Two years into the pandemic, Florida’s monitoring system for COVID has left the public blind to the arrival of highly contagious variants.
Florida sends only a tiny fraction of all positive COVID tests to labs for genetic sequencing to learn their strain of coronavirus — only 1% over the entire pandemic.
Some states, such as Washington, are sequencing up to 20% of all cases. With so few samples sequenced in Florida, health officials lack the ability to track variants and their prevalence across the state until cases surge.
The delta wave showed just how vulnerable Florida is to mutations that arrive undetected. Floridians learned of the first confirmed case of delta in the state in mid-June when the new variant was reported on a federal COVID tracker. By then, the number of cases had begun to soar, followed by hospitalizations, and then record deaths.
“What we have in Florida is inadequate,” said Dr. Glenn Morris, director of the Emerging Pathogens Institute at the University of Florida. “What we really need is a system that looks at selected strains across the state, does sequencing and puts it in a model to understand what strains are present and how they may be moving throughout different parts of the state.”
While hospitals, universities, public and private health labs sequence samples from patients to learn which variants are present, Florida lacks a comprehensive and cohesive system to analyze and share data. The Florida Department of Health documents the number of COVID cases, vaccinations and deaths weekly on its website, but does not publicly release the variants identified in the state or their proportion.
Scientists say sequencing alone won’t stop the arrival or spread of more variants, but better detection and communication would give Florida’s counties a chance to act as highly infectious strains becomes more prevalent.
Even now, as Florida emerges from the omicron wave, infections aren’t falling as fast as experts had forecasted. Could a subvariant known as “stealth omicron,” or BA.2, be spreading far more widely than detected? Florida so far has recorded 15 cases of the BA.2 omicron variant. Given how quickly the new subvariant has spread elsewhere, researchers believe it likely accounts for more.
BA.2 “probably was first introduced in Florida in early January, so it’s been here about a month,” said Thomas Hladish, a research scientist at the University of Florida. “Florida has always had problems with detection. Our surveillance system in Florida is not good.
“My spitball estimate: I would guess 50% of cases now are BA.2 or something on that order.”
With infection numbers still hovering around 10,000 a day in Florida, COVID-19 will continue to sicken more people and strain health care resources for longer than expected.
Morris said the best example of the need for early detection of new variants is what happened with monoclonal antibodies, the COVID treatment Florida’s governor has promoted during the past few months.
As the new omicron wave of COVID swept across Florida, clinics continued to use two monoclonal-antibodies treatments that worked against delta, including one made by Regeneron. Federal health officials warned those two treatments did not work against omicron.
“What we needed to know is where omicron was and in what areas it would still make sense to be using Regeneron and in which sections of the state it didn’t make sense at all,” Morris said. “When the state was transitioning from one variant to another that was the point where it would have been useful to know.”
Researchers are asking for better surveillance not just in Florida but throughout the United States, concerned because the coronavirus, like all viruses, mutates as it moves through large groups of people.
If a new highly contagious mutation emerges like omicron did in South Africa, it could move through the population quickly, causing harm before detected.
Dr. Jason Lane, chief medical officer for ChenMed, primary medical care centers for seniors, worries about that scenario. “If a variant is homegrown and turns out as devastating as delta, or evolves in the U.S. and we miss it, that’s what worries me about our deficiencies. Hopefully, there is a lot being done to beef it up.”
When asked if Florida has made any advancements in surveillance of variants or has improvements underway, Department of Health spokesman Jeremy Redfern responded:
“The Department of Health operates three laboratories capable of genomic sequencing, but our labs are just part of a larger picture. We work alongside multiple partners, like laboratories contracted by the Centers for Disease Control and Prevention (CDC) and academic institutions, that are capable of genomic sequencing. The CDC is the primary agency for all public health-related genomic surveillance in the United States. It is best to think of Florida as a puzzle piece that is part of the overall surveillance puzzle.”
The private sector jumps in
Seeing a need for real-time data, Walgreens has launched its own COVID-19 Index for the public to help identify the spread of virus variants across the U.S.
Its monitoring index will be updated using PCR tests administered by Walgreens and analyzed by its laboratory testing partner, Aegis Sciences.
The PCR tests come from patients at 5,000 Walgreens pharmacies, including 800 in Florida. The drugstore has one of the largest databases of COVID samples in the country.
Walgreens Chief Medical Officer Dr. Kevin Ball said Aegis is able to identify whether a sample is omicron in 24 hours. The Walgreens COVID-19 tracker shows 100% of its COVID samples in Florida are omicron.
Ball said the scope and timeliness of Walgreens’ national surveillance system should help catch future variants early and curb their spread. Eventually, he would like the tracker to reflect the makeup of cases within communities as well as provide a statewide overview.
“We would like to get to the geo-level. This is a process we are trying to get towards so we can identify an outbreak as it is occurring, what variant is driving it and offer guidance on what to do in those moments,” he said.
Florida’s universities and hospitals also are sequencing positive test samples, mostly to learn what strains are appearing in students or patients.
And while anyone who does sequencing reports findings into a global database, Florida lacks an infrastructure to extract and share that same data on a statewide scale — to catch a new variant early on.
“What one needs is to look statewide and get a sense of patterns emerging at a statewide level,” said Morris at UF. “We have the capacity to sequence and we have utilized it, but we are limited. We are looking at samples from within Alachua County primarily. We don’t know exactly what’s going on in other parts of Florida so we can’t create a unified picture of what’s happening.”
Morris said UF and other universities have specialized researchers who could interpret the data and detect mutation strains within the state. Having this information could guide public health response, he said. “There is not a statewide system in Florida which has fully pulled in the capacity present in the state.”
Wastewater may be the answer
Wastewater monitoring could be the way to find rapidly spreading variants faster.
Wastewater monitoring has been used during the omicron surge by scientists in New York City, Boston and Miami and at universities such as the University of Miami to identify surges of cases in certain neighborhoods or dorms even before a variant has been identified from test swabs.
People infected with the coronavirus shed it in their feces so a high level may show that a variant is at work, warranting a closer look.
In Florida, only Pinellas and Brevard counties participate in the CDC’s national wastewater surveillance and show COVID in 100% of their water samples submitted. Some states, such as North Carolina, have half their counties, or more, participating. The CDC dashboard provides a color-coded view of virus levels in wastewater in participating communities.
Miami-Dade does its own wastewater surveillance and updates a county website weekly.
Already, the monitoring has proved useful, said Raghavender Joshi, assistant director of wastewater operations for Miami-Dade Water & Sewer. When the wastewater showed a spike in cases in December, the findings gave the county hospitals a few extra days to prepare for the omicron surge.
Biobot, which does the sequencing and analysis of the sewage for Miami-Dade and counties in 35 states, said one county in Delaware used sewage analysis to more strategically place mobile testing centers and another in Massachusetts used the information to guide its schools’ policies.
CDC spokesman Brian Katzowitz said the agency is adding 400 new sites to the national wastewater surveillance system in the coming weeks and it is possible some will be in Florida.
