As the COVID delta variant spreads, do NJ labs have enough capacity to track it?
Dr. Barry Kreiswirth, research scientist for Hackensack Meridian Health system, explains on May 10, 2021 about lab work on COVID-19 variants in Nutley. NorthJersey.com
When the alpha variant of COVID-19 was found in New Jersey over the winter, state officials had little sense of its prevalence, which communities were being hit hardest and how rapidly it was transmitting — until cases and hospitalizations began to shoot up in March.
Now, as the highly contagious delta variant spreads through New Jersey, the state Health Department says it has improved its ability to track mutations and is no longer flying as blind as it was six months ago.
But is that enough to get an accurate picture of the delta variant's prevalence?
Laboratories in New Jersey have been sampling about 10% of all positive coronavirus tests in recent weeks to conduct complex, labor-intensive genomic sequencing that determines which variants are present in the samples.
“We believe that we are currently sequencing enough specimens to identify trends in variants and make reasonable estimates as to their prevalence,” said Nancy Kearney, a state Health Department spokeswoman.
Viruses are constantly mutating as they replicate from host to host. Most mutations are short-lived, but some become more robust strains that can react differently and be more contagious, more deadly and possibly resistant to treatment or vaccines. In preliminary studies in Britain, where delta is the dominant variant among new COVID cases, the variant is more transmissible but not significantly deadlier or resistant to vaccines.
The accuracy of the state's monitoring program is extremely important.
The reports show that delta's presence has increased significantly since it was first detected on May 22. At the time, it made up only 3.1% of variants. By June 19 — the latest date for which sequencing data is available — it represented 26.8% of new COVID cases. At that rate, delta is due to overtake the alpha variant as the most dominant strain by early July.
Understanding the prevalence of variants plays an important role in treating those infected, almost all of whom are unvaccinated in New Jersey these days.
Some variants put up a better fight against certain antibody cocktails over others, said David Perlin, chief scientific officer for Hackensack Meridian Health.
"It comes down to what kind of treatment a physician will choose based on what we're sequencing at the time," he said.
Helping those efforts is increased sequencing capacity at the state lab in Ewing. In addition, the state Health Department has formed partnerships with more commercial and academic labs in recent months, Kearney said.
In the latest round of testing, 545 samples were sequenced at the state laboratory and four private labs out of 5,609 positive test samples recorded over a four-week period from May 22 to June 19.
That 9.7% rate is an improvement from late February, when New Jersey had sequenced only 171 samples, less than 1% of the more than 96,000 positive COVID tests since the state's first confirmed case of the alpha variant on Jan. 22.
By early April, the number of positive COVID tests sequenced had doubled to 2%, with state officials vowing expansion. At 10%, the state should more confidently be able to project what is happening statewide, although there are regional pockets where the dominant variant may not be as prevalent, said Perlin, of Hackensack Meridian.
"Sequencing 10% statistically can give you a pretty good representation of what's out there," said Perlin, whose Nutley laboratory is seeing a rise in delta similar to what the state is reporting.
Sequencing has improved in some states over the past several months due to increased federal funding from the Centers for Disease Control and Prevention and the National Institutes of Health, said Edwin Oh, an expert in genomics and infectious diseases at the University of Nevada, Las Vegas, School of Medicine.
But it's still not where it needs to be on a national scale, Oh said.
"I do believe we are truly flying blind with regard to the surveillance of old, new and emerging variants," he said. "This is because we, as a country, have only started sequencing genomes across all states."
While sequencing is more robust in New Jersey, it still needs to be expanded because the virus is constantly mutating, said Keith Bostian, dean at Kean University’s Center for Science, Technology and Mathematics.
“Changes in viral strains can happen very quickly, on the order of two to four months,” said Bostian, who has been trying to partner his laboratory with the Health Department for months, to no avail. “The number of positive samples is low enough so that now it may be possible to detect the expansion of delta and other new variants more effectively.”
COVID delta variant growing in New Jersey
Test samples compiled over four weeks show how much the delta variant is increasing in proportion to all strains of COVID-19.
- June 19: 26.8%
- June 12: 15.6%
- June 5: 7.3%
- May 29: 5.1%
- May 22: 3.1%
Scott Fallon covers the environment for NorthJersey.com. To get unlimited access to the latest news about how New Jersey’s environment affects your health and well-being, please subscribe or activate your digital account today.