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Parallel evolution of influenza across multiple spatiotemporal scales
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor
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Universal primer set for the full-length amplification of all influenza A viruses
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Refinement of the influenza virus hemagglutinin by simulated annealing
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Influenza Virus Resistance to Antiviral Therapy
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Influenza A Virus Transmission Bottlenecks Are Defined by Infection Route and Recipient Host
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Emerging oseltamivir resistance in seasonal and pandemic influenza A/H1N1
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EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1038/442981aopenalex-snapshot
A global initiative on sharing avian flu data
inferredcites →https://doi.org/10.1038/nature04239openalex-snapshot
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution
inferredcites →https://doi.org/10.1038/nature06945openalex-snapshot
The genomic and epidemiological dynamics of human influenza A virus
inferredcites →https://doi.org/10.1038/nature12344openalex-snapshot
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations
inferredcites →https://doi.org/10.1038/nature13087openalex-snapshot
A predictive fitness model for influenza
inferredcites →https://doi.org/10.1038/ng.280openalex-snapshot
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1038/ng.3479openalex-snapshot
Quantifying influenza virus diversity and transmission in humans
inferredcites →https://doi.org/10.1038/nm992openalex-snapshot
HIV evolution: CTL escape mutation and reversion after transmission
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrg2583openalex-snapshot
Evolutionary analysis of the dynamics of viral infectious disease
inferredcites →https://doi.org/10.1073/pnas.1409171111openalex-snapshot
Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013–2014 influenza season
inferredcites →https://doi.org/10.1073/pnas.1525578113openalex-snapshot
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
inferredcites →https://doi.org/10.1084/jem.20130212openalex-snapshot
Immune history shapes specificity of pandemic H1N1 influenza antibody responses
inferredcites →https://doi.org/10.1086/425004openalex-snapshot
Influenza Infections after Hematopoietic Stem Cell Transplantation: Risk Factors, Mortality, and the Effect of Antiviral Therapy
inferredcites →https://doi.org/10.1086/508777openalex-snapshot
Characterization of Multidrug-Resistant Influenza A/H3N2 Viruses Shed during 1 Year by an Immunocompromised Child
inferredcites →https://doi.org/10.1086/520243openalex-snapshot
Antigenic Drift of Influenza A (H3N2) Virus in a Persistently Infected Immunocompromised Host Is Similar to That Occurring in the Community
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/cid/cit725openalex-snapshot
The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts
inferredcites →https://doi.org/10.1093/cid/civ272openalex-snapshot
Clinical Outcomes Associated With Respiratory Virus Detection Before Allogeneic Hematopoietic Stem Cell Transplant
inferredcites →https://doi.org/10.1093/molbev/msr044openalex-snapshot
The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus
inferredcites →https://doi.org/10.1111/2041-210x.12628openalex-snapshot
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
inferredcites →https://doi.org/10.1126/science.1090727openalex-snapshot
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
inferredcites →https://doi.org/10.1126/science.1122469openalex-snapshot
An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations
inferredcites →https://doi.org/10.1126/science.1244730openalex-snapshot
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
inferredcites →https://doi.org/10.1128/jvi.00112-10openalex-snapshot
Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus
inferredcites →https://doi.org/10.1128/jvi.00667-16openalex-snapshot
Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
inferredcites →https://doi.org/10.1128/jvi.01657-16openalex-snapshot
Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification
inferredcites →https://doi.org/10.1128/jvi.02469-09openalex-snapshot
Intrahost Evolutionary Dynamics of Canine Influenza Virus in Naive and Partially Immune Dogs
inferredcites →https://doi.org/10.1128/jvi.02683-07openalex-snapshot
Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus
inferredcites →https://doi.org/10.1128/jvi.03248-15openalex-snapshot
Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans
inferredcites →https://doi.org/10.1128/jvi.65.5.2340-2350.1991openalex-snapshot
Antigenic and genetic variation in influenza A (H1N1) virus isolates recovered from a persistently infected immunodeficient child
inferredcites →https://doi.org/10.1128/jvi.80.4.1637-1644.2006openalex-snapshot
Human Immunodeficiency Virus Type 1envEvolves toward Ancestral States upon Transmission to a New Host
inferredcites →https://doi.org/10.1128/mbio.02464-14openalex-snapshot
Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135920openalex-snapshot
Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation
inferredcites →https://doi.org/10.1371/journal.ppat.1006194openalex-snapshot
Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/genetics.112.143396openalex-snapshot
Clonal Interference in the Evolution of Influenza
inferredcites →https://doi.org/10.7554/elife.03568openalex-snapshot
Predicting evolution from the shape of genealogical trees
inferredcites →https://doi.org/10.7554/elife.11282openalex-snapshot
Population genomics of intrapatient HIV-1 evolution
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients
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Mutant strains of SARS-CoV-2 are more prone to infect obese patient: a review
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The healthy Nordic diet for blood glucose control: a systematic review and meta-analysis of randomized controlled clinical trials
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Influenza and obesity: its odd relationship and the lessons for COVID-19 pandemic
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Mapping the Evolutionary Potential of RNA Viruses
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SARS-CoV-2-host dynamics: Increased risk of adverse outcomes of COVID-19 in obesity
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Genotype–phenotype landscapes for immune–pathogen coevolution
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Adaption and parallel evolution of human-isolated H5 avian influenza viruses
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Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses
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A decade of genome sequencing has revolutionized studies of experimental evolution
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Population Genetics in the Human Microbiome
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Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
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Within-Host Evolution of Human Influenza Virus
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Extreme Competence: Keystone Hosts of Infections
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Fundamental concepts of convergent (parallel) evolution in human-pathogenic viruses and their implications for global health
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A decade of RNA virus metagenomics is (not) enough
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Persistent SARS-CoV-2 infection: significance and implications
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Innovation in active and passive immunisation of people who are immunocompromised: a call to action
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The evolution of seasonal influenza viruses
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Every flu evolves in the same way
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How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin
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Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae
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Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination
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Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks
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Individual immune selection pressure has limited impact on seasonal influenza virus evolution
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Influenza evolution with little host selection
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Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination
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Co-evolution of immunity and seasonal influenza viruses
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The consequences of SARS-CoV-2 within-host persistence
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Reconciling disparate estimates of viral genetic diversity during human influenza infections
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The potential impacts of human genetics on virus emergence
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Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale
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A heuristic neural network model in the research of properties of evolutionary trajectories
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Slowing Influenza Virus Evolution: A Role for Multiple Synergistic Antiviral Specificities in Vaccination Strategies
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Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters
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Virus Evolution in Prolonged Infections of Immunocompromised Individuals
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Comparative Population Genetics in the Human Gut Microbiome
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Estimating linkage disequilibrium and selection from allele frequency trajectories
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Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient
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Within-Host Rhinovirus Evolution in Upper and Lower Respiratory Tract Highlights Capsid Variability and Mutation-Independent Compartmentalization
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Inferring Epistasis from Genetic Time-series Data
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Linking influenza virus evolution within and between human hosts
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Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants
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Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status
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Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons
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Within-host genetic diversity of SARS-CoV-2 across animal species
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Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies
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Antigenic escape is accelerated by the presence of immunocompromised hosts
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A general approach to identify low-frequency variants within influenza samples collected during routine surveillance
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The Ecology and Evolution of Influenza Viruses
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2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic?
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Urbanization and humidity shape the intensity of influenza epidemics in U.S. cities
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Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
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Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo
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Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks
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Functional symmetry and reproducibility of the evolutionary process
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Convergent evolution as an indicator for selection during acute HIV-1 infection
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Two Pandemics Coalition: Covid-19 and Obesity
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Two Pandemics Coalition: COVID-19 and Obesity
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Impact of Obesity on Influenza A Virus Pathogenesis, Immune Response, and Evolution
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A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing
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Factors Associated with Increased Morbidity and Mortality of Obese and Overweight COVID-19 Patients
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Evolutionary Divergent Suppressor Mutations in Conformational Diseases
inferred← citeshttps://doi.org/10.3390/idr14030035openalex-snapshot
System Complexity in Influenza Infection and Vaccination: Effects upon Excess Winter Mortality
inferred← citeshttps://doi.org/10.3390/microorganisms8010133openalex-snapshot
Inter-Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes
inferred← citeshttps://doi.org/10.3390/v10080407openalex-snapshot
Mutation and Epistasis in Influenza Virus Evolution
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The Molecular Evolution of Type 2 Vaccine-Derived Polioviruses in Individuals with Primary Immunodeficiency Diseases
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Obesidade e infecção por SARS-CoV-2: papel da metainflamação
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How flu changes within the human body may hint at future global trends
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Within-host adaptive evolution is limited by genetic drift in experimental human influenza A virus infections
inferred← citeshttps://doi.org/10.64898/2026.04.10.717627openalex-snapshot
Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence
inferred← citeshttps://doi.org/10.7554/elife.32303openalex-snapshot
Extreme heterogeneity of influenza virus infection in single cells
inferred← citeshttps://doi.org/10.7554/elife.35962openalex-snapshot
Stochastic processes constrain the within and between host evolution of influenza virus
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A large effective population size for established within-host influenza virus infection
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Asynchrony between virus diversity and antibody selection limits influenza virus evolution
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Dynamically linking influenza virus infection kinetics, lung injury, inflammation, and disease severity
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Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children
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