South Carolina’s search for more contagious coronavirus variants faces a simple math problem: it’s not testing many people for them.
Each week, South Carolina performs more than 100,000 tests for the coronavirus and identifies more than 20,000 infected people. And it is analyzing the genetic material of just a few dozen virus samples to look for new versions of the germ, including variants that spread more quickly.
The Department of Health and Environment Control of SC reports that it is sequencing the genetic material of 24 samples per week. And it sends another 10 samples to the United States Centers for Disease Control and Prevention every two weeks.
This is a key time for the state’s virus surveillance efforts as new, more communicable variants begin to spread across the United States. Federal officials say variant B117, found for the first time in the UK, has been identified in seven states, including Georgia and Florida.
They have not yet been found in South Carolina, but experts suspect they may already be here. The true extent of its spread is a mystery why the United States sequences the genetic material of relatively few virus samples to look for changes in its composition.
At the current rate in South Carolina, scientists are analyzing the genomes of about 1 in every 1,000 known cases of COVID-19, the disease caused by the virus. If variant B117 is among the other 999, it will not be detected.
“I’m sure we have them,” said Dr. Helmut Albrecht, director of the Center for Infectious Disease Research and Policy at the University of South Carolina.
Monitoring the evolution of the virus is more than a mere curiosity, especially now. The emergence of a more transmissible version would be devastating, since the country’s hospitals are already filled to capacity with a record number of patients with coronavirus. And the mutations may eventually threaten the effectiveness of COVID-19 vaccines.
DHEC says it started sequencing virus samples internally 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 about 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 can study how it spread from place to place.
Researchers at USC, for example, used the information to trace an outbreak at a military base to a single dinner, Albrecht said. And in Louisiana, which has the highest sequencing rate in the southeast, researchers at the Louisiana State University Health Science Center in Shreveport have enough data to see how the virus spreads from city to city – how an outbreak in one place causes problems in another.
The information may even reveal how well nursing home facilities are protecting their residents from the virus, said Dr. Jeremy Kamil, who leads the LSU Health Shreveport sequencing effort. If infected residents have the same version of the virus, the outbreak may have started with a single error. If they have many different versions, the virus has been introduced several times.
The researchers say it is not surprising that the B117 variant was detected in the United Kingdom because that country has a coordinated effort to sequence massive virus samples.
The extent of his efforts is evidenced by the number of contributions the UK has made to a global coronavirus genome database administered by the GISAID Initiative, a non-profit organization that promotes data sharing among virus researchers. The database stores more than 360,000 sequences of coronavirus, allowing scientists to study the evolution of the outbreak worldwide.
The UK published about 49 genome sequences for every 1,000 COVID cases known there. In the United States, the state with the best rate, Hawaii, has published more than 28 for every 1,000 cases among its residents.
South Carolina, in turn, has 0.66 sequences per 1,000 cases. This is the 27th best rate in the USA, 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 US by hiring more laboratories to run samples as early as next week, but even with the expansion, the US will only sequence a small fraction of one percent of its known virus cases. Observers say the United States is slow to prioritize studying changes in the virus genome and is not coordinated by a national effort.
A study group assembled last year by the National Academies of Science, Engineering and Medicine asked the federal government to develop and fund a national strategy to sequence the virus in near real time. Doing so would help public health officials better understand where people are catching the virus and whether it is adapting to our defenses, the group said.
Understanding the change in the virus’s genetic makeup will become increasingly important as the United States begins to see an end in sight to the pandemic, Albrecht said. The virus will eventually be eliminated by vaccines, so public health officials need to be vigilant for mutations that make vaccines less effective. And since genetic information can identify the sources of individual outbreaks, it can be useful to put out the last embers of what is now a fire across the country.
For now, DHEC has indicated that its sequencing effort is focused on detecting variant B117, and the state’s public health laboratory is targeting samples that are flagged as possible variants by regular coronavirus tests.
When the laboratory 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 eliminated from its genetic code. So if a sample is positive for the other two sections, but not for the S gene, this is a clue.
DHEC says it plans to test all samples positive for COVID-19 that arrived since December and do not have the S gene. A new batch will be run on Monday.
Still, the US focus on the B117 variant may lose focus, said Kamil. Public health officials are focused on them because they know they exist, but without further sequencing, they will not know if other, more communicable variants are already here.
“There may be tons of them emerging in the United States, but we won’t see them until it’s too late. The UK saw it in time, ”said Kamil. “It’s like seeing a cockroach on the floor in the middle of the night. Do you think you will be the only one? “
Without sequencing more samples, the US will not know.