The Perfect Enemy | Florida researchers start to use AI to predict COVID waves

New COVID cases are picking up again in Florida, triggering concern the state will get hit with a winter wave like it has the last two years.

Previously, cases picked up right after Thanksgiving and surged to a peak in mid-January.

Now, Florida researchers believe they can get ahead of COVID waves by building an algorithm to spot new variants of concern before they spread.

“Imagine if we could get ahead of the curve,” said Marco Salemi, a professor of experimental pathology at the University of Florida. “Using artificial intelligence, we can learn patterns from a massive amount of data that are not easily distinguishable to the human observer.”

The researchers are taking publicly available information from a global database where scientists upload the sequences of the COVID virus from positive test samples. Their goal is to design an algorithm — a set of computerized instructions or rules — that would comb the data and find new variants that pose a threat.

“It could tell us if a variant has potential to be highly transmissible or pathogenic and give us some warning before the variant starts spreading on large scale,” Salemi said.

[ No one knows which variant, or multiple variants, will circulate at high levels this fall and winter. But most experts agree that the soup of emerging variants will fuel a rough few months ahead.

Some of the strains already are increasing in prevalence, evading some of the infection or vaccine-induced immunity. UF researchers want to be able to predict in advance if they will be as deadly or as transmissible as delta or omicron.

Salemi is an expert in the molecular evolution of viruses, and he is working with Mattia Prosperi, a UF professor who has expertise in applying AI to public health issues. Their work could produce a tool that would raise a red flag when a potential new variant of concern is uploaded to public databases.

“The value of using AI and machine learning is the algorithm can keep evolving to make even better predictions,” he said.

[ Salemi explained that while coronavirus will continue to mutate, only a limited number of combinations can make a virus a variant of concern. While the UF researchers have a prototype algorithm ready to go this winter, it may take a while to refine, he said.

Right now, strains that are circulating in the United States and Florida fall under the omicron umbrella.

“They seem to be less aggressive in terms of disease than the original omicron we saw last year,” Salemi said. “Whether this trend will continue and COVID becomes one of those benign viruses remains to be seen.”

The omicron subvariant BA.5 still holds the top spot in the US. It is one of the two omicron strains targeted by the new COVID boosters manufactured by Pfizer and Moderna authorized in September and recently approved for children over 5 years old.

Now, other strains such as BQ.1, BQ.1.1, BF.7, BA.4.6, BA.2.75, BA.2.75.2 are gaining traction in the U.S. Some experts believe several different lineages could end up circulating rather than one becoming dominant as has happened in the past.

Florida researchers start to use AI to predict COVID waves

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“The projections vary a little, but generally, most people feel somewhere in the middle of November that they’ll wind up being a substantial proportion and have bumped BA.5 off as the dominant variant,” Fauci told CNN.

[ “They all have similar ways to evade immunity,” said JT McCrone, a senior scientist for infectious diseases with Helix, which conducts surveillance using positive COVID test samples.

The updated COVID booster vaccines and antiviral drugs like Paxlovid likely will continue to protect against severe outcomes caused by the new variants. However, there has been poor uptake of the boosters both nationally and in Florida.

McCrone noted that relying on a previous infection may not be enough with these new strains. Waning immunity in people previously infected with COVID makes it highly likely that there will be a increase in cases in coming months, he said.

[ Several European countries are already starting to see cases trend back up, and some of the northeastern states in the U.S. have had an uptick in their wastewater results. In Florida, COVID levels tracked in wastewater in several counties throughout the state have risen slightly in the last few weeks. Still, at this time, Miami-Dade, Broward, and Palm Beach counties remained at a low COVID-19 risk level, even as the state continues to report new deaths from the disease.

“The increase in flu has begun and COVID should follow shortly,” McCrone said. “How large a wave and how much these variants will contribute, we don’t know.”

Sun Sentinel health reporter Cindy Goodman can be reached at cgoodman@sunsentinel.com.