Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens.
10.3343/alm.2016.36.3.255
- Author:
Moon Woo SEONG
1
;
Sung Im CHO
;
Hyunwoong PARK
;
Soo Hyun SEO
;
Seung Jun LEE
;
Eui Chong KIM
;
Sung Sup PARK
Author Information
1. Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea. sparkle@snu.ac.kr
- Publication Type:Brief Communication ; Research Support, Non-U.S. Gov't
- Keywords:
Pandemic H1N1 virus;
Influenza virus;
Nosocomial outbreak;
Next-generation sequencing;
Genome sequencing
- MeSH:
Databases, Genetic;
Genotype;
High-Throughput Nucleotide Sequencing;
Humans;
Influenza A Virus, H1N1 Subtype/classification/*genetics/isolation & purification;
Influenza, Human/diagnosis/*virology;
Nasopharynx/*virology;
Nucleic Acid Amplification Techniques;
Phylogeny;
RNA, Viral/analysis/metabolism;
Sequence Analysis, RNA;
Viral Proteins/genetics
- From:Annals of Laboratory Medicine
2016;36(3):255-258
- CountryRepublic of Korea
- Language:English
-
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.
