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News / 03.17.20

How the Broad Institute is helping understand and overcome COVID-19

Credit : NIAID
By Broad Communications

Broad researchers are contributing to Massachusetts’s COVID-19 diagnostic testing, developing new diagnostic technologies and data analysis tools, and generating new biological insights.

Last updated 4/7/20

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 ways, some of which are summarized here. We will continue updating this page with new developments.

Broad Institute’s CLIA-certified testing center begins processing COVID-19 patient samples

March 26, 2020

Working in partnership with the Commonwealth of Massachusetts, Massachusetts State Public Health Laboratory, and area hospitals, the CLIA-certified lab of the Broad Institute of MIT and Harvard has begun processing COVID-19 test samples from patients across New England. The lab returned its first batch of results back to physicians within 24 hours of receiving samples. As teams at the testing center apply additional automation, tests will take approximately 12 hours to complete from receipt. Learn more.

Medical providers: For precise instructions on how to prepare and send samples directly to the Broad Institute Clinical Research Sequencing Platform for processing, click here.

Sheila Dodge, general manager of the Broad Institute's Genomics Platform, talked about how she and her collaborators quickly scaled the testing center to create capacity to process approximately 2,000 COVID-19 tests per day.

How Broad Institute converted a clinical processing lab into a large-scale COVID-19 testing facility in a matter of days

March 27, 2020

Facing a pandemic, scientific and administrative teams across the institute raced to enable coronavirus testing. Click here to read the story of how the Broad's COVID-19 testing facility rapidly came together. 

New diagnostics development

(Note: These technologies and research protocols are not approved clinical diagnostic tests. Any diagnostic would need to be developed and validated for clinical use and would need to follow all local regulations and best practices.)

A 5-min RNA preparation method for COVID-19 detection with RT-qPCR (protocol)
April 6, 2020

Limited availability of RNA extraction kits has slowed the testing of COVID-19 patient samples. Alim Ladha, Julia Joung, core institute member Feng Zhang, and colleagues at the McGovern Institute for Brain Research at MIT describe a new one-step RNA preparation method that can be carried out in five minutes, a fraction of the time taken by other approaches, and uses an alternate commercially available extraction solution. Samples prepared using this protocol are compatible with the CDC’s RT-qPCR testing protocol for SARS-CoV-2.

CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design (preprint)
March 2, 2020

Hayden Metsky, Cameron Myhrvold, and their colleagues in the lab of institute member Pardis Sabeti of the Broad's Infectious Disease and Microbiome Program (IDMP) and Genomic Center for Infectious Diseases (GCID) have created a website containing CRISPR-Cas13-based assay designs, developed using a method called ADAPT, for detecting 67 viruses, including SARS-CoV-2 and related respiratory viruses, in which users can select single or multiplex panels. The team describes these resources in this preprint, focusing on a SHERLOCK assay for SARS-CoV-2.

A protocol for the detection of COVID-19 using CRISPR diagnostics (protocol)
February 14, 2020

Core institute member Feng Zhang, Omar Abudayyeh, and Jonathan Gootenberg have developed a research protocol, applicable to purified RNA, that may inform the development of CRISPR-based diagnostics for COVID-19.

The research protocol provides the basic framework for establishing a SHERLOCK-based COVID-19 test using paper strips.

Data and analysis resources

Broad scientists release COVID-19 best-practices workflows and analysis tools in Terra (Terra Blog post)
March 17, 2020

As our scientific collaborators at the Broad and around the world knuckle down to analyze the data that is starting to stream in, the Terra team in the Broad Data Sciences Platform (DSP) is prioritizing work to support their efforts. In collaboration with Daniel Park, group leader for viral computational genomics in the Broad IDMP and GCID, and his colleagues, the DSP is excited to release a first set of resources for COVID-19 analysis in Terra.

COVID-19 biology

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues (preprint)
March 17, 2020

To uncover the factors that regulate ACE2, the SARS-CoV-2 entry receptor, institute member Alex Shalek of the Klarman Cell Observatory, Jose Ordovas-Montanes, researchers from the Human Cell Atlas Lung Biological Network, and other collaborators investigated large single-cell RNA-sequencing datasets. They found that the gene encoding ACE2 is an interferon-stimulated gene in human upper airway epithelial cells, suggesting that SARS-CoV-2 may exploit interferon-driven upregulation of ACE2 to enhance infection. Learn more on the Shalek lab’s COVID-19 resources page.