Molecular Detection and Phylogenetic Relationships of Carrot Red Leaf Virus in Apiaceous Crop Production Areas

Abstract

Carrot red leaf virus (CtRLV), a phloem-limited polerovirus (family Solemoviridae) transmitted in a persistent, circulative manner by the willow-carrot aphid Cavariella aegopodii Scopoli, has emerged as an increasingly significant viral pathogen in Apiaceous crop production systems, inducing characteristic foliar reddening, stunting, root deformation, and marketable yield reductions in carrot (Daucus carota L.) and related umbelliferous crops under conditions conducive to aphid vector activity and population buildup. Despite the recognized economic impact of CtRLV in established carrot-producing regions, systematic molecular epidemiological surveys documenting virus incidence, geographic distribution, and phylogenetic diversity across Apiaceous production areas remain critically limited, constraining the development of targeted disease surveillance frameworks and vector management strategies calibrated to regional pathosystem dynamics. This study conducted systematic field surveys across commercial Apiaceous crop production areas to determine CtRLV incidence and spatial distribution, employing sensitive molecular detection protocols to characterize virus presence across symptomatic and asymptomatic plant samples. Total nucleic acid extractions from leaf tissue samples were subjected to reverse transcription polymerase chain reaction using genus-specific and species-specific primer pairs targeting conserved and variable genomic regions of the CtRLV coat protein and replicase genes. Positive detections were confirmed through direct sequencing of amplified products, and complete or near-complete genome sequences of representative isolates were obtained through high-throughput sequencing approaches. Pairwise nucleotide identity analyses and multilocus phylogenetic reconstructions based on coat protein, movement protein, and RNA-dependent RNA polymerase gene sequences were performed using maximum likelihood and Bayesian inference frameworks to resolve phylogenetic relationships among CtRLV isolates recovered from geographically distinct production areas and to assess interspecific relationships with related poleroviruses infecting Apiaceous hosts.