Florida researchers begin using AI to predict COVID waves

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New cases of COVID are on the rise again in Florida, raising fears that the state will be hit by a winter wave like the last two years.

Previously, cases spiked right after Thanksgiving and peaked in mid-January.

Now, Florida researchers believe they can get ahead of the COVID waves by building an algorithm that detects new variants of the concern before it spreads.

“Imagine getting 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 vast amounts of data that are not easily discernible to a human observer.”

The researchers draw on 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 computer instructions or rules—that would comb the data and find new variants that pose a threat.

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

No one knows which variant or variants will be circulating at high levels this fall and winter. But most experts agree that the soup of emerging variants will strengthen for several rough months ahead.

Some strains are already increasing in prevalence and are evading part of the infection or vaccine-induced immunity. UF scientists want to be able to predict in advance whether they will be as deadly or transmissible as delta or omicron.

Salemi is an expert on the molecular evolution of viruses and works with Mattia Prosperi, a UF professor with expertise in the application of artificial intelligence to public health issues. Their work could create a tool that would highlight a potential new variant of concern by uploading to public databases.

“The value of using artificial intelligence and machine learning is that the algorithm can constantly evolve to make even better predictions,” he said.

Salemi explained that while the coronavirus will continue to mutate, only a limited number of combinations can turn the virus into a variant that causes concern. While UF researchers have a prototype algorithm ready to run this winter, it may take some time to perfect, he said.

Right now, strains 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 continues 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’s one of two omicron strains targeted by new COVID boosters made by Pfizer and Moderna approved in September and recently approved for children over 5 years of age.

Now other strains such as BQ.1, BQ.1.1, BF.7, BA.4.6, BA.2.75, BA.2.75.2 are gaining ground in the USA. Some experts believe that several different lineages could end up circulating instead of one becoming dominant as it has in the past.

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“Projections vary a little bit, but generally most people feel somewhere around mid-November they’ll end up being a substantial part and they’ve eliminated BA.5 as the dominant option,” Fauci told CNN.

“They all have similar ways of escaping immunity,” said JT McCrone, senior infectious disease scientist at Helix, which conducts surveillance using positive COVID samples.

Updated COVID booster vaccines and antiviral drugs such as Paxlovid will likely continue to protect against serious consequences caused by the new variants. However, there was poor uptake of boosters both nationally and in Florida.

McCrone noted that relying on previous infection may not be enough for these new strains. The waning immunity of people who have previously been infected with COVID makes it highly likely that there will be an increase in cases in the coming months, he said.

Several European countries are already beginning to see an upward trend in cases, and some Northeastern states in the US have seen increases in sewage. In Florida, levels of COVID monitored in wastewater in several counties across the state have increased slightly over the past few weeks. Still, for now, Miami-Dade, Broward and Palm Beach counties remain at low risk for COVID-19, even as the state continues to report new deaths from the disease.

“Influenza has started to increase and COVID should soon follow,” McCrone said. “How big a wave and how much these variants will contribute, we don’t know.”

Sun Sentinel health reporter Cindy Goodman can be reached at [email protected]

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