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Updated: Jan 14, 2026

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Optimized library preparation, sequencing, and data analysis protocols for the generation of orbivirus consensus

Tillie J Dunham¹, Tyler J Sherman², Kirsten J Reed²

¹Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.

|January 13, 2026

Summary

Simplified whole genome sequencing (WGS) protocols for orbiviruses using next-generation sequencing (NGS) reduce time and cost. Optimized methods and the OrbiSeq pipeline enable high-quality viral genome sequencing for enhanced surveillance.

Keywords:

Library preparation Next-Generation sequencing (NGS)Nextflow OrbiSeq pipeline Orbivirus Reproducibility Sample preparation Segmented genome Viral genomics Whole genome sequencing (WGS)

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Area of Science:

Virology
Genomics
Bioinformatics

Background:

Orbiviruses are significant arboviruses with segmented double-stranded RNA genomes.
Traditional sequencing methods are time-consuming and costly.
Next-generation sequencing (NGS) offers potential for viral genetic diversity studies.

Purpose of the Study:

To simplify and optimize sample preparation, sequencing, and analysis for orbivirus whole genome sequencing (WGS).
To reduce the time and cost associated with orbivirus genome sequencing.
To develop a reproducible bioinformatics workflow for viral genome analysis.

Main Methods:

Optimized sample and library preparation protocols for Illumina and Nanopore sequencing platforms.
Development of OrbiSeq, a Nextflow workflow for orbivirus genome analysis.
Comparative analysis of optimized protocols against established methods.

Main Results:

Optimized protocols yielded high-quality whole genome sequences comparable to established methods.
Both Illumina and Nanopore platforms produced reliable orbivirus genome sequences.
The OrbiSeq pipeline efficiently generated consensus sequences for orbivirus genomes.

Conclusions:

Simplified WGS protocols enhance the feasibility of extensive orbivirus genomic surveillance.
The OrbiSeq workflow supports the analysis of both segmented and non-segmented viral genomes.
Optimized sequencing and analysis strategies provide deeper evolutionary insights into viruses.