How the Broad community is responding to COVID-19
Update June 12, 2023: COVID-19 is still with us, but the once-urgent need for PCR testing has subsided and can be addressed by other providers focused on diagnostics. So the Broad Institute is winding down its COVID-19 diagnostic testing program, with June 30, 2023 as the last day of operations. The Broad continues to conduct research and develop technologies to better understand, diagnose, and treat infectious diseases.
As the COVID-19 pandemic presents increasing public health challenges, scientists from around the world have responded with openness and unprecedented speed, studying the SARS-CoV-2 virus and working to develop new diagnostic technologies, treatments, and tools for researchers. Scientists at the Broad Institute of MIT and Harvard are contributing to this global effort in a variety of ways.
Learn more about data portals and analytic resources being developed by Broad data scientists and software engineers to support COVID-19-related research.
Data & portals
February 23, 2021
COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. COVID-19 CG, developed by Albert Tian Chen, Alina Chan, Ben Deverman and colleagues, will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.
November 23, 2020
With its high-resolution view of the cellular and molecular underpinnings of biological processes, single-cell genomics can help improve the understanding of COVID-19. Early foundational work utilized existing data to characterize the putative target cells of SARS-CoV-2 samples from diverse organs, but these efforts were limited to samples derived from uninfected donors and other previously sampled disease indications. Jose Ordovas-Montanes, Alex Shalek, Alexandra-Chloe Villani, and others in the Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia created and shared a single-cell data resource (covid19cellatlas.org) derived from samples from COVID-19 patients, with the goal of accelerating our collective understanding of COVID-19.
SARS-CoV-2 viral genomics workspace on Terra, containing data and analysis workflows from ongoing genomic epidemiological analysis of COVID-19 in Massachusetts
August 26, 2020
Broad’s viral genomics group and Data Sciences Platform have created a public Terra workspace containing 772 high quality (>98 percent complete) SARS-CoV-2 genomes collected from COVID-19 cases in Massachusetts. This dataset is described in this preprint and blog post. The analysis workflows contained in the workspace allow researchers to perform reference-based SARS-CoV-2 genome assembly, phylogenetic analysis, and data submissions to NCBI GenBank. Both the phylogenetic analysis and GenBank submission workflows can operate on genomes that were assembled within Terra or imported from external assembly software. The data is also available in NCBI GenBank and visualized on NextStrain.org, as well as auspice.broadinstitute.org.
How the Single Cell Portal team is supporting COVID-19 research
April 22, 2020
A video Q&A with Vicky Li Horst and Tim Tickle of the Broad’s Data Sciences Platform about how scientists studying individual cells are collaborating with the Single Cell Portal team to advance COVID-19 research.
Terra and Single Cell Portal teams release new COVID-19 resource pages
April 8, 2020
As scientists around the world analyze COVID-19 data, the Terra and Single Cell Portal teams in the Broad Data Sciences Platform (DSP) are prioritizing work to support the efforts. In collaboration with Broad scientists, these DSP teams have created the infrastructure for processing, analyzing, and sharing COVID-19 viral genomic data and single-cell sequencing data. Read more on the newly released COVID-19 resource pages from Terra and the Single Cell Portal.
