Efforts ramp up to detect COVID-19 variants
Patchwork system has some states aggressively seek variants while others lag behind
The nation dramatically stepped up its surveillance for coronavirus variants in recent weeks, but experts say there’s much further to go if the Washington region - and the rest of the country - wants to stay ahead of new and potentially dangerous versions of the virus.
Conducting the genetic sequencing to detect for variants is far more expensive, time-consuming and sophisticated than testing whether people have contracted the coronavirus, leading to a patchwork system where some states aggressively seek out variants and others lag behind.
“There are definitely states where they really champion this,” said Duncan MacCannell, chief science officer for the Centers for Disease Control and Prevention’s Office of Advanced Molecular Detection. “But, you know, there’s also a lot of blanks (on the map), dark spots, places where we just don’t have regular sequence data.”
In the D.C. region, Maryland
stands out for dramatically enhancing its search for variants, attempting to more than double its output and detect new versions as they emerge. Nationwide, sequencing volume has tripled since early February, but the country had been so far behind in its efforts that CDC and public health experts say nearly all states still need far more sequencing to create an accurate picture of variants already circulating.
The uneven information about variants circulating in the country comes as states race to vaccinate residents ahead of a potential fourth surge in cases fueled by more contagious and potentially more deadly variants. The Biden administration has put nearly $2 billion into helping the CDC ramp up variant surveillance efforts nationwide, including $1.75 billion included in the rescue package Congress passed last month.
MacCannell’s division leads the consortium to coordinate the country’s knowledge about variants, as well as recruits private labsand universities to surveil for them. Part of the challenge, he said, is that not all public health labs have the expertise to decode the genetic sequences deposited into the national database and then connect it to a community outbreak.
“Ironically, last year, we actually planned to roll out enhanced training for molecular skills for state and local public health departments, epidemiologists,” MacCannell said. “But that was somewhat derailed by the pandemic response.”
Public health experts and epidemiologists hope the nation’s growing system can quickly spot emerging variants before they gain a dangerous foothold.
“We’re making great progress. I still don’t think we are where we where we want to be or need to be,” Janet Hamilton, executive director of the Council of State and Territorial Epidemiologists, said in interview late last month. “We still have quite a few gaps in how the data is shared and how rapidly it’s shared. We still have labs that are conducting sequencing, and their data is not necessarily incorporated as part of the national picture.”
Maryland has had a sluggish start compared to West Coast states like California and Washington, where private labs and universities conducted surveillance since near the beginning of the pandemic.
But in March, after the federal government began sending states cash to help sequencing efforts, Republican Gov. Larry Hogan set a goal to sequence 10 percent of all positive coronavirus tests moving forward, a threshold some experts say is critical to detect both newly emerging variants and those known to be concerning.
Some states, such as Oklahoma and South Dakota, have sequenced less than 0.25 percent of their state’s positive tests since the pandemic began, according to CDC data. In places with low rates,those efforts are largely done by private commercial companies such as Quest Diagnostics and LabCorp that have contracts with CDC to do 6,000 sequences a week nationwide.
The best performing states, including Washington and Maine, have done more than 3 percent of their positive cases since January 2020. Virginia has done 0.88 percent and Maryland has done 1.46 percent, while D.C. data is not available.
While it takes a few hours for a well-trained lab technician to determine if a sample has the virus, sequencing that same sample calls for more sophisticated machinery and a highly trained scientist to then make sense of the virus’s genetic sequence, which is 30,000 nucleotides long. Sequencing work takes days, and Maryland has built a multipart operation involving a mix of university, public health and private labs to get enough samples screened.
A year ago, the genomics lab at the University of Maryland School of Medicine could have started sequencing coronavirus samples and searching for variants on a significant scale, if only there had been the money to launch it.
“Because of the lack of funding, because it’s not a very cheap enterprise to stand up, we basically never pursued it,” said Jacques Ravel, associate director of the school’s Institute for Genome Sciences. “There was no major interest in doing sequencing, unfortunately.”
Now that variants have spread widely and sparked deep concern about prolonging the pandemic, Ravel’s operation is in high output helping Maryland join the many states dramatically ramping up the search for versions of the virus that could spread faster, make people sicker or evade the vaccines designed to immobilize it.
Some of the state’s preliminary data, particularly around the variant first identified in the United Kingdom, is concerning.
The CDC announced last week the more transmissible and potentially more lethal variant had become the most prevalent version of the coronavirus in the United States. While it is less widespread in Maryland, D.C. or Virginia than in places such as Michigan, Maryland’s robust surveillance program shows it’s quickly on the rise: Two weeks ago, about a quarter of the 200 samples tested weekly in Ravell’s lab had the variant. As of Friday, the latest data showed it had risen to 38 percent overall, with as much as 60 percent of positive samples from a community testing site in Baltimore City, where the coronavirus case rate has risen sharply in recent weeks.
That threshold is potentially alarming.
“What we what we know from the experience of half a dozen countries - the first wave of countries that were really hit by the British variant - is that when the variant passed 50 percent of the variants being sampled, it really took off,” said Jonathan “Jono” Quick, a public health doctor with the Rockefeller Foundation and author of ‘The End of Epidemics.”
“The thing is, you don’t get a do over,” Quick said. “You can’t catch up. I mean, once you get a surge start happening, then it takes a herculean effort to turn it around.”