Just as the Covid-19 pandemic seemed to be well on its way to being vanquished, the “delta” variant of the coronavirus threatens to fuel a new surge. So far, 51 cases have been detected in Georgia—more than one in 10 samples tested from mid-May to mid-June. It may not sound like much, but experts say that is just a signal of what’s yet to come. Nationally, the delta variant dominates and, combined with the aftermath of July 4th get-togethers and lagging vaccination rates, is fueling a rise in Covid-19 cases across the nation for the first time in months.
Where this more transmissible version of the coronavirus is emerging in Georgia and how rapidly it is spreading remains unclear due to a lag in genomic surveillance and gaps in sampling. The state is working to ramp up its capacity to sequence the viral DNA that shows how the virus is mutating.
The Georgia Department of Public Health has been sending specimens to the Centers for Disease Control and Prevention for that testing, but a recent infusion of federal money will boost the state’s in-house capability. Genomic surveillance is the reconnaissance that detects which versions of the virus are causing the most infections.
Recent trends in states like Missouri show why variants matter. Delta-linked cases triggered a rise in hospital admissions in rural Missouri counties where residents shunned vaccination. Although there have been some “breakthrough” infections among people who are vaccinated, so far the Covid vaccines have been protective against the delta variant.
“The reality is, [people] either get the vaccine or [they’re] going to be getting Covid. That’s how transmissible the delta variant is,” says Amber Schmidtke, an epidemiologist and science communicator who has been tracking the pandemic in Georgia.
In Georgia, Chattahoochee County has the lowest vaccination rate in the state. Just 15 percent of residents in the sparsely populated county on the Alabama border near Columbus have received even one dose. For the past two weeks, the county has had the highest rate of new cases.
About 28 percent of Covid-19 PCR tests in Wheeler County in southeast Georgia came back positive in the past two weeks; the county has vaccinated just 19 percent of residents with a least one dose.
The search for specimens
This may sound like someone else’s problem, but variants have an opportunity to take hold where vaccination is low—and then spread elsewhere. “You want to make sure you’re doing really good genomic surveillance in areas with low vaccination rates,” says Schmidtke.
Yet getting those samples can be difficult in places that have strained health care resources. Eight hospitals have closed in rural Georgia since 2010.
The Georgia Public Health Laboratory has the capacity to sequence about 196 specimens each week from positive PCR tests for SARS-CoV-2. The specimens must meet certain requirements—most rapid (antigen) tests don’t qualify—and the labs don’t (or can’t) always store test samples for future DPH lab use, as requested, DPH epidemiologists said in an emailed response to Atlanta.
“The greatest challenge we have now is access to quality samples for sequencing,” the officials said. The agency “attempts to sequence 100 percent of positive specimens tested at the state laboratory that meet the quality standards.”
Even when samples are available, there’s a time lag before the results can be analyzed and reported. “[Variants] are almost certainly here before we’re really aware of them,” says Anne Piantadosi, an infectious disease physician whose Emory lab has been analyzing about 40 samples every two weeks. Those samples come from Emory Health Care and Grady Health System patients.
“In your mind, you can think of us as two or four weeks behind,” she says. “We should be thinking or planning or acting as if [variants] are already here.”
Is the delta variant in your neighborhood?
Ultimately, Covid risk is local—your likelihood of encountering someone who is infected while you’re in line at the grocery store or sitting at an indoor restaurant. “I tend to think people will take appropriate precautions if they understand what the risk is,” says Sam Scarpino, a biomathematician and director of the Emergent Epidemics Lab at Northeastern University in Boston. “The problem in the U.S. is that we haven’t done a good job of communicating what the risk is in your neighborhood.”
Genomic surveillance isn’t available at that granular level, but county health departments provide weekly reports that include maps of Covid cases by zip code. Overall, cases in metro Atlanta are down, as rates of vaccination (about 50 percent with at least one dose) are higher in metro counties than the state average (44 percent).
But there are pockets of vulnerability. In Fulton County, for example, 43 percent of the Covid cases reported in June were among young adults ages 20 to 39, and 61 percent were among Black residents—both demographics that have lower vaccination rates. The city of Atlanta had more cases than North or South Fulton, and the city of East Point had the highest rate of recent cases (measured in the last two weeks of June). In Cobb County, the Powder Springs area overall has had the highest number of cases.
Once a variant has been identified, specific PCR tests can be developed to look for it. Viruses naturally evolve through mutations, and genomic sequencing is the only way to discover that a new mutation has taken hold.
“In some ways, we’re only as strong as the weakest link when it comes to surveillance systems,” Scarpino says. “That means places without adequate genomic surveillance are creating gaps in our understanding of what’s going on.”
Are you protected against the delta variant?
At Emory, virologist Mehul Suthar is studying how strongly the immune system reacts to the Delta variant after vaccination. “One of the puzzles that needs to be unlocked is the durability of the antibody response—how well these vaccines still work six months to a year after vaccination,” he says.
One study, published in a “pre-print” or pre-publication form in May in a collaboration between Emory researchers and the National Institute of Allergy and Infectious Diseases, looked at five variants, which were first identified in the United Kingdom, South Africa, Brazil, California, and New York. The variant from Brazil (B.1.351, or beta) was the most successful at evading antibodies, but two doses of the Moderna vaccine still produced a “robust” response, the study authors concluded.
The beta variant did not become dominant in the United States; some mutations help the virus persist but others affect how easily it spreads, Suthar explains. If a variant emerges that spreads easily and also evades vaccine antibodies, then booster doses might become necessary, he says.
“Knowledge is power. Knowing where this virus is and how it’s spreading is critical to being able to develop a better plan of action,” Suthar says.
With $6.7 million from the American Rescue Plan for genomic surveillance, the Georgia Department of Public Health is beefing up its staff. “Genomic sequencing and molecular surveillance are the future of public health, and DPH and [the Georgia Public Health Laboratory] are dedicated to improving our capacity and understanding of pathogens impacting our community,” the state epidemiologists said.
Finding a path out of the pandemic depends on it.