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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.
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.
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.
