We are using infectious disease genomics to investigate how pathogenic viruses such as Zika, West Nile, Ebola, Lassa, and SARS-CoV-2 emerge and cause large-scale outbreaks. Using a combination of computational biology, experimentation, and field work, our hope is to transform outbreak response and change the way we develop vaccines and therapeutics.
At the Andersen Lab at Scripps Research we try to understand questions such as: how do viruses emerge, spread, evolve, and go from causing small-scale outbreaks to large-scale epidemics? How can we diagnose them better and discover novel ones? How do they develop resistance to countermeasures and what molecular and immunological factors govern the underlying mechanisms? Critically, by addressing these questions, can we develop new and effective vaccines and medicines, while informing outbreak responses? The research in our laboratory is aimed at tackling these questions using an integrated approach of computation, experimentation, genomics, and large-scale data analysis. We also more broadly employ quantitative approaches across scientific disciplines, ranging from microbiology to human immunology and genetics.
The Andersen Laboratory was established at Scripps Research in the summer of 2015 in beautiful La Jolla, California. We are strong proponents of open data and open science, and we are big believers in collaborating across scientific disciplines. To this end, we are actively engaged in several of our research initiatives, including the Global Health Initiative at Scripps Research, the Center for Viral Systems Biology, the Viral Hemorrhagic Fever Consortium, the West African Research Network for Infectious Diseases, and the WestNile 4K Project.
COVID-19 / SARS-CoV-2 Resources
The ongoing COVID-19 pandemic caused by SARS-CoV-2 is rapidly escalating emergency. To gain insights into the emergence, spread, transmission, and evolution of the virus, we are working with a large number of public health agencies, hospitals, biotechs, and academic partners. With funding from the CDC and NIH, we are sequencing hundreds of samples a week and all the data are made publicly available every week.
In response to the emergence of new variants of SARS-CoV-2, we have made several visualization tools to make the genomic data more useful to the public, scientists, and outbreak responders. Some of our primary tools include:
Lineage reports (e.g., B.1.1.7/Alpha, B.1.351/Beta, P.1/Gamma, B.1.617.2/Delta, etc.): https://outbreak.info/situation-reports
Location specific lineage reports, e.g., San Diego: https://outbreak.info/location-reports?loc=USA_US-CA_06073
Sequencing Dashboard visualizing the results from our sequencing efforts: https://searchcovid.info/sequencing-statistics/
More broadly speaking, we have made outbreak.info a go-to source for epi data, resources, and variant reports. The reports are updated four times daily where we download and reanalyze the entire genomic dataset on GISAID – which is now more than a million SARS-CoV-2 genomes.