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

MSphere
Yong-Li XiaoJeffery K Taubenberger

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 avi...Continue Reading

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Citations

Sep 4, 2019·Annual Review of Animal Biosciences·Amir GhorbaniChang-Won Lee
Jun 28, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Adam McNeeElma Tchilian
Dec 29, 2020·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Wanitchaya KittikraisakPhonepadith Xangsayarath

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Datasets Mentioned

BETA
SRR7444548

Methods Mentioned

BETA
nucleic acid sequencing
PCR
cDNA library
nucleic acid extraction
RNA-Seq
Illumina sequencing

Software Mentioned

Venny
PdbViewer
GenScript
MUSCLE
FigTree
Bowtie2
Swiss
FastTree
SAMtools mpileup
Tophat2

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