Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing

The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.

Automated summary

High-throughput sequencing (HTS) has been successfully applied for virus discovery in agricultural crops, providing insights into virus population structure and differentiation among virus variants contributing differently to disease etiology. This study developed a bioinformatic pipeline for CTV genotype detection, with a 50% genome coverage cut-off identified for non-target read mappings, validating it as a CTV genotyping assay.