Genetic Diversity and Phylogeny of Chilli Veinal Mottle Virus in Yunnan Tobacco-Planting Regions Based on the CP Gene

Chilli veinal mottle virus (ChiVMV, Potyvirus capsivenamaculae) can infect various Solanaceae crops, causing a decrease in yield and quality. In recent years, ChiVMV has become one of the most prevalent viruses affecting tobacco production, but its diversity and genetic structure are still elusive. In this study, 202 ChiVMV isolates were obtained from 13 tobacco-producing areas in Yunnan Province between 2021 and 2025. Analysis of the coat protein (CP) genes of the 202 isolates showed that there exist 193 haplotypes and abundant genetic diversity. The highest variation was observed at the N-terminus of ChiVMV CP. Further analysis displayed three high-confidence recombination events in the CP gene of ChiVMV Yunnan isolates, with isolate 25DLYP-7 from the Dali region playing a putative parental isolate for these recombinations. The results of neutral and selection pressure analyses indicated that the CP gene of ChiVMV Yunnan isolates exhibits purifying selection. Distribution analysis of these ChiVMV Yunnan isolates showed that geographical isolation is closely related to the genetic diversity of ChiVMV, and field weeds may serve as important initial sources of infection. Phylogenetic analysis demonstrated that ChiVMV Yunnan populations display close association with isolates from southwestern China, as well as isolates from South Asia and Europe.