Infectious Disease Genomics

Scientists at the Scripps Research Translational Institute use sequencing-based technologies to study the interaction and co-evolution between host and pathogen. By developing and applying both computational tools and experimental methods, we seek to gain a detailed picture of the viruses and microorganisms that infect humans. Our aim is to use this knowledge to transform infectious disease outbreak response and change the way we develop vaccines and therapeutics.

Ongoing Studies

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations, Nature Methods, February 2023

Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources, Nature Methods, February 2023

Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions, Nature Communications, August 2022

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades, Nature Communications, September 2022

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic, Science, July 2022

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission, Nature, July 2022

Emergence of an early SARS-CoV-2 epidemic in the United States, Cell, September 2021

Ebola virus transmission initiated by relapse of systemic Ebola virus disease, New England Journal of Medicine 2021

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States, Cell 2021

The proximal origin of SARS-CoV-2, Nature Medicine 2020

Travel suirveillance and genomics uncover a hidden Zika outbreak during the waning epidemic, Cell 2019

Precision epidemiology for infectious disease control, Nature Medicine 2019

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar, Genome Biology 2019

Tracking virus outbreaks in the twenty-first century, Nature Microbiology 2018

Systematic analysis of monoclonal antibodies against Ebola virus GP defines features that contribute to protection, Cell 2018

Pandemics: spend on surveillance, not prediction, Nature 2018

Genomic insights into Zika virus emergence and spread, Cell 2018

Genomic epidemiology reveals multiple introductions of Zika virus into the United States, Nature 2017

Establishment and cryptic transmission of Zika virus in Brazil and the Americas, Nature 2017

Zika Virus Evolution and Spread in The Americas, Nature 2017

Protocol Multiplex PCR Method for MinION and Illumina Sequencing of Zika and Other Virus Genomes Directly From Clinical Samples, Nature Protocols 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic, Nature 2017

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic, Cell 2016

The Evolution Of Ebola Virus: Insights From The 2013-2016 Epidemic, Nature 2016

Roots, Not Parachutes: Research Collaborations Combat Outbreaks, Cell 2016

Navigating the Zika panic, F1000Research 2016

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus, Cell 2015

Ebola Virus Epidemiology, Transmission and Evolution during Seven Months in Sierra Leone, Cell 2015

We have the best view yet of COVID-19's origins. What should we do about it?, Vox 2022

New research points to Wuhan market as pandemic origin, The New York Times 2022

Wuhan market was epicenter of pandemic's start, studies suggest, Nature 2022

San Diego County detects its first Omicron case, The San Diego Union-Tribune 2021

Covid origins: Scientists weigh up evidence over virus's origins, BBC News 2021

Coronavirus almost certainly came from an animal, not a lab leak, top scientists argue, CNN 2021

U.K. coronavirus variant spreading rapidly through United States, study finds, The Washington Post 2021

Scripps Research and UCSD wing $2.5M CDC contract to track COVID-19 spread across San Diego, The San Diego Union-Tribune 2020

No, COVID-19 coronavirus was not bioengineered. Here's the research that debunks that idea, Forbes 2020

Zika was soaring across Cuba. Few outside the country knew., The New York Times 2019

Infected travelers reveal Cuba's 'hidden' Zika outbreak, Science 2019

Cuba's Untold Zika Outbreak Uncovered, Nature 2019

How Zika Conquered The Americas, The Atlantic 2017

Epidemiology: Molecular mapping of Zika spread, Nature 2017

San Diego Lab Takes ‘Open Science’ Approach To Tracking Zika’s Arrival In US, KPBS 2017

How Ebola Adapted to Us, The Atlantic 2016

The Next Pandemic, Genome 2016

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