IGI Seminar Series: SARS-CoV-2 dynamics in Madagascar

Summary

Join us for this week's Seminar Series led by Cara Brook, Assistant Professor in the Department of Ecology and Evolution at the University of Chicago. The COVID-19 pandemic has impacted nearly every country on Earth, testing the limits of public health infrastructures globally. As the national reference laboratory for febrile illness in Madagascar, researchers at the Institut Pasteur of Madagascar were responsible for all SARS-CoV-2 testing during the first epidemic wave in Madagascar (March – September 2020)—and continue to undertake the vast majority of in-country surveillance to this day. With support from the Innovative Genomics Institute (IGI), Cara and her team developed and expanded this in-country COVID-19 testing lab during the early stages of the pandemic, and applied new methods leveraging quantitative information captured in the cycle threshold (Ct) output from the SARS-CoV-2 qPCR pipeline to fit nested viral kinetics and mechanistic, epidemiological models in the Susceptible-Exposed-Infectious-Recovered (SEIR) framework to the resulting data in order to quantify epidemic growth rates in real time and forecast ongoing epidemic trends.

In this talk, Cara will demonstrate the effectiveness of this Ct-based surveillance method in the low surveillance region of Madagascar. Additionally, she will discuss how her team leveraged IGI funding to expand their ongoing Gates-funded work in pathogen genomic sequencing in Madagascar, implementing the first-ever in country Illumina sequencing platform to undertake SARS-Cov-2 genomic surveillance. She will report results from the first year of this effort, identifying the timing and source of SARS-CoV-2 introductions to the island and patterns of within-country dispersal. Finally, she will close with a discussion of the evolutionary origins of SARS-CoV-2 emergence and her lab’s ongoing work in undertaking viral discovery, surveillance, and dynamical modeling in wild fruit bat coronavirus reservoirs in Madagascar. Read more about the Brook lab's research here or her IGI-funded project here.

Join us for the live event on Zoom. All participants and hosts are required to sign into a Zoom account prior to joining meetings.

Speaker

Cara Brook — Cara Brook is an Assistant Professor in the Department of Ecology and Evolution at the University of Chicago and a Branco Weiss ‘Society in Science’ Fellow. The Brook lab investigates the ecological and evolutionary dynamics of zoonotic infections, in particular those derived from wild bat hosts. Cara maintains a long-term field site studying fruit bat viruses on the island nation of Madagascar, where she work closely with students from the University of Antananarivo and Institut Pasteur de Madagascar. She is committed to conducting rigorous science while simultaneously promoting scientific development, education, and capacity building in Madagascar.

Prior to the University of Chicago, Cara spent time as a Miller Postdoctoral Fellow working with Mike Boots in the Department of Integrative Biology at the University of California, Berkeley. She received her Ph.D. in Ecology and Evolutionary Biology from Princeton University in 2017 and her B.S. in Earth Systems from Stanford University in 2010. Cara hails originally from beautiful Sonoma County, California. When not chasing bat viruses, you will find her hiking, backpacking, and camping across the North American West.