Characterization of a new cytorhabdovirus discovered in papaya (Carica papaya) plantings of Ecuador and its relationship with a bean-infecting strain from Brazil

Authors: MEDINA-SALGUERO, ANDRES - Escuela Superior Politecnica Del Litoral; CORNEJO-FRANCO, JUAN - Centro De Investigaciones Biotecnologicas Del Ecuador; Grinstead, Sam; Mollov, Dimitre; Mowery, Joseph; FLORES, FRANCISCO - Escuela Superior Politecnica Del Litoral; QUITO-AVILA, DIEGO - Centro De Investigaciones Biotecnologicas Del Ecuador

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2019
Publication Date: 6/20/2019
Citation: Medina-Salguero, A., Cornejo-Franco, J., Grinstead, S.C., Mollov, D.S., Mowery, J.D., Flores, F., Quito-Avila, D. 2019. Characterization of a new cytorhabdovirus discovered in papaya (Carica papaya) plantings of Ecuador and its relationship with a bean-infecting strain from Brazil. PLoS One. https://doi.org/10.1371/journal.pone.0215798.
DOI: https://doi.org/10.1371/journal.pone.0215798

Interpretive Summary: Papaya is a tropical fruit consumed fresh in many parts of the world. Papaya plants in Ecuador were observed with virus-like symptoms. Plants were initially found to be infected with papaya ringspot virus but further investigation was warranted based on the symptoms. Next generation sequencing analysis revealed a second and new virus belonging to the plant rhabdovirus group. The complete genomic sequence of this virus was determined and used to developed primers that can be used for its detection. Plants from five papaya growing regions in Ecuador were screened using the new detection procedure. The new rhabdovirus was found in all areas co-infecting papaya trees with papaya ring spot virus. These findings will help understand the complex nature of viral diseases affecting papaya and facilitate improved management strategies. This information will be useful to growers and regulatory agencies.

Technical Abstract: The complete genome of a new rhabdovirus infecting papaya (Carica papaya L.) was sequenced and characterized. The genome consists of 13,469 nucleotides with six canonical open reading frames (ORFs) predicted from the antigenomic strand. In addition, two overlapping short ORFs were predicted between ORFs 3 and 4. Phylogenetic analyses using amino acid sequences from the nucleocapsid, glycoprotein and polymerase, grouped the virus with members of the genus Cytorhabdovirus, with rice stripe mosaic virus, yerba mate chlorosis-associated virus and Colocasia bobone disease-associated virus as closest relatives. The 3’ leader and 5’ trailer sequences were 144 and 167 nt long, respectively. Each end contains complementary sequences prone to form panhandle structures. The motif 3’-AUUCUUUUUG-5’, conserved across rhabdoviruses, was identified in all but one intergenic regions; whereas the motif 3’-ACAAAAACACA-5’ was found in three intergenic junctions. This is the first complete genome of a cytorhabdovirus infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the most important papaya producing province of Ecuador. During the final stage of this manuscript preparation, the genome of a bean-associated cytorhabdovirus became available. Nucleotide identity (97%) between both genomes indicated that the two viruses are strains of the same species, for which we propose the name papaya cytorhabdovirus E.