June 06, 2022

Scripps Research and GISAID release application programming interface (API) for accessing COVID-19 variant data Open science collaboration will support global genomic surveillance efforts to track coronavirus variants.

June 06, 2022

LA JOLLA, CA The Center for Viral Systems Biology (CViSB) at Scripps Research is collaborating with GISAID, a global data science initiative that facilitates public access to SARS-CoV-2 genomic data, to effectively track the global evolution of SARS-CoV-2 variants on Outbreak.info. Today, CViSB announces its collaboration with GISAID on an application programming interface (API) that enables access to all processed data on Outbreak.info.

The API further realizes our goal of making data as easily accessible as possible for downstream analyses, says Karthik Gangavarapu, PhD, a scientific collaborator in the laboratory of Kristian Andersen, PhD, at Scripps Research and a co-lead on the project. Our collaboration with GISAID makes it possible to track these mutations, thanks to the efforts of thousands of labs that share their data through GISAID in an unparalleled global effort.

Enabling the effort by Scripps Research with high-quality data shared via GISAID is another example of how an open, but transparent exchange of outbreak data empowers the scientific community to produce better public health outcomes that aid global health security, says GISAID Vice President Ben Branda.

Since the onset of the pandemic, researchers around the world have been arduously working to identify, track and understand mutations in the SARS-CoV-2 genome, the virus that causes COVID-19. GISAID is an essential driver of the global response and the primary source of genomic data for SARS-CoV-2 and influenza viruses which enables public health decision-making and medical breakthroughs. SARS-CoV-2 data shared through GISAID are aggregated and standardized in Outbreak.info, a web application developed by researchers at Scripps Research to facilitate visualizations of many key data inquiries to track the evolution and spread of Variants of Concern. These results allow researchers to focus on data interpretation and avoid duplicative efforts.

Since the first whole-genome sequences of the emerging coronavirus were made available through GISAID on January 10, 2020, over 11 million viral genomes from 210 countries and territories have been processed and annotated by GISAID's global curation team and made available to the public in record time. This has enabled the rapid development of lifesaving countermeasures to COVID-19, including the first vaccines (Polack et al. N Engl J Med 2020) and the first diagnostic tests to detect SARS-CoV-2 (Bohn et al. Clin Chem Lab Med 2020). The unprecedented magnitude of data shared through GISAID makes timely data analysis a challenge for researchers. This API, however, enables researchers to query the large dataset and find answers faster.

Genomic surveillance has been at the forefront during the ongoing COVID-19 pandemic, says Laura Hughes, PhD, an institute investigator at Scripps Research and the project lead for Outbreak.info. We created Outbreak.info to efficiently analyze these sequences and support research and public health efforts with tools to visually compare and analyze variants.

The Outbreak.info team, enabled thanks to the effective data sharing of the GISAID community, has been doing an exceptional job in responding to the global need to track variants during the rapidly evolving pandemic and making their data publicly available to the rest of the scientific community, says Eric Topol, MD, founder and director of the Scripps Research Translational Institute. I applaud their exemplary collaborative efforts.

The release of the API adds to the collection of APIs offered on Outbreak.info, as the site also provides access to COVID-19 epidemiology data and other resources, including COVID-19 journal articles, preprints, clinical trials. These APIs build on the open data projects Bjorn, created by the Andersen lab at Scripps Research, and BioThings Suite, developed by the Su and Wu labs at Scripps Research, which make the development of high performance biomedical APIs possible.

According to Hughes, Sharing information and contributing to a centralized body of knowledge is ever important in a rapidly evolving situation. The more researchers around the world continue to work on a unified front, the greater the impact that can be achieved.

The Center for Viral Systems Biology is funded by the National Institute of Allergy and Infectious Diseases (5U19 AI135995-03).

Outbreak.info is supported with funding from the National Institute for Allergy and Infectious Diseases (3 U19 AI135995-04S3, 3 U19 AI135995-03S2, U01AI151812, R01 AI162611, R01 AI153044), National Center for Data to Health (5 U24 TR002306), Centers for Disease Control and Prevention (75D30120C09795), and the National Institute of General Medical Sciences (R01GM083924).

About Scripps Research

Scripps Research is an independent, nonprofit biomedical institute ranked the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more at www.scripps.edu.

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