T. Bedford

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

This study develops a high-throughput sequencing-based neutralization assay to measure antibody titers against multiple influenza strains and finds that vaccination effects vary by individual and prior vaccination history.

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.

An Atlas of Adaptive Evolution in Endemic Human Viruses

The paper identifies ten endemic human viruses that undergo antigenic evolution, showing higher mutation rates in surface proteins compared to SARS-CoV-2.

Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference

This paper introduces a method to quantify plasmid movement in Shigella species over time, finding higher transfer rates for small plasmids and recent dissemination of a multidrug-resistant plasmid.

State-dependent evolutionary models reveal modes of solid tumor growth

This paper introduces a Bayesian state-dependent evolutionary model to infer spatially varying cell division rates in tumors using multi-region sequencing data, finding peripheral cells divide 3-6x faster than central cells.

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

The paper quantifies adaptive evolution in SARS-CoV-2 by analyzing mutation accumulation and selection pressures across the genome, finding rapid adaptive changes in spike S1 and other genes.

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

The paper analyzes SARS-CoV-2 within-host diversity and transmission bottlenecks in acute infections, finding limited diversity and narrow bottlenecks that restrict variant spread.

Recombination patterns in coronaviruses

This paper introduces a method to infer recombination networks in coronaviruses and shows recombination is common and potentially beneficial in seasonal human coronaviruses.

Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

The paper evaluates the quality of specimens and results from a home-based respiratory surveillance study to assess its feasibility for community-level monitoring of respiratory pathogens.

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

This study shows that OC43 and 229E coronaviruses are evolving in immune-targeted regions, suggesting antigenic drift may drive immune evasion and vaccine reformulation needs.

Limited predictability of amino acid substitutions in seasonal influenza viruses

This study assesses the predictability of amino acid substitutions in seasonal influenza viruses and finds that current frequency is the strongest predictor of fixation, while other features like epitope occurrence or LBI have limited predictive power.

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

This study develops a forecasting framework for influenza A/H3N2 evolution by integrating phenotypic antigenic drift data with sequence-based fitness estimates, showing improved long-term predictions.

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes

This study tracks genetic and phenotypic changes in Helicobacter pylori isolates from a single host over six years, revealing sub-populations with distinct genetic and functional traits.

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

The paper uses genetic sequence data and patient metadata to analyze local influenza transmission dynamics in Basel, Switzerland, finding that temperature trends correlate with transmission and that elderly and school children drive different transmission networks.

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

The paper analyzes H5N1 influenza virus evolution in humans and ducks in Cambodia, finding human-adapting mutations but limited within-host evolution due to selection pressures.

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

The paper analyzes seasonal influenza circulation patterns from September 2019 to September 2020, identifying dominant clades and antigenic changes in A/H3N2, A/H1N1pdm, B/Vic, and B/Yam viruses.

Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

The paper maps how amino-acid mutations in influenza's hemagglutinin affect neutralization by polyclonal human sera, showing individual variation in escape mutations not observed in ferrets.

Dengue antigenic relationships predict evolutionary dynamics

This study identifies specific genetic substitutions and clusters contributing to dengue antigenic diversity and shows their impact on population dynamics and vaccine design.

Comprehensive mapping of avian influenza polymerase adaptation to the human host

This study maps amino-acid mutations in avian influenza PB2 polymerase that enhance growth in human cells, identifying new adaptive mutations and their evolutionary constraints.

Real-time analysis and visualization of pathogen sequence data

This paper reviews recent developments in real-time analysis of pathogen sequence data with a focus on visualization and integration of sequence and phenotypic data.

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

The paper experimentally measures the effects of all single amino-acid mutations in H3N2 influenza HA on viral growth and shows their correlation with evolutionary success in natural lineages.

Nextstrain: real-time tracking of pathogen evolution

Nextstrain provides real-time tracking of pathogen evolution by integrating viral genome data with other public health data through a database, bioinformatics pipeline, and visualization platform.

Modern-Day SIV viral diversity generated by extensive recombination and cross-species transmission

The paper uses phylogenetic analysis to study SIV recombination and cross-species transmission among primates, identifying 14 novel host switches and varying host-switching abilities across lentiviral lineages.