Active Projects
Ebola Epidemiology
Epidemiological data for the ongoing Ebola outbreak in the DRC.
HLA Typing from Ebola and Lassa Patients
HLA genotype calls from Ebola and Lassa patients admitted in Sierra Leone.
SARS-CoV-2 Evolution
Investigations of the origin and evolution of SARS-CoV-2.
SARS-CoV-2 Genomics
Genome sequencing of SARS-CoV-2 from COVID-19 patients.
West Nile Genomics – California
West Nile virus sequences from California.
West Nile Genomics – WestNile 4K
West Nile virus sequences from across the United States.
Zika Functional Evolution
Experimental studies testing Zika virus evolution.
Archived Projects
Bat Metagenomics
Metagenomic survey of bats from Uganda. The anti-PREDICT Project.
Dengue Florida Genomics
Full-length dengue virus genomes from the 2013 outbreak in Martin County, Florida.
Zika Genomics
Sequence data from the Zika virus outbreak in Florida and beyond – mostly local cases from humans and mosquitoes, but also travel-associated cases.
Zika Epidemiology
We’re compiling Zika case numbers from endemic countries. Our data is based on bar graphs reported and compiled by PAHO.
Zika Phylogeography
Phylogeographical analysis of Zika virus spread.
Recent Data-related Blog Posts
English: To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from patients in San Diego and across the border in Tijuana. In this preliminary analysis we look at the how the outbreaks are connected between California, USA and Baja California, (more…)
To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from infected patients in San Diego. This is our first preliminary analysis. (more…)
Summary: Using local and travel-associated case reporting from American and European public health systems, we identified an unreported Zika outbreak in Cuba during 2017. Virus sequencing from travelers revealed that the Zika outbreak in Cuba was sparked by multiple introductions of the virus from elsewhere in the Caribbean and Central America during 2016 that persisted into 2017. The recent Zika virus…