Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya.

The mutation prone RNA genome of Papaya ringspot virus could be a driving force behind its geographical spread and dissemination. Here we present the molecular investigations on atypical PRSV–P strain identified from Pakistan with genome sequence phylogenetic and recombination analysis. The PRSV-P, Pakistan outbreak strain showing a geographic spread across India and Bangladesh in phylogenetic lineage. In major recombination events, it has acquired genome variation in amino terminal of PRSV coat protein gene, whereas the gene for helper component-proteinase (HC–Pro), a nonstructural coding region of multi-domain provenance, also evolves at nucleotide and amino acid levels. The phylogenetic analysis of another highly variable P1 region showed evolutionary dynamics with respect to other geographical strains, particularly the Indian isolate from North East region (Meghalaya). PRSV–PK holds high levels of genetic divergence in comparison to American, Australian and Asian isolates. The genetic and phylogeographic analyses indicate that a spatial recombination has occurred from first PRSV, however temporal evolution is within the region of occurrence. The genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.