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Within-Host Evolution of Human Influenza Virus

https://doi.org/10.1016/j.tim.2018.02.007

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inferredcites →https://doi.org/10.1128/jvi.00667-16openalex-snapshot

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Viral Mutation Rates

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inferredcites →https://doi.org/10.1128/jvi.01162-15openalex-snapshot

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inferredcites →https://doi.org/10.1128/jvi.01623-05openalex-snapshot

Kinetics of Influenza A Virus Infection in Humans

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

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The Influenza Virus Resource at the National Center for Biotechnology Information

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Intrahost Evolutionary Dynamics of Canine Influenza Virus in Naive and Partially Immune Dogs

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Evolution of Equine Influenza Virus in Vaccinated Horses

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Antigenic and genetic variation in influenza A (H1N1) virus isolates recovered from a persistently infected immunodeficient child

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Neuraminidase Is Important for the Initiation of Influenza Virus Infection in Human Airway Epithelium

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Human Immunodeficiency Virus Type 1envEvolves toward Ancestral States upon Transmission to a New Host

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Comparison of the Mutation Rates of Human Influenza A and B Viruses

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Constraints, Drivers, and Implications of Influenza A Virus Reassortment

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Coordinated Evolution of Influenza A Surface Proteins

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Continuous Influenza Virus Production in Cell Culture Shows a Periodic Accumulation of Defective Interfering Particles

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Error baseline rates of five sample preparation methods used to characterize RNA virus populations

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Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature

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Quasispecies Theory and the Behavior of RNA Viruses

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Evolution of an Eurasian Avian-like Influenza Virus in Naïve and Vaccinated Pigs

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Influenza Virus Reassortment Occurs with High Frequency in the Absence of Segment Mismatch

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Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses

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The effective rate of influenza reassortment is limited during human infection

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Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients

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Parallel evolution of influenza across multiple spatiotemporal scales

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Stochastic processes constrain the within and between host evolution of influenza virus

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The consequences of SARS-CoV-2 within-host persistence

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Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models

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Evolutionary Parasitology

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Preface

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List of common acronyms

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Glossary

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Parasites and their significance

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0002openalex-snapshot

The study of evolutionary parasitology

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The diversity and natural history of parasites

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0004openalex-snapshot

The natural history of defences

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0005openalex-snapshot

Ecological immunology

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0006openalex-snapshot

Parasites, immunity, and sexual selection

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0007openalex-snapshot

Specificity

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0008openalex-snapshot

Parasite immune evasion and manipulation of host phenotype

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0009openalex-snapshot

Transmission, infection, and pathogenesis

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0010openalex-snapshot

Host–parasite genetics

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0011openalex-snapshot

Between-host dynamics (Epidemiology)

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0012openalex-snapshot

Within-host dynamics and evolution

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0013openalex-snapshot

Virulence evolution

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0014openalex-snapshot

Host–parasite co-evolution

inferred← citeshttps://doi.org/10.1093/oso/9780198832140.003.0015openalex-snapshot

Ecology

inferred← citeshttps://doi.org/10.1093/ve/veaa010openalex-snapshot

Linking influenza virus evolution within and between human hosts

inferred← citeshttps://doi.org/10.1093/ve/veaa088openalex-snapshot

Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants

inferred← citeshttps://doi.org/10.1093/ve/veac052openalex-snapshot

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

inferred← citeshttps://doi.org/10.1093/ve/veae034openalex-snapshot

Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status

inferred← citeshttps://doi.org/10.1093/ve/veae042openalex-snapshot

Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks

inferred← citeshttps://doi.org/10.1093/ve/veaf101openalex-snapshot

Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection

inferred← citeshttps://doi.org/10.1093/ve/veag027openalex-snapshot

Linkage-aware inference of fitness from short-read time-series genomic data

inferred← citeshttps://doi.org/10.1097/inf.0000000000005140openalex-snapshot

Respiratory Syncytial Virus Genotype ON1 Within-host Populations in Hospitalized Children: Deletion of the 72-Nucleotide Duplication in the G Gene

inferred← citeshttps://doi.org/10.1099/jgv.0.001584openalex-snapshot

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

inferred← citeshttps://doi.org/10.1101/2020.02.20.959015openalex-snapshot

Influenza A viruses serially passaged in different MDCK cell lines exhibit limited sequence variation across their genomes, with the exception of the hemagglutinin gene

inferred← citeshttps://doi.org/10.1101/2020.04.03.023135openalex-snapshot

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

inferred← citeshttps://doi.org/10.1101/2020.04.20.051011openalex-snapshot

Limited SARS-CoV-2 diversity within hosts and following passage in cell culture

inferred← citeshttps://doi.org/10.1101/2020.06.26.173203openalex-snapshot

Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2

inferred← citeshttps://doi.org/10.1101/2021.03.20.436248openalex-snapshot

Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

inferred← citeshttps://doi.org/10.1101/2023.08.18.23293746openalex-snapshot

Emergence of neutralizing antibodies associates with clearance of SARS-CoV-2 during HIV-mediated immunosuppression

inferred← citeshttps://doi.org/10.1101/2025.04.28.650738openalex-snapshot

Low level of viral intra-host diversity is associated with severe SFTS disease

inferred← citeshttps://doi.org/10.1101/cshperspect.a038489openalex-snapshot

The Ecology and Evolution of Influenza Viruses

inferred← citeshttps://doi.org/10.1111/cmi.12989openalex-snapshot

The Class IV human deacetylase, HDAC11, exhibits anti‐influenza A virus properties via its involvement in host innate antiviral response

inferred← citeshttps://doi.org/10.1111/jeb.13890openalex-snapshot

Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors

inferred← citeshttps://doi.org/10.1126/scisignal.adg7867openalex-snapshot

Miz1 represses type I interferon production and limits viral clearance during influenza A virus infection

inferred← citeshttps://doi.org/10.1128/jvi.01403-22openalex-snapshot

Detection of Airborne Influenza A and SARS-CoV-2 Virus Shedding following Ocular Inoculation of Ferrets

inferred← citeshttps://doi.org/10.1128/jvi.01710-19openalex-snapshot

Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts

inferred← citeshttps://doi.org/10.1128/jvi.01969-19openalex-snapshot

Silent Infection of B and CD8 + T Lymphocytes by Influenza A Virus in Children with Tonsillar Hypertrophy

inferred← citeshttps://doi.org/10.1128/mbio.00887-23openalex-snapshot

Efficacy of oseltamivir treatment in influenza virus-infected obese mice

inferred← citeshttps://doi.org/10.1128/mbio.02030-21openalex-snapshot

Structural Dynamics and Molecular Evolution of the SARS-CoV-2 Spike Protein

inferred← citeshttps://doi.org/10.1128/mmbr.00242-24openalex-snapshot

Coinfection by multiple Trypanosoma cruzi clones: a new perspective on host-parasite relationship with consequences for pathogenesis and management of Chagas disease

inferred← citeshttps://doi.org/10.1128/msphere.01043-20openalex-snapshot

Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza

inferred← citeshttps://doi.org/10.1128/spectrum.00257-21openalex-snapshot

Clinically Relevant Influenza Virus Evolution Reconstituted in a Human Lung Airway-on-a-Chip

inferred← citeshttps://doi.org/10.1128/spectrum.01166-23openalex-snapshot

Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types

inferred← citeshttps://doi.org/10.1146/annurev-immunol-072621-084422openalex-snapshot

Evolutionary Landscapes of Host-Virus Arms Races

inferred← citeshttps://doi.org/10.1371/journal.ppat.1009499openalex-snapshot

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

inferred← citeshttps://doi.org/10.1371/journal.ppat.1009811openalex-snapshot

From one to many: The within-host rise of viral variants

inferred← citeshttps://doi.org/10.1371/journal.ppat.1013294openalex-snapshot

Complex interactions in the life cycle of a simple parasite shape the evolution of virulence

inferred← citeshttps://doi.org/10.14271/dms-21453-deopenalex-snapshot

Impfungen – Aspekte aus Steiners Werk

inferred← citeshttps://doi.org/10.15167/2421-4248/jpmh2021.62.2s1openalex-snapshot

Journal of Preventive Medicine and Hygiene, Vol. 62 No. 2s1 (2021): Health Technology Assessment (HTA) dell’introduzione della vaccinazione antinfluenzale per la popolazione giovanile italiana con il vaccino Fluenz Tetra®

inferred← citeshttps://doi.org/10.1534/genetics.118.301510openalex-snapshot

Effects of Transmission Bottlenecks on the Diversity of Influenza A Virus

inferred← citeshttps://doi.org/10.17760/d20383671openalex-snapshot

Characterization of the germline mtDNA bottleneck using third generation sequencing and computational modeling

inferred← citeshttps://doi.org/10.21203/rs.3.rs-144416/v1openalex-snapshot

Intra-host dynamic variations in SARS-CoV-2

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v3openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v4openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v5openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v6openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21608/mid.2023.204080.1501openalex-snapshot

Two linked clinical cases of avian influenza in Cambodia: what threat to public health in southeast Asia does this pose?

inferred← citeshttps://doi.org/10.31219/osf.io/bdkg8openalex-snapshot

Protective Immunity against COVID-19

inferred← citeshttps://doi.org/10.3389/fcimb.2020.575613openalex-snapshot

Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities

inferred← citeshttps://doi.org/10.3389/fgene.2022.859508openalex-snapshot

An Evolutionary Insight Into the Heterogeneous Severity Pattern of the SARS-CoV-2 Infection

inferred← citeshttps://doi.org/10.3389/fimmu.2019.02806openalex-snapshot

BCG-Induced Cross-Protection and Development of Trained Immunity: Implication for Vaccine Design

inferred← citeshttps://doi.org/10.3389/fmed.2021.585358openalex-snapshot

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

inferred← citeshttps://doi.org/10.3389/fmicb.2018.02596openalex-snapshot

Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing

inferred← citeshttps://doi.org/10.3390/bios13080822openalex-snapshot

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

inferred← citeshttps://doi.org/10.3390/jcm8111974openalex-snapshot

Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study

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/v10110627openalex-snapshot

Causes and Consequences of Spatial Within-Host Viral Spread

inferred← citeshttps://doi.org/10.3390/v11080754openalex-snapshot

Cyprinid herpesvirus 3 Evolves In Vitro through an Assemblage of Haplotypes that Alternatively Become Dominant or Under-Represented

inferred← citeshttps://doi.org/10.3390/v12010087openalex-snapshot

Caspase-Mediated Cleavage of Human Cortactin during Influenza A Virus Infection Occurs in Its Actin-Binding Domains and Is Associated with Released Virus Titres

inferred← citeshttps://doi.org/10.3390/v12030319openalex-snapshot

A Turkey-origin H9N2 Avian Influenza Virus Shows Low Pathogenicity but Different Within-host Diversity in Experimentally Infected Turkeys, Quail and Ducks

inferred← citeshttps://doi.org/10.3390/v13050751openalex-snapshot

Within-Host and Between-Host Evolution in SARS-CoV-2—New Variant’s Source

inferred← citeshttps://doi.org/10.3390/v14030554openalex-snapshot

Low Pathogenicity H7N3 Avian Influenza Viruses Have Higher Within-Host Genetic Diversity Than a Closely Related High Pathogenicity H7N3 Virus in Infected Turkeys and Chickens

inferred← citeshttps://doi.org/10.3390/v16010131openalex-snapshot

Influenza A Virus and Acetylation: The Picture Is Becoming Clearer

inferred← citeshttps://doi.org/10.3390/v17020152openalex-snapshot

Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients

inferred← citeshttps://doi.org/10.3390/v17050686openalex-snapshot

A Bioluminescent Imaging Mouse Model for Seasonal Influenza Virus Infection Based on a Pseudovirus System

inferred← citeshttps://doi.org/10.3390/v18050585openalex-snapshot

Genomic Evidence for Novel Introduction and Intra-Host Diversity of DENV-2 in Dar es Salaam, Tanzania

inferred← citeshttps://doi.org/10.3390/vaccines12091068openalex-snapshot

Adjuvant Use of the Invariant-Natural-Killer-T-Cell Agonist α-Galactosylceramide Leads to Vaccine-Associated Enhanced Respiratory Disease in Influenza-Vaccinated Pigs

inferred← citeshttps://doi.org/10.5808/gi.21077openalex-snapshot

Genome characterization and mutation analysis of human influenza A virus in Thailand

inferred← citeshttps://doi.org/10.58837/chula.the.2021.22openalex-snapshot

Analysis of influenza a genomes and bacterial microbiota in upper respiratory tracts of influenza patients

inferred← citeshttps://doi.org/10.64898/2025.12.01.691650openalex-snapshot

bronko: ultrafast, alignment-free detection of viral genome variation

inferred← citeshttps://doi.org/10.70675/0b1afe7cz91c0z456azb240ze87b7040d573openalex-snapshot

Virus influenza aviaires : analyse du risque d'évolution vers les formes hautement pathogènes

inferred← citeshttps://doi.org/10.70675/0e41c216zcba3z4458zbd5dzde8d5a912099openalex-snapshot

Coévolution de la balance fonctionnelle de l’hémagglutinine et la neuraminidase chez les virus influenza de type A

inferred← citeshttps://doi.org/10.70675/fdbf1b0az5559z406ezbb68z8a1a5ad58e89openalex-snapshot

Mise en place d'une approche de métagénomique pour la surveillance des infections respiratoires virales

inferred← citeshttps://doi.org/10.7249/rra1482-2openalex-snapshot

Technological Approaches to Human Performance Enhancement

inferred← citeshttps://doi.org/10.7554/elife.68917openalex-snapshot

Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

inferred← citeshttps://doi.org/10.7554/elife.78618openalex-snapshot

Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs

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