COVID-19 cases reached high levels, and variants of the virus, like delta, are even more contagious than the original strain. So how exactly are we tracking this?
For many years, Washington state has used a technology called genome sequencing. Genome sequencing is basically a way of mapping the fingerprints (or blueprints) of an organism, or cell. Doctors and scientists use this information to track various diseases and viruses. This is crucial to make predictions (or models) to help keep people safe.
We spoke with State Epidemiologist for Communicable Diseases, Dr. Scott Lindquist, to learn how genome sequencing is used to help us uncover important information about viruses, like COVID-19.
Before we dive in, it’s important to understand just what a virus is. According to Genome.gov, a virus is a small collection of genetic code, either DNA or RNA, surrounded by a protein coat. Viruses cannot replicate, or make copies of themselves, alone. They must infect a “host cell” and use parts of that cell in order to replicate. Often, the host cell is destroyed in the process, which results in damage to the host organism. Now onto our interview:
Thanks for sitting down with us Dr. Lindquist! What is genome sequencing?
It’s a laboratory method used to determine the entire genetic makeup of a specific organism. For infectious diseases, it is used on viruses, bacteria, and even parasites.
What can genome sequencing be used for?
Genome sequencing can help identify a viral or bacterial outbreak as well as identify virus variants. For example, let’s look at an E.coli (bacteria) outbreak. Say there are 700 reported cases of E.coli in a short time window. Those samples are sequenced and it’s found that three samples are exactly alike. Then, you can go back to the three people who tested for those matching strains and find out what they had in common, like where or what they ate before they got sick, thus determining the origin of the outbreak.
In the past, we used genome sequencing to detect tuberculosis outbreaks; to classify a hepatitis outbreak and trace it back to the first case; and to make sense of clusters or outbreaks of a virus.
How has genome sequencing been used during the COVID-19 pandemic?
Genome sequencing was crucial for learning more about COVID-19. The COVID-19 (SARS-CoV-2) virus has RNA codes that can be read by genome sequencing. Genome sequencing isolates the virus, unpacks the RNA, and maps it out — it goes piece-by-piece and reconstructs the RNA sequence.
Once the sequence is determined, scientists can begin to recognize patterns and compare sequences to detect things like the most common virus variants at any given time.
Why is this important?
It’s important for understanding how variants spread. Using this technology, Washington scientists determined that over 98 percent of the viruses they’re currently testing are the Delta variant. During the month of July 2021, Washington sequenced 20.5 percent of all positive cases confirmed with a molecular test. The proportion of positive cases we are sequencing ranks us among the highest in the nation, according to the Centers for Disease Control and Prevention (CDC).
We’re using genome sequencing to track all COVID-19 variants in Washington. For detailed information and current data (updated weekly) about COVID-19 variants in Washington state, check out the DOH Sequencing and Variants Report.
What has been Washington’s biggest discovery with genome sequencing so far?
The amount of COVID-19 variants has been one of the biggest recent discoveries! DOH provides weekly reports on eight [current] variants of COVID-19 that have appeared in our state.
What does the future of genome sequencing look like in Washington?
Washington has been one of the leaders of genome sequencing in the U.S. and has invested heavily in genome sequencing. Once the COVID-19 pandemic subsides, we will use the technology to detect, track, and monitor other viruses like hepatitis, tuberculosis, and any other type of viral or bacterial outbreak.
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