J. Huddleston

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.

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.

Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

This study maps mutations in the SARS-CoV-2 spike RBD that escape antibody recognition, revealing escape mutation patterns and enabling the design of antibody cocktails.

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.

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.

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.