# Comprehensive Virome Analysis of Commercial Lilies in South Korea by RT-PCR, High-Throughput Sequencing, and Phylogenetic Analyses

## TL;DR

This study analyzed viruses in lilies from South Korea and found high infection rates, multiple virus co-infections, and identified new viral variants.

## Contribution

The study provides the first comprehensive virome analysis of commercial lilies in South Korea using RT-PCR, HTS, and phylogenetic methods.

## Key findings

- 87% of lily samples were infected, with lily mottle virus and Plantago asiatica mosaic virus being the most prevalent.
- Mixed infections were twice as common as single infections and caused more severe symptoms, especially in triple-virus combinations.
- Phylogenetic analysis showed close relationships between Korean and Chinese isolates and host-related clustering in Plantago asiatica mosaic virus.

## Abstract

Viral diseases pose a significant threat to lily (Lilium spp.) cultivation; however, large-scale assessments of virus prevalence and diversity in South Korea are limited. This study combined RT-PCR surveys, high-throughput sequencing (HTS), and analyses of 48 lily hybrid transcriptomes to characterize the lily virome. RT-PCR screening of 100 samples from 13 regions showed that 87% were infected, primarily with lily mottle virus (LMoV, 65%), Plantago asiatica mosaic virus (PlAMV, 34%), cucumber mosaic virus (CMV, 34%), and lily symptomless virus (LSV, 25%). Mixed infections were approximately twice as frequent as single infections and were associated with greater symptom severity, particularly in triple-virus combinations. High-throughput sequencing expanded detection to six viruses, including milk vetch dwarf virus (MDV) and lily virus B (LVB), the latter confirmed as a variant of strawberry latent ringspot virus (SLRSV). Near-complete genomes of several viruses were assembled and validated through RT-PCR. Transcriptome mining identified eight virus species across 26 cultivars; PlAMV was the most common, and viral loads varied significantly among hybrids. Phylogenetic analyses revealed close relationships between Korean and Chinese isolates and host-related clustering in PlAMV. These findings highlight the complexity of lily viromes in South Korea and provide essential resources for diagnostics, disease management, and biosecurity.