Omicron is now the dominant COVID-19 variant in Miami-Dade, genomic surveillance shows
Omicron has become the dominant strain of the coronavirus circulating in Miami-Dade, overtaking the delta variant in a matter of weeks and becoming the primary driver of new COVID-19 cases in the county, according to new genomic surveillance data released Monday.
Genetic sequencing of the virus in Miami-Dade shows omicron’s rapid growth from a tiny fraction of hundreds of samples tested during the first week of December to nearly three of every four samples monitored last week.
“It is absolutely astonishing how contagious this variant has proven to be,” said Miami-Dade Mayor Daniella Levine Cava, whose office provided the genomic surveillance data.
Major jump in Miami omicron cases, positivity rates in December
The latest report from NOMI Health, the healthcare company contracted by Miami-Dade to conduct testing, vaccination and sequencing in the county, found that 76% of 504 COVID-19 samples taken Dec. 14-15 were the omicron variant — compared to 64% of 378 samples collected Dec. 10-13.
Among the 373 samples collected Dec. 1-5, about 1.3% or 5 omicron cases were detected.
Levine Cava said she also was struck by the spike in Miami-Dade COVID-19 tests coming back positive, now at about 10% versus 1% a month ago, according to county data. Last week, she reinstated in Miami-Dade an order requiring daily bed inventories and COVID patient counts from hospitals across the county.
“It’s definitely here,” Levine Cava said of the omicron variant, “And it’s on us to protect ourselves and still the most important thing we can do is vaccinate.”
Omicron’s prevalence in Miami-Dade was not confirmed by the Florida Department of Health, which conducts genetic sequencing of the coronavirus at state labs and works with federal, local and private groups to collect and analyze genomic surveillance data.
Weesam Khoury, director of communications for the health department, declined to comment Monday on Miami-Dade’s findings.
“It is unfortunate that the county has decided it is more important to share these data with the press rather than coordinating with the Florida Department of Health or Centers for Disease Control and Prevention,” she said. “The Department can only make determinations based on verifiable evidence.
Khoury added that, “It would benefit the state of Florida and the entire scientific community if these local officials uploaded their sequencing data into a transparent and verifiable data base. ... The Department expects to see a rise of the omicron variant in Florida.”
While Florida requires healthcare providers to report all COVID-19 test results, it is not clear what requirements or processes are in place for NOMI Health or Miami-Dade to report the findings of genetic sequencing to the state.
‘I would be concerned about omicron’
The findings from Miami-Dade’s genomic surveillance report track with the results of local genetic sequencing and PCR testing conducted by University of Miami physicians and infectious disease experts.
Dr. David Andrews, an associate professor in the Department of Pathology and Laboratory Medicine at UM’s Miller School of Medicine, is leading the university’s genomic surveillance of COVID-19 in Miami-Dade.
Andrews said that 94% of 70 samples collected and genetically sequenced last week detected the omicron variant. He added that UM also has monitored for the variant using polymerase chain reaction or PCR tests that can detect mutations unique to omicron.
“There’s no question that omicron is dominant in Miami-Dade,” he said.
Andrews said he worried that omicron’s spread could be fueled in part by asymptomatic or mild cases.
“Intuitively, I would be concerned about omicron, just as was the case for delta, because it’s so transmissible that any patient that’s asymptomatic and carrying it is probably going to spread it,” he said. “It’s hard to believe that a virus can arrive and in three to four weeks predominate in a large population.”
Andrews said early indications are that omicron mostly causes mild symptoms in those who are vaccinated and those who have had a prior COVID-19 infection, though he emphasized that there is still a lot to learn about the long-term effects of the disease.
“Where I think there’s an unknown is: What is the array of symptoms and what is the disease it causes in patients who are unvaccinated? ... With this rate of prevalence, we’re going to know pretty soon.”
Omicron’s dominance was not unexpected. The variant’s extensive mutations appear to increase its ability to escape vaccine and natural immunity, according to experts, and many people are relaxing on prevention measures such as masking and social distancing.
“These characteristics can result in a rapid acceleration of cases, especially in the absence of consistent public health messaging and layered approaches to mitigation,” said Jason Salemi, an epidemiologist at the University of South Florida who has tracked the state’s COVID data.
Risk of patient surges at hospitals
But even if omicron causes mild disease, the variant’s increased ability to spread — including among those who are vaccinated or have had the disease before — raises the risk of patient surges and sickened staff at hospitals, said Justin Senior, CEO of the Safety Net Hospital Alliance of Florida, a consortium of public hospital systems.
“It creates a difficult situation,” Senior said. “You have to put a lot of procedures and protocols in place to make sure other patients and your staff don’t get infected.”
Senior said he’s also concerned about the rising number of COVID-19 tests returning positive because that has been a precursor to increased hospital admissions during prior surges. However, he said, it’s too early for Florida hospitals to know what they can expect from omicron.
The rate of vaccination, boosters and prior infections in a community — in addition to the overall age of the population — can have an impact on disease severity, hospitalizations and deaths, he said.
“You prepare for the worst and hope for the best,” he said.
Accounting for 73 percent of new U.S. infections
Omicron was first detected in South Africa in November and has rapidly spread around the globe. The variant is now the dominant version of the coronavirus in the United States, accounting for 73% of all new infections for the week ending Dec. 18 — a nearly six-fold increase in omicron’s share of infections in one week, according to the CDC.
The first cases of omicron in Florida were reported on Dec. 7. Miami-Dade’s mayor confirmed the county’s first case of the variant on Dec. 10. The variant also has been detected in Miami-Dade’s wastewater, though such monitoring does not give public health officials an indication of how prevalent the strain is in the community.
After two months of declining cases in Florida following the summer’s delta variant-fueled surge, cases are rising once again — with Miami-Dade leading all counties in new infections with a case rate of 400 per 100,000 population during the week that ended Dec. 16, according to the Florida Department of Health’s COVID situation report.
South Florida’s three most populous counties saw the largest increase in cases over the prior week — with new infections rising by 322% in Miami-Dade, 213% in Broward and 160% in Palm Beach.
During the first week of December, 22 states — including Florida — reported at least one COVID-19 case attributed to the omicron variant, according to the CDC. Among the 43 U.S. cases with initial follow-up, one hospitalization and no deaths were reported.
On Monday, Miami-Dade hospitals reported 279 inpatients with COVID-19, including 35 in intensive care.
As doctors, scientists, public health officials and hospital administrators keep a close eye on omicron to see how its effects may vary from prior variants, there’s no mystery that vaccines are the most effective way for people to protect themselves from serious illness, hospitalization and death, said Salemi, the USF epidemiologist.
“I would expect cases to continue to rise and an increasing proportion of cases to be based on infection with an omicron lineage,” he said. “How much, where, in whom, and the extent to which this translates into increased hospitalizations and deaths … well, a lot of that depends on how well we utilize the tools we have to fight omicron.”
This story was originally published December 20, 2021 at 9:05 PM.
