Next-generation sequencing for virus detection: covering all the bases.
Virol J
; 13: 85, 2016 Jun 02.
Article
en 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.Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Virus ARN
/
Viroides
/
Genoma Viral
/
Análisis de Secuencia de ADN
/
Secuenciación de Nucleótidos de Alto Rendimiento
Tipo de estudio:
Diagnostic_studies
Idioma:
En
Revista:
Virol J
Asunto de la revista:
VIROLOGIA
Año:
2016
Tipo del documento:
Article
País de afiliación:
Sudáfrica