Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions.
Virus Genes
; 56(3): 288-297, 2020 Jun.
Article
em En
| MEDLINE
| ID: mdl-32193781
ABSTRACT
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) offers advantages in speed and length of detection over second-generation sequencing (SGS). Here, we presented the end-to-end workflows for both Oxford Nanopore MinION and Pacbio Sequel on a viral disease emergency event, along with Ion Torrent PGM as a reference. A specific pipeline for comparative analysis on viral genomes recovered by each platform was assembled, given the high errors of base-calling for TGS platforms. All the three platforms successfully identified and recovered at least 85% Norovirus GII genomes. Oxford Nanopore MinION spent the least sample-to-answer turnaround time with relatively low but enough accuracy for taxonomy classification. Pacbio Sequel recovered the most accurate viral genome, while spending the longest time. Overall, Nanopore metagenomics can rapidly characterize viruses, and Pacbio Sequel can accurately recover viruses. This study provides a framework for designing the appropriate experiments that are likely to lead to accurate and rapid virus emergency response.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vírus
/
Viroses
/
Saúde Pública
/
Emergências
/
Sequenciamento de Nucleotídeos em Larga Escala
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Virus Genes
Assunto da revista:
BIOLOGIA MOLECULAR
/
VIROLOGIA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
China