Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
Annals of Laboratory Medicine
;
: 255-258, 2016.
Article
Dans Anglais
| WPRIM
| ID: wpr-56700
ABSTRACT
Rapid and accurate identification of an influenza outbreak is essential for patient care and treatment. We describe a next-generation sequencing (NGS)-based, unbiased deep sequencing method in clinical specimens to investigate an influenza outbreak. Nasopharyngeal swabs from patients were collected for molecular epidemiological analysis. Total RNA was sequenced by using the NGS technology as paired-end 250 bp reads. Total of 7 to 12 million reads were obtained. After mapping to the human reference genome, we analyzed the 3-4% of reads that originated from a non-human source. A BLAST search of the contigs reconstructed de novo revealed high sequence similarity with that of the pandemic H1N1 virus. In the phylogenetic analysis, the HA gene of our samples clustered closely with that of A/Senegal/VR785/2010(H1N1), A/Wisconsin/11/2013(H1N1), and A/Korea/01/2009(H1N1), and the NA gene of our samples clustered closely with A/Wisconsin/11/2013(H1N1). This study suggests that NGS-based unbiased sequencing can be effectively applied to investigate molecular characteristics of nosocomial influenza outbreak by using clinical specimens such as nasopharyngeal swabs.
Texte intégral:
Disponible
Indice:
WPRIM (Pacifique occidental)
Sujet Principal:
Phylogenèse
/
Protéines virales
/
ARN viral
/
Partie nasale du pharynx
/
Analyse de séquence d'ARN
/
Techniques d'amplification d'acides nucléiques
/
Bases de données génétiques
/
Grippe humaine
/
Sous-type H1N1 du virus de la grippe A
/
Séquençage nucléotidique à haut débit
Type d'étude:
Étude pronostique
Limites du sujet:
Humains
langue:
Anglais
Texte intégral:
Annals of Laboratory Medicine
Année:
2016
Type:
Article
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