First report of Cowpea mosaic virus (CPMV, Comovirus vignae) and molecular characterization of Indian strain RNA2

The RNA2 sequence of Cowpea mosaic virus (CPMV, Comovirus vignae) is submitted from India for the first time. At present, only seven CPMV isolates from different countries possess a fully characterized genome. High throughput sequencing method (Illumina Hi seq) of entire RNA extract from cowpea plants taken from Haryana and Delhi elucidated the genomic sequence. RNA-2 is 3484 nucleotides in length, excluding the poly (A) tail, and exhibits a sequence identity ranging from 94.11% to 99.17% with other CPMV isolates. The serological test, such as DAS-ELISA, confirmed the presence of the infection. Mechanically inoculated plants exhibited symptoms similar to CPMV. Transmission electron microscopy (TEM) revealed the significant cytoplasmic changes in the infected plant. The open reading frames (ORFs) are analyzed, and the potential polyprotein cleavage sites are observed. Phylogenetic analysis and recombination study clarify the evolutionary relationship and the virus’s dynamic properties. The identified purifying selection pressure signifies the evolutionary constraints of maintaining the essential viral functions.