Projects & Data

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

ages_tests

Age distribution of COVID-19 cases in San Diego County

| Data | No Comments
To understand the spread of COVID-19 in San Diego, we looked at the age distribution of COVID-19 over time (Figure 1). Data for this analysis was provided by the Epidemiology and Immunization Services Branch of the County of San Diego Health and Human Services agency through the San Diego Open GIS Data Portal. The visualization was inspired by Gytis Dudas's…
narrative

Narrative 2 | Cross-border virus transmission

| Data, Narrative | No Comments
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…)
narrative

Narrative 1 | Genomic Epi in San Diego

| Data, Narrative | No Comments
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…)