Molecular diversity of Papaya ringspot virus in India: genetic recombination and mutations between the isolates from different hosts and geo-climatic locations are role players in virus evolution

Among 10 proteins encoded by Papaya ringspot virus (PRSV), only coat protein (CP) has been studied extensively from mainly the papaya-originated isolates i.e. PRSV-P. In this study, besides CP, the helper component proteinase (HC-pro) and nuclear inclusion protein-a (NIa-pro) coding regions from 19 PRSV-P and -W isolates originating from different geo-climatic locations and hosts were analyzed. Unlike CP, both HC-pro and NIa-pro did not reveal the variability in their length. HC-pro and NIa-pro sequences revealed less than 10% deduced amino acid (daa) diversity worldwide, the CP was found highly variable (up to 20% daa diversity). Highest variability in CP sequence was noticed among the cucurbit-originating PRSV-P Indian isolates, especially from Warm semi-arid climate, which was attributed to a large number of aa insertions/deletions. However, papaya-originating PRSV-P isolates from the Oceanic climate were less variable (up to 5% daa diversity). In NIa-pro, besides already known host/pathotype-specific switching of aa Lys/Asp27, switching of Lys27 → Arg27 and Asp27 → Glu27 was identified within P and W pathotypes. Additionally, a novel aa switching from Ser/Met134 → Thr134 between P and W pathotypes respectively was identified. The phylogeny of PRSV isolates was largely based on the geo-climatic locations and hosts. Through recombination detection analysis, three recombinant isolates were detected based on both NIa-pro and CP sequences, which possessed cucurbit-originated PRSV (either -P or -W) isolates as one of their parents (either major or minor.) Patterns of codon usage among the three protein coding sequences generated further revealed that the CP gene is under maximum selection pressure (with six sites) followed by NIa-pro gene (with one site). This investigation shows that the genetic recombination between the isolates originating from different hosts and geo-climatic locations as well as mutations are the significant mechanisms playing their role in generating diverse populations of PRSV.