South Carolina’s hunt for more contagious variants of the coronavirus faces a problem of simple math: It’s not testing many people for them.
Every week, South Carolina is running more than 100,000 tests for the coronavirus and identifying more than 20,000 people infected. And it’s analyzing the genetic material of only a few dozen virus samples to look for new versions of the germ, including variants that spread more readily.
The S.C. Department of Health and Environmental Control says it is currently sequencing the genetic material of 24 samples each week. And it sends another 10 samples to the U.S. Centers for Disease Control and Prevention every other week.
This is a key moment for the state’s virus surveillance effort as new, more transmissible variants begin to spread throughout the United States. Federal authorities say the B117 variant, which was first found in the United Kingdom, has been identified in seven states, including Georgia and Florida.
They have not yet been found in South Carolina, but experts suspect they could already be here. The true extent of their spread is a mystery because the U.S. sequences the genetic material of relatively few virus samples to look for changes in their makeup.
At the current rate in South Carolina, scientists are analyzing the genomes of about 1 of every 1,000 known cases of COVID-19, the disease caused by the virus. If the B117 variant is among the other 999, it will go undetected.
“I’m certain we have them,” said Dr. Helmut Albrecht, director of the University of South Carolina’s Center for Infectious Disease Research and Policy.
Tracking the virus's evolution is more than a mere curiosity, especially now. The emergence of a more transmissible version would be devastating since the nation's hospitals are already filled with a record number of coronavirus patients. And mutations could eventually threaten the effectiveness of COVID-19 vaccines.
DHEC says it began sequencing virus samples in-house in June, using equipment that reads the virus’s genetic code and converts it into a long string of letters. Each virus is represented by nearly 30,000 As, Ts, Cs and Gs — the pieces that tell cells how to make new copies. With enough samples, scientists can track how the virus is changing, and they can study how it spread from place to place.
USC researchers, for instance, have used the information to track an outbreak on a military base back to a single dinner, Albrecht said. And in Louisiana, which has the highest sequencing rate in the Southeast, researchers at Louisiana State University’s Health Sciences Center in Shreveport have enough data that they can see how the virus spreads from town to town — how an outbreak in one place triggers problems in another.
The information can even reveal how well facilities like nursing homes are protecting their residents from the virus, said Dr. Jeremy Kamil, who leads LSU Health Shreveport’s sequencing effort. If infected residents have the same version of the virus, the outbreak may have begun with a one-time mistake. If they have many different versions, the virus was introduced multiple times.
Researchers say it’s little surprise that the B117 variant was detected in the United Kingdom because that country has a coordinated effort to sequence virus samples en masse.
The extent of its efforts is made clear by the number of contributions the U.K. has made to a global database of coronavirus genomes run by the GISAID Initiative, a nonprofit that fosters data-sharing among virus researchers. The database stores more than 360,000 coronavirus sequences, enabling scientists to study the outbreak's evolution around the world.
The U.K. has published about 49 genome sequences for every 1,000 known COVID cases there. In the U.S., the state with the best rate, Hawaii, has published more than 28 for every 1,000 cases among its residents.
South Carolina, for its part, has 0.66 sequences per 1,000 cases. That’s the 27th best rate in the U.S., according to a Post and Courier analysis of GISAID data.
The CDC says it is trying to improve the level of genome sequencing in the U.S. by hiring more labs to run samples as early as next week, but even with the expansion, the U.S. will sequence only a small fraction of a percent of its known virus cases. Observers say the U.S. has been slow to prioritize studying the virus's changing genome and lacks the coordination of a nationwide effort.
A study group assembled last year by the National Academies of Sciences, Engineering, and Medicine called on the federal government to develop and fund a national strategy to sequence the virus in close to real time. Doing so would help public health authorities better understand where people are catching the virus and whether it is adapting to our defenses, the group said.
Understanding the virus’s changing genetic makeup will become increasingly important as the U.S. begins to see an end in sight for the pandemic, Albrecht said. The virus will ultimately be brought to heel by vaccines, so public health authorities need to be vigilant for mutations that make the shots less effective. And because genetic information can identify the sources of individual outbreaks, it could be useful to snuff out the last embers of what’s now a nationwide wildfire.
For now, DHEC has indicated that its sequencing effort is focused on detecting the B117 variant, and the state public health lab is targeting samples that are flagged as possible variants by regular coronavirus tests.
When the lab tests a nose swab for the coronavirus, its machines look for three specific parts of the virus’s genetic code. But when the virus mutated to create the B117 variant, one of those three sections, called the S gene, was dropped from its genetic code. So if a sample is positive for the other two sections but not the S gene, that's a clue.
DHEC says it plans to eventually test every COVID-19 positive sample that has come in since December and lacks the S gene. A new batch will be run Monday.
Still, the U.S.’s focus on the B117 variant may miss the point, Kamil said. Public health authorities are focused on them because it knows they exist, but without more sequencing, they won’t know whether other, more transmissible variants are already here.
“There may be tons of them emerging in the U.S., but we’re not going to see them until it’s too late. The U.K. saw this one in time,” Kamil said. “It’s like seeing a cockroach on the floor in the middle of the night. You think it’s going to be the only one?”
Without sequencing more samples, the U.S. won’t know.