Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift

ABSTRACT Influenza A virus (IAV) infections are a major public health concern, including annual epidemics, epizootic outbreaks, and pandemics. A significant IAV epizootic outbreak was the H7N9 avian influenza A outbreak in China, which was first detected in 2013 and which has spread over 5 waves fro...

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Autores principales:	Yong-Li Xiao, Lili Ren, Xi Zhang, Li Qi, John C. Kash, Yan Xiao, Fan Wu, Jianwei Wang, Jeffery K. Taubenberger
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	DNA sequencing H7N9 avian viruses Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1f706eab79644aba8e580fa9481e1a2f
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spelling	oai:doaj.org-article:1f706eab79644aba8e580fa9481e1a2f2021-11-15T15:22:26ZDeep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift10.1128/mSphereDirect.00462-182379-5042https://doaj.org/article/1f706eab79644aba8e580fa9481e1a2f2018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphereDirect.00462-18https://doaj.org/toc/2379-5042ABSTRACT Influenza A virus (IAV) infections are a major public health concern, including annual epidemics, epizootic outbreaks, and pandemics. A significant IAV epizootic outbreak was the H7N9 avian influenza A outbreak in China, which was first detected in 2013 and which has spread over 5 waves from 2013 to 2017, causing human infections in many different Chinese provinces. Here, RNA from primary clinical throat swab samples from 20 H7N9-infected local patients with different clinical outcomes, who were admitted and treated at one hospital in Shanghai, China, from April 2013 to April 2015, was analyzed. Whole-transcriptome amplification, with positive enrichment of IAV RNA, was performed, all 20 samples were subjected to deep sequencing, and data from 16 samples were analyzed in detail. Many single-nucleotide polymorphisms, including ones not previously reported, and many nonsynonymous changes that could affect hemagglutinin head and stalk antibody binding epitopes were observed. Minor populations representing viral quasispecies, including nonsynonymous hemagglutinin changes shared by antigenically variant H7N9 clades identified in the most recent wave of H7N9 infections in 2016 to 2017, were also identified. IMPORTANCE H7N9 subtype avian influenza viruses caused infections in over 1,400 humans from 2013 to 2017 and resulted in almost 600 deaths. It is important to understand how avian influenza viruses infect and cause disease in humans and to assess their potential for efficient person-to-person transmission. In this study, we used deep sequencing of primary clinical material to assess the evolution and potential for human adaptation of H7N9 influenza viruses.Yong-Li XiaoLili RenXi ZhangLi QiJohn C. KashYan XiaoFan WuJianwei WangJeffery K. TaubenbergerAmerican Society for MicrobiologyarticleDNA sequencingH7N9avian virusesMicrobiologyQR1-502ENmSphere, Vol 3, Iss 5 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA sequencing H7N9 avian viruses Microbiology QR1-502
spellingShingle	DNA sequencing H7N9 avian viruses Microbiology QR1-502 Yong-Li Xiao Lili Ren Xi Zhang Li Qi John C. Kash Yan Xiao Fan Wu Jianwei Wang Jeffery K. Taubenberger Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
description	ABSTRACT Influenza A virus (IAV) infections are a major public health concern, including annual epidemics, epizootic outbreaks, and pandemics. A significant IAV epizootic outbreak was the H7N9 avian influenza A outbreak in China, which was first detected in 2013 and which has spread over 5 waves from 2013 to 2017, causing human infections in many different Chinese provinces. Here, RNA from primary clinical throat swab samples from 20 H7N9-infected local patients with different clinical outcomes, who were admitted and treated at one hospital in Shanghai, China, from April 2013 to April 2015, was analyzed. Whole-transcriptome amplification, with positive enrichment of IAV RNA, was performed, all 20 samples were subjected to deep sequencing, and data from 16 samples were analyzed in detail. Many single-nucleotide polymorphisms, including ones not previously reported, and many nonsynonymous changes that could affect hemagglutinin head and stalk antibody binding epitopes were observed. Minor populations representing viral quasispecies, including nonsynonymous hemagglutinin changes shared by antigenically variant H7N9 clades identified in the most recent wave of H7N9 infections in 2016 to 2017, were also identified. IMPORTANCE H7N9 subtype avian influenza viruses caused infections in over 1,400 humans from 2013 to 2017 and resulted in almost 600 deaths. It is important to understand how avian influenza viruses infect and cause disease in humans and to assess their potential for efficient person-to-person transmission. In this study, we used deep sequencing of primary clinical material to assess the evolution and potential for human adaptation of H7N9 influenza viruses.
format	article
author	Yong-Li Xiao Lili Ren Xi Zhang Li Qi John C. Kash Yan Xiao Fan Wu Jianwei Wang Jeffery K. Taubenberger
author_facet	Yong-Li Xiao Lili Ren Xi Zhang Li Qi John C. Kash Yan Xiao Fan Wu Jianwei Wang Jeffery K. Taubenberger
author_sort	Yong-Li Xiao
title	Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
title_short	Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
title_full	Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
title_fullStr	Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
title_full_unstemmed	Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift
title_sort	deep sequencing of h7n9 influenza a viruses from 16 infected patients from 2013 to 2015 in shanghai reveals genetic diversity and antigenic drift
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/1f706eab79644aba8e580fa9481e1a2f
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Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift

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