Dr. Pardis Sabeti, MD, DPhil
Professor, Harvard University School of Public Health
Institute Member, Broad Institute of Harvard and MIT
Investigator, Howard Hughes Medical Institute
What are you and your institution currently working on regarding COVID-19?
As soon as the SARS-CoV-2 genomes were released, we worked with our colleagues in West Africa to establish diagnostic testing in Nigeria, Sierra Leone, and Senegal. When US hospitals were given regulatory permission to set up Lab Developed Tests, we worked with our Massachusetts General Hospital partners to get FDA approval and begin testing. Through the Massachusetts Consortium for Pathogen Readiness, we supported many hospitals in the region to establish testing, and novel technologies in their development path. At the same time, we began whole genome sequencing and phylogenetic analysis of hundreds of complete SARS-CoV-2 genomes from Boston, identifying numerous introductions to the area, and linking seemingly unconnected populations and superspreading events.
We have also developed novel tools and technologies for diagnostics, including CARMEN, SHINE, and ADAPT. CARMEN massively multiplexed nucleic acid detection with CRISRP-Cas13, and shows its performance on 170 human associated viruses. SHINE is an integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. In our most recent publication on BioRxiv, we successfully optimized SHERLOCK into a single-step reaction, the results of which register by fluorescence, or on a lateral flow assay which can be interpreted by a companion smartphone application. With ADAPT, we used genomically-comprehensive machine learning to develop and share assay designs for detection of 67 viral species and subspecies related to SARS-CoV-2. We are also deploying our Sentinel mobile application and dashboard technologies, including a large-scale roll-out across Colorado in August.
We are also deploying our education module, Operation Outbreak, (OO) which includes usage of Bluetooth technology on phones to spread a virtual virus to simulate an outbreak. As campuses re-open in the fall, and many working groups hope to better understand virus transmission, OO can serve as a tool to better understand how viruses spread, as well as how to protect against them.
Could you describe your genomic sequencing research and training programs?
My group is highly committed to understanding and combatting locally circulating pathogens, and have been involved in this work for some time. We have longstanding partnerships in West Africa where we have been conducting sequencing and surveillance of various outbreaks including Ebola and Lassa. We were able to establish connections in 11 countries in the Americas to carry out sequencing amidst the Zika epidemic, and now continue to work in Honduras. We also work locally in the Massachusetts Department of Health, where we have studied Mumps and Hepatitis A.
Education is also a passion of my lab. With our partners in the African Center of Excellence of Genomics of Infectious Disease, (ACEGID), we developed training programs for infectious disease surveillance in genomics, diagnostics, sequencing, and bioinformatics at various levels, including summer-long certifications and Masters/PhD programs for 169 students from 7 countries. ACEGID has also provided short courses for over 914 scientists and health care workers from throughout West and Central Africa. With our partners at the Massachusetts Department of Public Health (DPH) and CDC we have also provided short courses in genomics and bioinformatics for 52 individuals from 8 U.S. DPHs.
Dr. Pardis Sabeti is a Professor at Harvard University, the Harvard School of Public Health, the Broad Institute of Harvard and MIT, and a Howard Hughes Medical Institute Investigator. Her computational genomic lab has contributed to widely varying fields — including human evolutionary biology, viral sequencing, information theory, rural disease surveillance and education efforts in West Africa. They aim to create comprehensive approaches for detecting, containing, and treating deadly infectious diseases, including Lassa virus, Ebola virus, Zika virus, and Babesiosis microtia. Dr. Sabeti completed her undergraduate degree at MIT, her graduate work at Oxford University as a Rhodes Scholar, and her medical degree summa cum laude from Harvard Medical School as a Soros Fellow. Sabeti’s awards and honors include World Economic Forum (WEF) Young Global Leader, National Geographic Emerging Explorer, the National Academy of Sciences Richard Lounsbery Award, Smithsonian American Ingenuity Award for Natural Science, TIME magazine’s “Person of the Year” as one of the Ebola fighters, and one of TIME’s 100 Most Influential People
About at the Center for Systems Biology and Department of Organismic and Evolutionary Biology
The Department of Organismic and Evolutionary Biology (OEB) is committed to training scientists who pursue a greater understanding of the evolution of the earth’s life processes. The department’s faculty and students conduct field and laboratory studies that are key to understanding the evolution of organisms, how biodiversity is generated and maintained, how organisms work, and how organisms interact with their environment.