skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Influenza-Omics and the Host Response: Recent Advances and Future Prospects

Journal Article · · Pathogens
 [1]; ORCiD logo [2]
  1. Battelle Memoria Institute, Aberdeen, MD (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Influenza A viruses (IAV) continually evolve and have the capacity to cause global pandemics. Because IAV represents an ongoing threat, identifying novel therapies and host innate immune factors that contribute to IAV pathogenesis is of considerable interest. This review summarizes the relevant literature as it relates to global host responses to influenza infection at both the proteome and transcriptome level. Here, the various –omics infection systems that include but are not limited to ferrets, mice, pigs and even controlled infection of humans are reviewed. Discussion focuses on recent advances, remaining challenges, and knowledge gaps as it relates to influenza-omics infection outcomes.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1378027
Report Number(s):
PNNL-SA-126286; PATHCD; 453060036
Journal Information:
Pathogens, Vol. 6, Issue 2; ISSN 2076-0817
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 11 works
Citation information provided by
Web of Science

References (67)

Systems-Level Comparison of Host-Responses Elicited by Avian H5N1 and Seasonal H1N1 Influenza Viruses in Primary Human Macrophages journal December 2009
Review of Influenza A Virus in Swine Worldwide: A Call for Increased Surveillance and Research journal April 2013
A Host Transcriptional Signature for Presymptomatic Detection of Infection in Humans Exposed to Influenza H1N1 or H3N2 journal January 2013
Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis journal April 2015
Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross journal February 2013
A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections journal January 2011
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor journal May 2007
Influenza A Virus Challenge Models in Cynomolgus Macaques Using the Authentic Inhaled Aerosol and Intra-Nasal Routes of Infection journal June 2016
H7N9 and Other Pathogenic Avian Influenza Viruses Elicit a Three-Pronged Transcriptomic Signature That Is Reminiscent of 1918 Influenza Virus and Is Associated with Lethal Outcome in Mice journal July 2014
Transcriptomic Characterization of the Novel Avian-Origin Influenza A (H7N9) Virus: Specific Host Response and Responses Intermediate between Avian (H5N1 and H7N7) and Human (H3N2) Viruses and Implications for Treatment Options journal December 2013
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice journal January 2013
NCBI GEO: mining tens of millions of expression profiles--database and tools update journal January 2007
Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems journal January 2011
Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort Study journal June 2015
Animal models for influenza virus transmission studies: a historical perspective journal August 2015
2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models journal January 2012
Analysis of cellular proteome alterations in porcine alveolar macrophage cells infected with 2009 (H1N1) and classical swine H1N1 influenza viruses journal March 2012
Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses journal October 2013
Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers journal January 2012
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism journal February 2016
Gene expression changes in the host response between resistant and susceptible inbred mouse strains after influenza A infection journal April 2010
The 1918 Influenza Virus PB2 Protein Enhances Virulence through the Disruption of Inflammatory and Wnt-Mediated Signaling in Mice journal December 2015
Host Gene Expression Signatures Discriminate between Ferrets Infected with Genetically Similar H1N1 Strains journal July 2012
Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus journal April 2013
Transcription analysis on response of swine lung to H1N1 swine influenza virus journal August 2011
The landscape of viral proteomics and its potential to impact human health journal May 2016
Systems biology and systems genetics—novel innovative approaches to study host–pathogen interactions during influenza infection journal June 2014
Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages journal May 2011
Causal analysis approaches in Ingenuity Pathway Analysis journal December 2013
Influenza Research Database: An integrated bioinformatics resource for influenza virus research journal September 2016
Virus–host interactions: from systems biology to translational research journal August 2009
iTRAQ-based quantitative proteomics reveals important host factors involved in the high pathogenicity of the H5N1 avian influenza virus in mice journal December 2016
A comprehensive collection of systems biology data characterizing the host response to viral infection journal October 2014
Identification of Host Genes Linked with the Survivability of Chickens Infected with Recombinant Viruses Possessing H5N1 Surface Antigens from a Highly Pathogenic Avian Influenza Virus journal December 2011
Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response journal July 2011
Proteomics Analysis of Differential Expression of Chicken Brain Tissue Proteins in Response to the Neurovirulent H5N1 Avian Influenza Virus Infection journal August 2010
Ion-Current-Based Temporal Proteomic Profiling of Influenza-A-Virus-Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier journal January 2016
RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection journal September 2015
De-Novo Transcriptome Sequencing of a Normalized cDNA Pool from Influenza Infected Ferrets journal May 2012
Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection journal November 2016
Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes journal October 2009
Immune Response to Seasonal Influenza A Virus Infection: A Proteomic Approach journal August 2012
Dynamic changes in host gene expression associated with H5N8 avian influenza virus infection in mice journal November 2015
A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance journal August 2015
Genome Wide Host Gene Expression Analysis in Chicken Lungs Infected with Avian Influenza Viruses journal April 2016
Comparative proteome analysis of tracheal tissues in response to infectious bronchitis coronavirus, Newcastle disease virus, and avian influenza virus H9 subtype virus infection journal April 2014
Transcriptomic and Epigenetic Profiling of the Lung of Influenza-Infected Pigs: A Comparison of Different Birth Weight and Susceptibility Groups journal September 2015
Proteomic analysis of the lungs of mice infected with different pathotypes of H5N1 avian influenza viruses journal June 2012
Ferrets exclusively synthesize Neu5Ac and express naturally humanized influenza A virus receptors journal December 2014
The use of nonhuman primates in research on seasonal, pandemic and avian influenza, 1893–2014 journal May 2015
Informatics resources for the Collaborative Cross and related mouse populations journal July 2015
Respiratory Mucosal Proteome Quantification in Human Influenza Infections journal April 2016
Antiviral innate immunity through the lens of systems biology journal June 2016
Anomaly Detection in Host Signaling Pathways for the Early Prognosis of Acute Infection journal August 2016
Will omics help to cure the flu? journal May 2014
Post-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces journal June 2020
Identification of Host Genes Linked with the Survivability of Chickens Infected with Recombinant Viruses Possessing H5N1 Surface Antigens from a Highly Pathogenic Avian Influenza Virus journal April 2012
Quantitative Proteomic Analyses of Influenza Virus-Infected Cultured Human Lung Cells journal August 2010
Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection journal May 2010
Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics journal September 2006
Epidemiology, Evolution, and Recent Outbreaks of Avian Influenza Virus in China journal June 2015
Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections journal September 2010
Increased Viral Loads and Exacerbated Innate Host Responses in Aged Macaques Infected with the 2009 Pandemic H1N1 Influenza A Virus journal August 2012
Sequencing, Annotation, and Characterization of the Influenza Ferret Infectome journal December 2012
A(H7N9) Virus Results in Early Induction of Proinflammatory Cytokine Responses in both Human Lung Epithelial and Endothelial Cells and Shows Increased Human Adaptation Compared with Avian H5N1 Virus journal February 2015
2009 Pandemic H1N1 Influenza Virus Causes Disease and Upregulation of Genes Related to Inflammatory and Immune Responses, Cell Death, and Lipid Metabolism in Pigs journal September 2011
Into the Eye of the Cytokine Storm journal March 2012

Cited By (3)

Host and viral determinants of influenza A virus species specificity journal November 2018
Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations journal August 2019
Influenza Virus Infection, Interferon Response, Viral Counter-Response, and Apoptosis journal August 2017