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Ann Lab Med. 2016 May;36(3):255-8. doi: 10.3343/alm.2016.36.3.255.
Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens.
Seong MW1, Cho SI1, Park H1, Seo SH1, Lee SJ1, Kim EC1, Park SS2.
Author information
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.
KEYWORDS:
Genome sequencing; Influenza virus; Next-generation sequencing; Nosocomial outbreak; Pandemic H1N1 virus
PMID: 26915615 [PubMed - in process] Free full text
Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens.
Seong MW1, Cho SI1, Park H1, Seo SH1, Lee SJ1, Kim EC1, Park SS2.
Author information
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.
KEYWORDS:
Genome sequencing; Influenza virus; Next-generation sequencing; Nosocomial outbreak; Pandemic H1N1 virus
PMID: 26915615 [PubMed - in process] Free full text