Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.
Virol J
; 17(1): 24, 2020 02 13.
Article
em En
| MEDLINE
| ID: mdl-32054488
ABSTRACT
BACKGROUND:
Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome.METHODS:
We evaluated a method designed to address this challenge, using the 'Primal Scheme' multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis.RESULTS:
The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested ([Formula see text] = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17-99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69-99.92%). However, coding-region coverage was reduced at this depth ([Formula see text] = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin.CONCLUSION:
The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma Viral
/
Análise de Sequência de DNA
/
Vírus da Dengue
/
Nanoporos
/
Reação em Cadeia da Polimerase Multiplex
Tipo de estudo:
Evaluation_studies
Limite:
Humans
País/Região como assunto:
Asia
Idioma:
En
Revista:
Virol J
Assunto da revista:
VIROLOGIA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Reino Unido