For the last several months, the Centers for Disease Control and Prevention (CDC) has publicly shared information about the percentage of COVID-19 variants that are circulating in the U.S. at any given time. That data helped scientists know when the Omicron wave was happening, and it also allows everyone to keep tabs on COVID variants as a whole.
The CDC is able to offer up this information through genomic sequencing, but there’s been a lot of questions lately about how this works and what it means for your personal data. In fact, there have even been some claims floating around online that the CDC is analyzing your DNA through this program, which experts say is far from the truth. “That’s not how this works,” says Thomas Russo, M.D., professor and chief of infectious disease at the University at Buffalo in New York.
But what is genomic sequencing for COVID-19 strains, and how does this whole process work? Here’s what you need to know.
What is genomic sequencing?
At baseline, genomic sequencing is a process that breaks down the genetics of an organism or pathogen, Dr. Russo explains. A virus like SARS-CoV-2, which causes COVID-19, has a unique RNA sequence that’s made up of chemical building blocks called nucleotide bases, the CDC says online.
Through genomic sequencing, scientists break down the order of those bases in any given sample of the virus. This allows them to determine the COVID-19 strain and other features of a particular sample.
This process isn’t unique to COVID-19—scientists can do this with a range of viruses and pathogens, including the flu.
Why does the CDC do genomic sequencing?
Genomic sequencing helps give public health officials more information about viruses and other pathogens that cause illness, the CDC says. Per the CDC, scientists specifically use genomic sequencing to do the following:
Detect, investigate, monitor, and control pathogens
Understand how people became exposed to pathogens
Learn where pathogens are popping up
Trace the source and transmission of outbreaks
Learn more about pathogens evolving and to keep tabs on things like the development of drug resistance
In the case of COVID-19, though, the CDC largely does genomic sequencing “to determine which variants are circulating,” says infectious disease expert Amesh A. Adalja, M.D., a senior scholar at the Johns Hopkins Center for Health Security.
How the genomic sequencing process works
The CDC has a national genomic surveillance system that collects SARS-CoV-2 specimens (i.e. positive COVID tests) through the National SARS-CoV-2 Strain Surveillance program, along with ones from commercial or academic laboratories contracted by the CDC and state or local public health laboratories. Basically, they have a wide variety of sources that give them positive tests that they can then do genomic sequencing on.
It’s important to note that these samples are de-identified—meaning, the CDC does not have your personal information when they get the samples, Dr. Russo says. Instead, they just get the samples without your name, social security number, or any other major identifiers that would link the sample back to you.
The CDC gets these samples from different regions across the U.S., analyzes them, and makes calculations on things like variant proportions based on the data.
For the actual sequencing, “parts of the genetic material of the virus are put through a process that determines its exact genetic code, which is then compared with the code from known variants,” Dr. Adalja explains.
Again, Dr. Russo stresses, this only involves the virus’ genetic material and not your own. “Human genomic DNA is not being sequenced as part of the process,” he says.
Is there any way to know if your sample was sequenced by the CDC?
Unfortunately no. Only a small portion of COVID-19 tests that are taken are passed on as samples to the CDC and, again, they’re de-identified at that point. So, even if you wanted to know what happened to your sample and which COVID-19 strain you have, there’s no easy way of tracking it down, Dr. Adalja says.
That doesn’t mean you’re clueless about the variant you may have. Dr. Russo points out that the CDC’s variant proportion data paints a pretty accurate picture of what’s happening in the country and in your region, so “you can guesstimate which variant you have at this point.” Worth noting: Omicron is by far the dominant strain circulating in the country right now. So, if you test positive for COVID-19, odds are very high you have the Omicron variant. "Things were a little trickier when Delta was more common," Dr. Russo says.
Dr. Russo notes that the country didn’t do a lot of genomic sequencing at the start of the pandemic, but this data is now incredibly valuable for the public health community to help identify new strains of COVID-19 and appropriate treatments. “It’s extraordinarily important moving forward,” he says.
The post How Genomic Sequencing Actually Works for COVID Strains appeared first on Prevention.