USF researchers develop web portals to map COVID-19 by ZIP code, forecast outbreaks

When we think of the scientists leading COVID-19 research, we might imagine a PPE-clad medical researcher bent over her lab instruments -- focused on making sense of coronavirus at the cellular level, in a petri dish. But what if we step away from the microscope; pinch-and-zoom our gaze outward for a bird's eye view of the pandemic in our neighborhood?

What, then, might an anthropologist who specializes in geoscience and archaeology, and a computer whiz with a background in aquatic environmental science bring to the table? In terms of map-minded data sets that flesh out the big picture of COVID-19, it turns out: quite a bit. 

Dr. Lori Collins, Research Associate Professor in Geosciences and Co-Director of the USF Library Digital Heritage and Humanities Collections (DHHC), specializes in landscape preservation and archaeological documentation. Prior to the pandemic, much of her research focused on documenting and preserving Mesoamerican rock art using terrestrial laser scanning applications for archaeological visualization. 

DHHC's GIS Project Manager Ben Mittler worked as a GIS analyst with the Florida Department of Environmental Protection and the Hillsborough County Sheriff's Office before he joined the USF Library team in 2018. He earned his Master of Science in Aquatic Environmental Science from FSU in 2014 and is a Certified Geographic Information Systems (GIS) Professional.

Collins and Mittler are both self-professed map geeks. Early in the pandemic, they discussed how tracking and visualizing the spread of coronavirus in spatial terms, using GIS technology, could help staunch its spread. 

"We were already looking at [COVID-19] when it was still a Wuhan problem. We were seeing what was happening and understanding spatial spreads, and approaching it from that sort of mindset -- so we started, really early on, planning that we've got to get on board with this. We knew it was coming," Collins says.

Mittler helped develop the USF Library Florida COVID-19 Hub, a publicly-accessible web portal that offers real-time COVID-19 GIS data, infection-mapping tools, and statewide coronavirus news. It launched in late March.

"The Florida Department of Health has county-level data they publish. It's just not in a useful spatial format ... We've taken a number of these crucial data sets -- primarily related to pediatrics and in nursing homes -- and turned the paper reports, which publish on a daily or weekly basis, into spatial data sets we can incorporate into our dashboards and hub," Mittler explains.

Florida COVID-19 Hub visitors can access dashboards that track infections statewide daily by ZIP code across a color-coded map of Florida. There's also visual data specific to Florida nursing homes and pediatrics, and a Tampa Bay Area dashboard that curates data localized to the region where USF's three campuses reside.

"I think the spatial aspects we add are critical in communicating with the public. It's much easier for someone to understand a heat map or something that visually shows the impact happening around them -- whereas it might be difficult to look critically at charts and graphs where a person might not understand the math being used," Collins says.

Early in tracking the pandemic, Mittler noted the Department of Health was overwriting its daily data. This is an efficient way to keep Floridians up to speed on the latest infection numbers, but it comes at the expense of providing a more panoramic view of the virus over time, Collins says.

"They're not in the library business like we are -- so they were keeping numbers updated, but not necessarily archiving by day the data sets. But we knew numbers of researchers would need these data to do critical analysis," she explains.

Mittler began graphing cases by day and processing it in a variety of formats available for download. He also created an open archive of the data sets.

"A number of researchers from USF get the data that we're grabbing and they're processing it in a way they can use -- some are coding it spatially; some doing more tabular things like graphs and charts, and more mathematical and statistical processes. That long-term archive is important for researchers as we continue to move forward with the pandemic," Collins says. 

Florida COVID-19 Hub houses critical data for researchers and planning officials

USF's GIS dashboards pull state data from the Florida Department of Health and global data from Johns Hopkins University's global GIS dashboard, but the Florida COVID-19 Hub is unique in its inclusion of maps that are curated for local residents and stakeholders. These include Tampa General Hospital, emergency planning officials, and the USF community.
 
The Florida COVID-19 Hub is unique in its inclusion of maps that are curated for local residents and stakeholders. These include Tampa General Hospital, emergency planning officials, and the USF community.
"When our team started working on this, we wanted to make sure we specifically designed it for USF to be able to manage and understand what was happening on our campuses. [USF has] been noticed as having a really sound decision-making policy around COVID. I like to think our dashboard has played a big role in helping our leadership understand what's happening," Collins says.

"To me, this ZIP code feature Ben created is so powerful for the decision-makers talking about mask mandates and making policy decisions. This gives them real, tangible data to look at, in a very simple way, to understand what's happening around them," she adds.

The Florida COVID-19 Hub is tweaked to harness data the USF research community and its partners at Tampa General Hospital can apply to their own research. USF studies applying Mittler's spatial data sets range from policy-shaping research in the College of Public Health to mathematical applications in the Muma College of Business. 

"Looking at space-based imagery to use automated processes for counting cars in parking lots, for instance, is an easy way we can calculate impacts to businesses and critical infrastructure. These might not be our direct area of interest, but we can support all these diverse areas of interest," Collins says.

USF Library, College of Public Health collaborate on a COVID-19 forecasting model

Dr. Collins and epidemiologist, Dr. Edwin Michael, are co-investigators on a College of Public Health project called "COVID-19 Integrated Contagion Modeling for Community Policy and Governance." Distinguished USF Health Professor Dr. Thomas Unnasch is the principal investigator. The project is funded in part by the latest round of USF's COVID-19 Rapid Response Grant. 

The project seeks to establish a mathematical model that can predict the course of COVID-19 outbreaks across communities. In his role, Dr. Michael, who specializes in the spread and control of infectious tropical diseases using computational approaches, was tasked to create a tool for community planning officials who seek to stay one step ahead of the virus. Florida Blue is a funding partner.

Dr. Michael created SEIRcast, a dashboard that produces simulations and predictions about the epidemic at the population level; for instance, by ZIP code. SEIRcast feeds a variety of data through its agent-based model to create predictions that, Michael says, are "as close as possible to realism" regarding the possibility of coronavirus' spread throughout a population.

Much of SEIRcast's statistical data comes from the USF Library GIS dashboard, which lends the clarity of its spatial modeling approach and archive of the virus' progression across Florida since March. SEIRcast also pulls from population-level and policy data. It asks: how many schools are in a ZIP code; how many households and workplaces? Where are college dorms located, and nursing homes, and entertainment centers where the public gathers -- like sports arenas? 

"These are complex systems that become alive because they're interacting. … [SEIRcast] is a dynamic mathematical model, as opposed to a statistical model like GIS, which is very static," Michael says.

"We need to know where are the susceptibles and infected cases, so they bring in the data and locate it on a GIS -- onto locations -- which will be the foundation for our work. The [USF Library GIS system] does the heavy lifting for [SEIRcast]," he explains.

SEIRcast simulations combine this spatial COVID case data with policy and population data, and, after feeding these data into its system, the model calculates spatial risk factors, social contact networks, social behavior, and host mobility to predict how and where the virus could spread.

"Once we have a population located on the GIS map, we can introduce infections … How will disease spread if a random infected person enters the population?’’ Michael explains. "You can also get archival data if you trace back to early March. Then you can see that, 'in this spot the first cluster took place.' You can look at that, and given people's movements, where they are meeting other people, it helps predict which are the areas that will become a problem?"

Michael says in some ways, SEIRcast resembles another forecasting model Floridians know well: hurricane forecasting. Like weather models, COVID conditions can change by the day, making the predictions hazier the further out the forecast. Still, Michael says -- staying ahead of the virus matters -- especially as the scientists who are hunched over Petri dishes race toward a vaccine.

"Where are the most vulnerable populations? If you don't control it there, what's going to happen? The idea [with SEIRcast] is to be able to go to whoever holds the purse strings and say, 'if we don't stop it in those sections, it'll lead to an even larger problem,'" Michael says.

Could support from social sciences solve a pandemic? 

"The time crunch is the biggest challenge," Michael says, as the global COVID-19 timeline creeps up on one year.

"SEIRcast is up and running and now vaccines are coming, so there's pressure on us to give the first simulations. Everybody wants answers yesterday. It also means, in terms of science, that we're pushing ahead so fast we're not paying attention to the uncertainties in what we're doing. We have no time to sit down and reflect. And that's how we get smacked in the face."

Dr. Michael reports his SEIRcast work to the CDC, which he says is building a repository of models like his own "so that when the next epidemic comes, we have the modeling to get us up to speed quickly.

"But the problem in dealing with pandemics like they're a biomedical problem is that it's like putting on a bandaid. The bigger issues below that are things like: how do we treat the natural environment? Animal husbandry? How we do trade? And we need to make changes there," Michael says.

To accomplish those changes -- and to be prepared for the next pandemic, which the epidemiologist assures is inevitable, Dr. Michael says: bring in the social sciences.

"[COVID-19] has shown that it's not just epidemiology we need. We need to bring in social scientists. Many epidemiologists don't know the history of pandemics like the Spanish Flu. Where are the historians? The response to pandemics varies between countries. So, why did Asian countries do better? Is it their population? Is it governance? 

"This needs to cut across into sociology, into management, into governance -- because [pandemic preparedness] is a bigger problem" than biomedical science can solve on its own, Michael says.

That's where the librarians -- and the anthropologists and the environmentalists and historians; the spatial map geeks like Collins and Mittler with their diverse backgrounds, and their unique perspectives as digital archivists -- are as indispensable in the fight to stamp out the pandemic as their lab coat-clad colleagues in the medical STEM disciplines.

"At USF, we're looking to create new courses as we move forward in generating the next generation of students in public health -- students who can deal with this broad-spectrum view of global health also incorporating social sciences. There are things I think need to change -- and that change is coming. I do have hope," Michael says.

Links:
  1. USF Library Digital Heritage and Humanities Collections
  2. Florida COVID-19 Hub
  3. USF College of Public Health
  4. SEIRcast
     

Read more articles by Jessi Smith.

Jessi Smith (she/they) is a freelance writer who is passionate about sustainability, community building, and the power of the arts and transformative storytelling. A fourth-generation Floridian, Jessi received her B.A. in Art History and English from Florida International University and began reporting for 83 Degrees in 2009. When she isn't writing, Jessi enjoys taking her deaf rescue dog on outdoors adventures, unearthing treasures in backroads antiques and thrift shops, D.I.Y. upcycling projects, and Florida-friendly gardening.
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