High-throughput sequencing identification and multiplex RT-PCR detection of pepper viruses

Peppers are susceptible to a variety of virus infections. Early and accurate detection of virus species is the prerequisite for the virus disease prevention and management to reduce yield and quality losses. This study utilized small RNA sequencing to investigate the viruses in Guizhou peppers. Through extensive bioinformatics analysis, we identified ten virus species infecting Guizhou peppers and obtained the sequences of the conserved protein encoded by these viruses. Our phylogenetic analyses clarified the taxonomic status of the obtained viral isolate. A rapid and cost-effective multiplex PCR method for simultaneous virus detection was developed. By testing the novel developed method using field samples, we found that CMV, PCV1 and BBWV2 were the three most common viruses. This research offers a comprehensive list of viruses affecting peppers in Guizhou and presents an efficient detection method, facilitating our understanding and practical management of pepper virus infections.