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Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens

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...

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Autores principales: Seong, Moon-Woo, Cho, Sung Im, Park, Hyunwoong, Seo, Soo Hyun, Lee, Seung Jun, Kim, Eui-Chong, Park, Sung Sup
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Korean Society for Laboratory Medicine 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773267/
https://www.ncbi.nlm.nih.gov/pubmed/26915615
http://dx.doi.org/10.3343/alm.2016.36.3.255
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author Seong, Moon-Woo
Cho, Sung Im
Park, Hyunwoong
Seo, Soo Hyun
Lee, Seung Jun
Kim, Eui-Chong
Park, Sung Sup
author_facet Seong, Moon-Woo
Cho, Sung Im
Park, Hyunwoong
Seo, Soo Hyun
Lee, Seung Jun
Kim, Eui-Chong
Park, Sung Sup
author_sort Seong, Moon-Woo
collection PubMed
description 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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spelling pubmed-47732672016-05-01 Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens Seong, Moon-Woo Cho, Sung Im Park, Hyunwoong Seo, Soo Hyun Lee, Seung Jun Kim, Eui-Chong Park, Sung Sup Ann Lab Med Brief Communication 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. The Korean Society for Laboratory Medicine 2016-05 2016-02-23 /pmc/articles/PMC4773267/ /pubmed/26915615 http://dx.doi.org/10.3343/alm.2016.36.3.255 Text en © The Korean Society for Laboratory Medicine. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Brief Communication
Seong, Moon-Woo
Cho, Sung Im
Park, Hyunwoong
Seo, Soo Hyun
Lee, Seung Jun
Kim, Eui-Chong
Park, Sung Sup
Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title_full Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title_fullStr Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title_full_unstemmed Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title_short Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens
title_sort genotyping influenza virus by next-generation deep sequencing in clinical specimens
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773267/
https://www.ncbi.nlm.nih.gov/pubmed/26915615
http://dx.doi.org/10.3343/alm.2016.36.3.255
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