Trevor Bedford

Principal investigator
Google Scholar

I’m a Professor at the Fred Hutchinson Cancer Research Center in the Vaccine and Infectious Disease Division and the Computational Biology Program, affiliate faculty in the Department of Genome Sciences and the Department of Epidemiology at the University of Washington, and an Investigator at the Howard Hughes Medical Institute.

My research program focuses on using viral genome sequences to understand virus evolution and to gain insight into factors driving viral outbreaks, epidemics and pandemics. Much of this work has been instantiated in the Nextstrain platform to conduct real-time genomic epidemiology and to share results broadly. This platform has seen substantial public health adoption to improve seasonal influenza vaccines, combat Ebola outbreaks and to understand and curb SARS-CoV-2 transmission. More broadly, I’ve sought to progress genomic surveillance and with the Seattle Flu Study, lead the design and implementation of a next-generation infectious disease surveillance system that greatly impacted state and local response to the COVID-19 pandemic.


An atlas of adaptive evolution in endemic human viruses

Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences

Tracking the horizontal transfer of plasmids in Shigella sonnei and Shigella flexneri using phylogenetics

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition

State-dependent evolutionary models reveal modes of solid tumor growth

Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county

Trends in risk factors and symptoms associated with SARS-CoV-2 and rhinovirus test positivity in King County, Washington: A test-negative design study of the greater Seattle Coronavirus Assessment Network

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

A Bayesian approach to infer recombination patterns in coronaviruses

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

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

Diagnostic accuracy of an at-home, rapid self-test for influenza: prospective comparative accuracy study

Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

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

Tracing the origin, spread, and molecular evolution of Zika virus, Puerto Rico, 2016–2017

SARS-CoV-2 epidemiology on a public university campus in Washington State

Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

SARS-CoV-2 variants in patients with immunosuppression

Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

Comparison of symptoms and RNA levels in children and adults With SARS-CoV-2 infection in the community setting

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

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

A remote household-based approach to influenza self-testing and antiviral treatment

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

Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Ebola virus transmission initiated by relapse of systemic Ebola virus disease

Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Limited predictability of amino acid substitutions in seasonal influenza viruses

Evaluating specimen quality and results from a community-wide, home-based respiratory surveillance study

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

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Remote household observation for non-influenza respiratory viral illness

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

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

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

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

Characteristics of COVID-19 in homeless shelters: A community-based surveillance study

Cryptic transmission of SARS-CoV-2 in Washington State

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

Cross-sectional prevalence of SARS-CoV-2 among skilled nursing facility employees and residents across facilities in Seattle

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

Ten recommendations for supporting open pathogen genomic analysis in public health

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Evidence for limited early spread of COVID-19 within the United States, January–February 2020

Early detection of Covid-19 through a citywide pandemic surveillance platform

CpG-creating mutations are costly in many human viruses

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

Early prediction of antigenic transitions for influenza A/H3N2

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

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

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

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

Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain

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

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

Dengue genetic divergence generates within-serotype antigenic variation, but serotypes dominate evolutionary dynamics

Clustered mutations at the murine and human IgH locus exhibit significant linkage consistent with templated mutagenesis

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Estimating vaccine-driven selection in seasonal influenza

Real-time analysis and visualization of pathogen sequence data

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

Nextstrain: real-time tracking of pathogen evolution

Massive iatrogenic outbreak of human immunodeficiency virus type 1 in rural Cambodia, 2014-2015

Within-host evolution of human influenza virus

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

Predictive modeling of influenza shows the promise of applied evolutionary biology

MERS-CoV spillover at the camel-human interface

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

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

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

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

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Virus genomes reveal factors that spread and sustained the Ebola epidemic

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

Seasonal influenza circulation patterns and projections for 2017-2018

Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus

Viral factors in influenza pandemic risk assessment

Did a single amino acid change make Ebola virus more virulent?

Seasonal influenza circulation patterns and projections for 2016-2017

Explaining the geographical origins of seasonal influenza A (H3N2)

Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

Quantifying and mitigating the effect of preferential sampling on phylodynamic inference

Persistent HIV-1 replication maintains the tissue reservoir during therapy

Genetic diversity and protective efficacy of the RTS,S/AS01 malaria vaccine

Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak

Assessing phenotypic correlation through the multivariate phylogenetic latent liability model

Quantifying evolutionary constraints on B cell affinity maturation

nextflu: real-time tracking of seasonal influenza virus evolution in humans

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Eight challenges in phylodynamic inference

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

Reassortment between influenza B lineages and the emergence of a co-adapted PB1-PB2-HA gene complex

Seasonality in the migration and establishment of H3N2 influenza lineages with epidemic growth and decline

Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

The early spread and epidemic ignition of HIV-1 in human populations

Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2

Integrating influenza antigenic dynamics with molecular evolution

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories

Viral phylodynamics

The roles of competition and mutation in shaping antigenic and genetic diversity in influenza

Canalization of the evolutionary trajectory of the human influenza virus

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty

Spatial guilds in the Serengeti food web revealed by a Bayesian group model

Strength and tempo of selection revealed in viral gene genealogies

Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)

Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

Optimization of gene expression by natural selection

Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster

Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila

Overdispersion of the molecular clock varies between yeast, Drosophila and mammals

Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum

Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites

Gene conversion as a source of nucleotide diversity in Plasmodium falciparum

Evolvability of Hsp70 expression under artificial selection for inducible thermotolerance in independent populations of Drosophila melanogaster


fauna - RethinkDB database to support real-time virus analysis

cli - The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch. - The Nextstrain website

augur - Pipeline components for real-time phylodynamic analysis

ncov - Nextstrain build for novel coronavirus SARS-CoV-2

id3c - Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

auspice - Web app for visualizing pathogen evolution

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

baltic - baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

nextflu - Real-time tracking of influenza evolution

sismid - Pathogen evolution, selection and immunity

sacra - Cleaning scripts for real-time pathogen analysis

mitii - Pathogen evolution, selection and immunity

phylodynamics-lecture - Lecture on viral phylodynamics

ncov-wa-phylodynamics - Analyses of the hCoV-19 outbreak in Washington State

ncov-wa-d614g -

zika-usvi - Evolutionary analysis of USVI Zika epidemic

ncov-cryptic-transmission - Cryptic transmission of SARS-CoV-2 in Washington State

gs541-phylodynamics - Lectures and materials for GS541 Introduction to Computational Molecular Biology

janus - Build and deploy Nextstrain

ncov-phylodynamics - Phylodynamic estimation of nCoV incidence and prevalence

genomic-horizon - Temporal horizons of genomic epidemiology

h5n1-cambodia - Within-host diversity in H5N1-infected humans and poultry in Cambodia

h3n2-reassortment - Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

zika-colombia - Genetic analysis of the Zika epidemic in Colombia

dengue-antigenic-dynamics - Dengue antigenic variation and evolutionary dynamics

zika-seq - Pipelines to do MinION sequencing of Zika virus

global-migration - Analysis of global migration patterns of seasonal influenza viruses

mers-structure - Looking into MERS-CoV dynamics through the structured coalescent lens

roka - Evolutionary and epidemiological analysis of Roka HIV outbreak

unsampled - Estimating unsampled viral diversity

siv-cst - Dynamics of cross-species transmission in SIV

yellow-fever - Evolutionary dynamics of yellow fever virus

chikv - Evolutionary dynamics of chikungunya virus

medium-data - Talk on data and visualization

infectious-pulse - Many-strain SIR epidemiological model

sctrace - Simulating migration patterns using charged particles

flutrace - Visualizing influenza global circulation patterns

PACT - Posterior Analysis of Coalescent Trees

coaltrace - Simulating genealogies using charged particles

antigen - Simulating virus evolution and epidemiology

haplotypes - Visualizing evolution as a network of shared mutations

ancestry - Tracing coalescent histories

stem - Picking influenza stem strains

dynamics-practical - Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data

divergence - Illustration of Darwin's Principle of Divergence


Openings for bioinformatician and full-stack developer to contribute to Nextstrain platform

Cryptic transmission of novel coronavirus revealed by genomic epidemiology

Early warnings of novel coronavirus from genomic epidemiology and the global open scientific response

Forecasting influenza virus evolution to Sep 2020

Developer for real-time genomic epidemiology platform

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

Establishment and spread of Zika in the Americas

Zika in the USVI genome announcement

Seasonal influenza circulation patterns and projections for 2017-2018

Open Science Prize and relaunch

The Open Science Prize and a shared scientific endeavor

Seasonal influenza circulation patterns and projections for 2016-2017

Summer 2016

Zika sequencing in Brazil (or Trevor does fieldwork)

Programmer for real-time phylodynamic analysis

Seasonal influenza circulation patterns and future projections

Strain-specific vaccine efficacy in the RTS,S malaria vaccine

Analysis and visualization of influenza antigenic evolution

Seasonal influenza circulation patterns and future projections

Pathogen evolution, selection and immunity

New recruits

On scientific publishing practices in the face of public health crises

Ebola transmission and evolution revealed through genomic analysis

Tracking down the sneeze that started seasonal flu

Global circulation patterns of seasonal influenza viruses

Real-time analysis of Ebola evolution and geographic spread

Postdoc in immune repertoire dynamics

Observations of recent influenza evolution and predictions for the 2015-2016 flu season

Real-time tracking of influenza virus evolution

Seasonal migration of influenza lineages

Is Ebola adapting?

Bayesian estimation of phylogenetic signal

Reassortment between influenza B lineages

Uncovering the "hidden history" of HIV emergence and spread

Challenges in phylodynamics

Avian influenza diversity and persistence

Assessing correlated trait evolution

Molecular evolution of the human B cell repertoire

Reassortment patterns between influenza B lineages

Predicting flu migration patterns

Publishing with eLife

Postdoc in viral phylogenetics and evolution

Identifying sites responsible for antigenic change in influenza

Comparing amino acid distance to BLOSUM as a predictor of antigenic drift

Phylowood phylogeographic visualization

Version 2.0

Newton Institute presentation

Issue tracking reviewer criticisms

Integrating influenza antigenic dynamics with molecular evolution

Tutorial on inferring spatiotemporal dynamics from sequence data

Wikipedia x PLoS topics page on viral phylodynamics

Fixation of new alleles

Influenza diversity across spatial scales

Visualizing evolution as a network of shared mutations

What limits the rate of virus adaptation?

Plotting interpretable phylogenies

Comparing performance of Processing.js and D3.js

Simulating virus evolution and epidemiology

Running the numbers for Contagion... they don't come out well

Model comparison through path sampling and AICM

Visualizing the global circulation of the human influenza virus

Some thoughts on a GitHub of Science

Estimating global flu diversity

LaTeX manuscript template with web display

Interactive visualization of the Serengeti food web

Spatial guilds in the Serengeti food web revealed by a Bayesian group model

Reproducible peer review

Canalization of the evolutionary trajectory of the human influenza virus

Visualizing mortality data

Estimating the effective population size of swine flu

Illustrating Darwin's Principle of Divergence

Wright-Fisher population genetic simulation

Strength and tempo of selection revealed in viral gene genealogies

Matching R0 to cumulative prevalence in the H1N1 influenza pandemic

Counting parameters in a phylogeny

Multi-strain multi-deme model with SIRS dynamics

Updating coaltrace to use Javascript

Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

Reuters: "Who to blame for flu? Maybe the US, study finds"

Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)

Presentation on

Population genetic simulation on a mutational landscape

Compilation of most interesting Wikipedia articles

PACT: Posterior Analysis of Coalescent Trees

Basic coalescent simulation with physics-based layout