protein genes placed PSFaV in a group within a well-supported clade that shares a recent ancestor with Sclerotium rolfsii RNA virus 2 and Phlebiopsis gigantea mycovirus dsRNA 2, two fungus-associated fusagraviruses. Genomic features and phylogenetic relatedness suggest that PSFaV, along with its closest relative BabMelV, represent a species of novel plant-associated virus classified within the recently established family Fusagraviridae.

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Data availability

The complete genome sequence reported here is available in the GenBank database under the accession number ON226840.

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Acknowledgments

Plant samples were collected under Genetic Resource Access permit number MAE-DNB-CM-2018-0098, granted by the Department of Biodiversity of the Ecuadorean Ministry of the Environment. The authors thank the papaya growers from all of the fields sampled in this study.

Funding

This work was partially funded by the Secretaría de Educación Superior, Ciencia, Tecnología e Innovación (Ecuadorean Science and Technology Secretariat) under the INEDITA Project Initiative (project number PIC-21-INE-ESPOL-001).

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Authors

Contributions

Study conception and design: D.Q-A. Material preparation, data collection, and analysis were performed by D.Q-A, J.F-C, E.R-P, R.A-Q, and F.F. The first draft of the manuscript was written by J.F-C, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Diego F. Quito-Avila.

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The authors declare that they have no conflict of interest.

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This research does not contain any experiments involving human participants or animals.

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Communicated by Massimo Turina

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Electronic Supplementary Material

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Supplementary Material 1

705_2024_6075_MOESM2_ESM.jpg

Online Resource 2: (A) Predicted 3D structures of full-length coat proteins (CPs) of PSFaV, babaco meleira-like virus (BabMelV), papaya meleira virus isolate Espirito Santo (PMeV-ES), and papaya meleira virus isolate Rio Grande do Norte (PMeV-RN). Dotted boxes indicate the most conserved regions, which are magnified in B. (B) Extracted region from PSFaV (321–1167), BabMelV (309–1155), PMeV-RN (328–1173), and PMEV-ES (293–1139) showing higher structural and sequence similarity.

Supplementary Material 2

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Cornejo-Franco, J.F., Reyes-Proaño, E., Alvarez-Quinto, R.A. et al. Complete genome sequence and phylogenetic analysis of a newly discovered fusagra-like virus infecting Carica papaya in Ecuador. Arch Virol 169, 151 (2024). https://doi.org/10.1007/s00705-024-06075-7

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