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Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing.

Rachelle Bester1, Glynnis Cook2, Hans J Maree1,3

  • 1Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.

Viruses
|January 27, 2021
PubMed
Summary
This summary is machine-generated.

High-throughput sequencing (HTS) offers comprehensive plant virus detection, including mixed infections. This study validates HTS for accurate citrus tristeza virus (CTV) genotyping, aiding disease management.

Keywords:
CTVHTSnext-generation sequencingvariants

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Area of Science:

  • Plant Pathology
  • Virology
  • Bioinformatics

Background:

  • High-throughput sequencing (HTS) is crucial for virus discovery and understanding disease causes in crops.
  • HTS provides a complete viral profile, revealing mixed infections and informing population dynamics.

Purpose of the Study:

  • To evaluate high-throughput sequencing (HTS) for citrus tristeza virus (CTV) genotype detection.
  • To develop and validate a bioinformatics pipeline for accurate CTV genotyping.

Main Methods:

  • Constructed a bioinformatics pipeline for CTV genotype detection.
  • Evaluated the pipeline using simulated and real datasets to distinguish true genotype coverage from false positives.
  • Determined a 50% genome coverage cut-off for non-target read mappings.

Main Results:

  • The bioinformatics pipeline successfully discriminated between true and false positive read mappings for CTV.
  • A 50% genome coverage threshold was identified as a reliable parameter for non-target reads.
  • HTS, coupled with the pipeline, proved effective for CTV genotyping.

Conclusions:

  • HTS is a powerful tool for comprehensive plant virus analysis, including mixed infections.
  • The developed bioinformatics pipeline and HTS method offer a validated assay for CTV genotyping.
  • This approach enhances our ability to study virus ecology, evolution, and disease etiology.