Author: Trevor Bedford

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Preprints

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

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Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York

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Cryptic transmission of SARS-CoV-2 in Washington State

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A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

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Effects of weather-related social distancing on city-scale transmission of respiratory viruses

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SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

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Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

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MERS-CoV spillover at the camel-human interface

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

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Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

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Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

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Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

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Seasonal influenza circulation patterns and projections for 2016-2017

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  • Site-wide: 13,922
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The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

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Seattle Flu Study - Swab and Send: Study Protocol for At-Home Surveillance Methods to Estimate the Burden of Respiratory Pathogens on a City-Wide Scale

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Dengue antigenic relationships predict evolutionary dynamics

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Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

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Real-time analysis and visualization of pathogen sequence data

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

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Genetic characterization of the Zika virus epidemic in the US Virgin Islands

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

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  • Site-wide: 35,085
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Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

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The ability of single genes vs full genomes to resolve time and space in outbreak analysis

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Comprehensive mapping of avian influenza polymerase adaptation to the human host

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Recombination patterns in coronaviruses

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Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

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  • Site-wide: 44,396
  • In genomics: 3,544
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Nextstrain: real-time tracking of pathogen evolution

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  • In evolutionary biology: 2,594
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  • Site-wide: 78,195

Limited predictability of amino acid substitutions in seasonal influenza viruses

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

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  • Site-wide: 91,486
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Early Prediction of Antigenic Transitions for Influenza A H3N2

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Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

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  • In genomics: 4,369
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Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

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Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019

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  • Site-wide: 63,511
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Modern-Day SIV viral diversity generated by extensive recombination and cross-species transmission

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Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

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  • Site-wide: 80,034
  • In evolutionary biology: 4,185
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  • Site-wide: 149,609
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Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

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dms-view: Interactive visualization tool for deep mutational scanning data

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  • In bioinformatics: 7,724
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  • Site-wide: 69,703

Seasonal influenza circulation patterns and projections for 2017-2018

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  • Site-wide: 94,432
  • In evolutionary biology: 4,871
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Operationalizing genomic epidemiology during the Nord-Kivu Ebola outbreak, Democratic Republic of the Congo.

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SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

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Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

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  • Site-wide: 103,543
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Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

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  • Site-wide: 105,639
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Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

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  • Site-wide: 119,328
  • In evolutionary biology: 5,998
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Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes

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A Remote Household-Based Approach to Influenza Self-Testing and Antiviral Treatment

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

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