The COVID-19 pandemic has required an unprecedented level of collaboration between individuals from all disciplines and specializations, as the need for an effective, wide ranging response requires insight from a variety of viewpoints. Since the first case of COVID-19 was identified in the U.S. over 19 months ago, this trans-disciplinary collaboration has been exemplified by the Network Systems Science and Advanced Computing division of the U.Va. Biocomplexity Institute, which has played an important role in tracking the spread of the coronavirus across the U.S. and Commonwealth.
The Biocomplexity Institute opened in 2000 with the mission of investigating human life at every level and observing the complex interaction of systems that results from it. The institute houses research teams composed of 100 members from various scientific backgrounds and is led by Madhav Marathe, division director of NSSAC and co-leader of the COVID-19 response team, and executive director Christopher Barrett. In 2018, it partnered with the University, taking up residency in Charlottesville.
“Our institute, as the term suggests, works on problems that span the entire spectrum of problems that arise when studying complex biological problems,” Marathe said.
The Biocomplexity Institute’s projects include the tracking of pandemics, but also urban transport planning, understanding large scale disasters and even comprehending economic systems. In light of the COVID-19 pandemic, the focus of the NSSAC division has been on forecasting the spread of and planning the response to this disease. But the rarity of global pandemics made it difficult for the team to gather the data required to create a complex model of the spread of the virus, forcing them to find data from federal institutes or even social media and quickly put it to use.
In order to accomplish this, the Biocomplexity Institute has worked closely with the Centers for Disease Control and Prevention to project the spread of COVID-19 and share potential responses to the pandemic with both CDC and state leaders.
This cooperation between the CDC and the Biocomplexity Institute has been present for about a decade, with the Institute consistently participating in CDC-sponsored challenges to forecast the timing, peak and intensity of the current year’s flu season.
The Biocomplexity Institute’s COVID-19 projections are created through the use of various simulations and models, said Bryan Lewis, associate research professor and co-leader of the Biocomplexity Institute’s COVID-19 response team. Models allow the team to analyze different what-if scenarios and use them to provide situational data that may be unknown at the time the projection is made.
“The key thing that I think is a little bit different from a lot of approaches we use is that we try to make a mechanistic model,” Lewis said. “If you look at a car moving by and you're trying to say where that car is going to go, you can watch it, measure its speed and look at its trajectory, and you can say that it maintains constant speed or changes with that hill. We can roughly test where it will be in 10 seconds, and that’s a pretty statistical look at the world.”
When picturing population-level disease dynamics, mechanistic models and what-if scenarios can be used and grant more detail beyond the primary observations, Lewis said. This allows for certain actions to be tested — such as restaurants being closed or other restrictions — and enables researchers to see how they affect the spread of the virus. These projections are given to those with the ability to enact these changes to help see what steps they should take to curb the spread of disease.
As seen in a CDC paper made up of the data of not only the Biocomplexity Institute, but numerous universities and institutes across the country, the widespread distribution of the COVID-19 vaccines and implementation of nonpharmaceutical intervention means that cases could decline by August and potentially reach a new low by September if preventative measures are distributed effectively and are strictly followed.
But with reluctance of some to obtain vaccinations as well as new variants of COVID-19, the Biocomplexity Institute’s work is far from over. The recent spread of the delta variant across the United States has added a new layer of challenges to the biocomplexity institute’s work, with the prevalence and transmissibility of the strain forcing the University to reinstate then extend an indoor masking policy for the beginning of the 2021 fall semester.
In order to inform the public of the current state of the pandemic, as well as help the Virginia Department of Health make decisions on responses to the pandemic, the biocomplexity institute releases weekly forecasting updates. In their most recent update, the institute projects that the number of cases in Virginia will grow, the vaccination rate will remain slow and that there will be surges of the delta variant in several states.
The forecasting of an ever-evolving disease is not a simple matter. In order for accurate predictions to be made, data has to constantly be collected and implemented. Graduate research assistant Akhil Sai Peddireddy is one of the many team members facing the challenge of predicting the spread of a virus that could change unexpectedly at any moment.
“This is an ongoing effort — both the surveillance and the forecasting,” Peddireddy said. “We have to adapt to the rapidly changing circumstances of the pandemic, and then include these changes in our code and in our pipelines, and it has to be done every week. It’s similar to maintenance.”
Peddireddy explained that different vaccination rates and levels of herd immunity seen throughout both the state and country cause changes in their calculations.
The U.Va biocomplexity institute has also collaborated with international organizations to share forecasts and projections in an attempt to gain a deeper understanding of how the virus has affected the world.
“Pandemics don't respect national boundaries,” Marathe said. “So it's important to try and understand what's happening with this virus outside the U.S.”
The Biocomplexity Institute is working closely with various international partners to try and discover how the virus has been affecting other countries. For the past two months, the Biocomplexity Institute has been sharing forecasts with the European Center for Disease Control and Prevention, which accounts for most of the European countries. With the recent emergence of the delta variant in India — which spread rapidly throughout the country and has now become the most prominent strain in India and Great Britain — the Institute has also been working closely with the Indian Institute of Science in order to study vaccine allocation and prioritization, as well as help forecast the spread of cases in India.
“You cannot solve real world societal problems just individually,” Marathe said. “You really have to have a team to do it.”