Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan

Abstract Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted investigate genetic variability of CMV isolates infecting pea and spinach Pothwar region Serological-based surveys during 2016-2017 revealed 31.70% overall disease incidence from crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) that all positive belong subgroup II. Two selected cDNA ELISA-positive samples representing each crops were PCR-amplified (ca.1100 bp) sequenced corresponding CP gene which shared 93.7% nucleotide identity with other. Both sequences (AAHAP) (AARS) Pakistan submitted GenBank as accession nos. MH119071 MH119073, respectively. BLAST analysis 93.4% sequence AAHAP isolate SpK (KC763473) Iran while AARS maximum (94.5%) strain 241 (AJ585519) Australia clustered some reference II UK (Z12818) USA (AF127976) Neighbour-joining phylogenetic reconstruction. A total 59 polymorphic (segregating) sites (S) diversity (?) 0.06218 evident no INDEL event observed Pakistani isolates. evolutionary distance recorded 0.0657 other 0.0574-0.2964 reported elsewhere world. frequent flow (Fst = 0.30478 <0.33) between earlier In differentiation analysis, value three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), Ks* (4.04042) non-significant. values 2.02535, 0.01468, 0.71862 Tajima's D, Fu, & Li’s F* D* respectively, demonstrating population under balancing selection.