Next-generation sequencing for virus detection: covering all the bases

作者：Visser Marike; Bester Rachelle; Burger Johan T; Maree Hans J^*

来源：Virology Journal, 2016, 13(1): 85.

DOI：10.1186/s12985-016-0539-x

• CTV
• Closterovirus
• Genome coverage
• GLRaV-3
• Next-generation sequencing
• Sequencing depth
• Virus detection

Background: The use of next-generation sequencing has become an established method for virus detection. Efficient study design for accurate detection relies on the optimal amount of data representing a significant portion of a virus genome.
Findings: In this study, genome coverage at different sequencing depths was determined for a number of viruses, viroids, hosts and sequencing library types, using both read-mapping and de novo assembly-based approaches. The results highlighted the strength of ribo-depleted RNA and sRNA in obtaining saturated genome coverage with the least amount of data, while even though the poly(A)-selected RNA yielded virus-derived reads, it was insufficient to cover the complete genome of a non-polyadenylated virus. The ribo-depleted RNA data also outperformed the sRNA data in terms of the percentage of coverage that could be obtained particularly with the de novo assembled contigs.
Conclusion: Our results suggest the use of ribo-depleted RNA in a de novo assembly-based approach for the detection of single-stranded RNA viruses. Furthermore, we suggest that sequencing one million reads will provide sufficient genome coverage specifically for closterovirus detection.

• 出版日期2016-6-2