Molecular characterization and genetic diversity of papaya meleira virus 2 associated with papaya sticky disease in northeast Brazil

Papaya sticky disease is one of the main diseases of agricultural crops in Brazil. It is characterized by the spontaneous exudation of latex in the fruits, which oxidizes, giving the fruit a sticky appearance. These symptoms are associated with a mixed infection formed by the papaya meleira virus and the newly discovered papaya meleira virus 2 (PMeV2). This work aimed to molecularly characterize the first PMeV2 isolate from northeastern Brazil; to estimate the phylogenetic relationships of this isolate with the other viruses of the Tombusviridae family; and in addition, to estimate the genetic diversity and phylogenetic relationships between PMeV2 isolates. The obtained sequence was named PMeV2-RN, which has 4,435 nucleotides and showed 94% identity with the isolate PMeV2-ES from Espírito Santo, Brazil. The sequence contains two predicted open reading frames (ORFs) in different reading phases. ORF1 encodes a 238 amino acid polypeptide that has 88% identity with the corresponding PMeV2-ES protein. ORF2 encodes a protein of 473 amino acids that presents 100% identity with the RNA-dependent RNA polymerase (RdRp) protein of PMeV2-ES. Phylogenetic analyses showed a greater proximity between isolate PMeV2-ES and isolates papaya virus Q (PpVQ) and PMeV-Mx than with PMeV2-RN, which seems to belong to a distinct lineage of this virus in Brazil. The comparative analysis of the nucleotide sequences among the isolates obtained in different producing regions of the northeast region of Brazil indicated a high degree of similarity between the sequences. It showed a high degree of conservation among the isolates, which did not form geographically structured groups.