Abstract
Papaya ringspot virus (PRSV), the causative agent of a devastating and widespread ringspot disease in papaya (Carica papaya L.), belongs to the family Potyviridae. Here, we report the first complete genome characterization of a severe PRSV isolate (PRSV-Pune; GenBank accession No. MH311882) from papaya in the Pune district, western India. The genome size of PRSV-Pune is 10,326 nucleotides (nt), excluding the poly-A tail, encoding a polyprotein of 3345 amino acids (aa). The PRSV-Pune showed identity ranging from 82 to 86% and 87–90% at the nucleotide and amino acid levels, respectively, with 29 complete PRSV-P genomes from all over the world. Variations in amino acid composition at and around two polyprotein cleavage sites of PRSV-Pune were observed: MEQY/S instead of MEQY/N in P1/HC-Pro and DYHQ/N instead of VYHQ/S in CI/6K2. Phylogenetic analysis revealed the clustering of PRSV-Pune, along with the majority of Indian PRSV isolates, with isolates of American lineage. Putative recombination events in P1, HC-Pro, CI, NIb and CP coding regions were detected in PRSV-Pune. Negative selection pressure predicted in all cistrons indicates purifying selection. Our results highlight unique attributes of the severe PRSV-Pune from papaya.
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