Next-generation sequencing for virus detection: covering all the bases.
Virol J
; 13: 85, 2016 Jun 02.
Article
em En
| MEDLINE
| ID: mdl-27250973
ABSTRACT
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.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vírus de RNA
/
Viroides
/
Genoma Viral
/
Análise de Sequência de DNA
/
Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Diagnostic_studies
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article