Complex diversityin papaya ringspot virus (PRSV) populations is governed by the host species and the geo-climatic locations

Abstract Papaya ringspot virus (PRSV) is one of the most important viral pathogens limiting papaya and cucurbit production globally. However, the evolutionary processes governing its population structure across diverse agro-ecological environments remain insufficiently understood. This study examined the genetic diversity, recombination patterns, and population structure of PRSV-P and PRSV-W isolates collected from different hosts and geo-climatic regions of India. Twenty-seven PRSV isolates originated from papaya and multiple cucurbit species were analyzed based onthe sequences of three protein coding regions: helper component proteinase (HC-Pro), nuclear inclusion proteinase-a (NIa-Pro), and coat protein (CP). The CP gene displayed substantial variation, ranging from 837 to 876 nucleotides, with the amino acid (aa)sequence diversities reaching up to 20%. Higher diversity was observed among cucurbit-derived PRSV-P isolates from warm semi-arid (WSA) regions, primarily through frequent aainsertion and deletion events. Phylogenetic analyses revealed varying evolutionary patterns among genomic regions. CP sequences grouped according to geo-climatic origin, whereas NIa-Pro differentiated based on host-& pathotype-associated lineages (PRSV-P and PRSV-W), while HC-Pro showed no distinct clustering patterns. Recombination analysis identified gene-specific evolutionary dynamics, with recombination detected in CP and NIa-Pro but not in HC-Pro. Population genetic analyses indicated extremely high haplotype diversity ( Hd = 0.996), strong population subdivision ( Snn = 0.88889–1.00000; p ≤ 0.004), and moderate to high genetic differentiation ( Fst = 0.1899–0.7713), despite restricted gene flow ( Nm = 0.20). Negative Tajima’s D values suggested recent population expansion and/or strong purifying selection. Overall, environmental variation, host association, and gene-specific constraints jointly influence PRSV evolution, while genetic isolation and limited gene flow promote diversification and ecological adaptation across distinct geo-climatic regions.