ArticleAnnals of laboratory medicine2016
Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens.
Article in Annals of laboratory medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The peculiar characteristics and advancement in diagnostic methodologies of influenza A virus.Frontiers in microbiology · 2024Review
- From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.Vaccines · 2022Article
- Influenza A (H1N1): outbreak management in a dialysis unit and clinical outcomes of infection in chronic hemodialysis patients.Jornal brasileiro de nefrologia · 2020Article
- Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material.Ecology and evolution · 2019Article
- Progress and Current Status of Influenza Researches in China.Journal of translational internal medicine · 2019Article
- Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak.The Journal of infectious diseases · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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