(Q37448365)

English

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification

scientific article published on 05 October 2016

In more languages

default values for all languages

No label defined

No description defined

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification (English)

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

influenza A virus

object named as

Influenza A Virus

1 reference

based on heuristic

inferred from title

Robert Lambkin-Williams

object named as

Robert Lambkin-Williams

11

0 references

David E. Wentworth

4

object named as

David E Wentworth

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Rebecca A Halpin

5

object named as

Rebecca A Halpin

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Timothy B Stockwell

8

object named as

Timothy B Stockwell

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Suman Ranjan Das

9

object named as

Suman R Das

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

14

object named as

Katia Koelle

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Gavin J.D. Smith

3

object named as

Gavin J D Smith

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

author name string

Ashley Sobel Leonard

1

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Micah T McClain

2

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Xudong Lin

6

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Amy Ransier

7

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Anthony S Gilbert

10

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Geoffrey S Ginsburg

12

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Christopher W Woods

13

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

language of work or name

0 references

publication date

5 October 2016

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Journal of Virology

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

90

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

24

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

11247-11258

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Quantifying influenza virus diversity and transmission in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Influenza A Virus Protein PA-X Contributes to Viral Growth and Suppression of the Host Antiviral and Immune Responses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Mammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Improved detection of artifactual viral minority variants in high-throughput sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Within-host nucleotide diversity of virus populations: insights from next-generation sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Influenza A virus transmission bottlenecks are defined by infection route and recipient host.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Library preparation for highly accurate population sequencing of RNA viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Circulating avian influenza viruses closely related to the 1918 virus have pandemic potential.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Within-host whole-genome deep sequencing and diversity analysis of human respiratory syncytial virus infection reveals dynamics of genomic diversity in the absence and presence of immune pressure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

A host-based RT-PCR gene expression signature to identify acute respiratory viral infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Evolution of equine influenza virus in vaccinated horses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

An overlapping protein-coding region in influenza A virus segment 3 modulates the host response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Airborne transmission of influenza A/H5N1 virus between ferrets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Preexisting influenza-specific CD4+ T cells correlate with disease protection against influenza challenge in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

H3N2 influenza infection elicits more cross-reactive and less clonally expanded anti-hemagglutinin antibodies than influenza vaccination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Rhinovirus genome evolution during experimental human infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Intra- and interhost evolutionary dynamics of equine influenza virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Intrahost evolutionary dynamics of canine influenza virus in naive and partially immune dogs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

The Sequence Alignment/Map format and SAMtools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Fast and accurate short read alignment with Burrows-Wheeler transform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Homologous recombination is very rare or absent in human influenza A virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Statistical methods for detecting molecular adaptation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Ultra-deep sequencing for the analysis of viral populations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

23 August 2017

Mutations affecting the stability of the haemagglutinin molecule impair the immunogenicity of live attenuated H3N2 intranasal influenza vaccine candidates lacking NS1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

14 September 2017

The impact of key amino acid substitutions in the hemagglutinin of influenza A (H3N2) viruses on vaccine production and antibody response

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

14 September 2017

Efficacy of inactivated influenza A virus (H3N2) vaccines grown in mammalian cells or embryonated eggs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

26 June 2018

Egg- or cell culture-derived hemagglutinin mutations impair virus stability and antigen content of inactivated influenza vaccines.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

2 September 2018

Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

2 September 2018

Influenza A virus molecular virology techniques

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

2 September 2018

Single amino acid substitutions in the hemagglutinin of influenza A/Singapore/21/04 (H3N2) increase virus growth in embryonated chicken eggs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

2 September 2018

Molecular changes associated with adaptation of human influenza A virus in embryonated chicken eggs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5126380

2 September 2018

Two residues in the hemagglutinin of A/Fujian/411/02-like influenza viruses are responsible for antigenic drift from A/Panama/2007/99

1 reference

https://pubmed.ncbi.nlm.nih.gov/27707932

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1128/JVI.01657-16

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

release_arfygorkorg47docnfkvjasf5m

1 reference

https://api.fatcat.wiki/v0/release/arfygorkorg47docnfkvjasf5m

24 November 2022

based on heuristic

mapped directly with Wikidata item

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

20 August 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q37448365&oldid=1955842602"