So, for the past 16 months and counting, it’s been all things COVID-19, all the time, for researchers at the institute’s Network Systems Science and Advanced Computing Division, which Marathe directs and where Lewis is a research associate professor.
Five to six researchers do the core work for the weekly forecasts the institute produces, Lewis explained, and another 20 provide “nuggets” to support its modeling; these include statisticians providing survey analysis and bioinformaticians analyzing the latest information on COVID-19 variants. One of the core researchers is a computational biologist, Przemyslaw (Przemek) Porebski, who had just started working with the institute when COVID-19 hit; his work has optimized the computations that provide data on variants and was “a key component of our team’s contribution to the CDC paper,” Lewis noted. (All 14 UVA researchers who contributed to the paper are listed at the end of this article.)
Marathe, UVA’s principal investigator for the Virginia Department of Health, said the Biocomplexity Institute was in touch with VDH and the state Department of Emergency Management early in 2020, and shortly thereafter started collaborating with the Department of Education.
The Art, Science and Value of Forecasting
UVA’s COVID-19 forecasting team has internal “sync” meetings, where researchers pitch ideas on what to analyze week to week, explained Lewis, who draws upon his own experience and epidemiological knowledge, as well as what’s trending in headlines, scientific literature, others’ modeling, intel from standing calls with agencies, and even social media. The latter may seem like an odd resource for scientists, but Chinese researchers were posting their findings in real-time on Twitter when COVID-19 first emerged, said Lewis, and “we began producing our weekly forecasts a few weeks later.”
“What has been unique to this pandemic is the degree to which rapid information sharing among the scientific community took place,” he said. The use of the “rxiv” sites – “archive” sites where scientists could pre-publish a paper awaiting peer review as a way to share information quickly in a fast-changing, emergency situation – “really helped everyone’s efforts,” Lewis said.
The team also worked with VDH from November to March on a contact-tracing paper. Marathe and Lewis advised the state to create smaller health centers that could be put up and taken down easily, instead of larger, more permanent testing and vaccination sites.