DETROIT – From the start of the pandemic, we knew that the SARS-CoV-2 virus (COVID-19 is caused by that virus) was changing as it spread.
Some of these smaller mutations even made it easier to track its progress around the globe and within countries. It quickly became apparent that some of these mutations were becoming dominant; at that point, these variants of concern needed to be tracked.
Ultimately, being given Greek letter names by the WHO, COVID-19 variants like Alpha, Delta, and Omicron would spread worldwide and here in Michigan. Tracking and identifying them has become a crucial tool to protect the public.
Read: How are at-home COVID test results impacting overall case numbers?
Many people don’t realize that the technology necessary to identify variants in individual patient samples has only become available outside of research labs in recent years. To give you a sense of how these tests are run in the state lab, we went to Lansing to see them firsthand.
The lab that does genetic sequencing for SARS-CoV-2 samples from around the state has been doing this remarkable high-tech work since the pandemic started. Even for someone like me, with a solid background in biochemistry and genetics, the complex nature of genomic sequencing can seem like magic.
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How COVID samples are processed
Doctor Heather Blankenship is the Director of Genomic Sequencing at the MDHHS Bureau of Laboratories and was my tour guide.
After a COVID-19 nasal swab is processed in a lab, a small amount of leftover liquid still contains the necessary viral RNA from the SARS-CoV-2 virus that the lab can analyze.
These residual patient samples get sent to Blankenship’s lab for sequencing. They only need 20 ul (microliters) of the leftover sample, less than a drop of liquid. A microliter is one-millionth of a liter.
The processing of the sample to prepare it for sequencing is the most time and labor-intensive part of the process. During the processing, contaminants are removed, the RNA is turned into DNA that the sequencer can analyze, and the 30,000 base pair long strand of genetic material is cut into short 250 character long strands that can be handled by the sequencer.
Once the sample is prepared, it, along with samples from 95 other patients, is loaded into a matchbook-sized cartridge called a flow cell.
These 96 patient samples are only two drops of liquid, and each patient sample is only 10 ul. The processing inside the sequencer takes almost two days and what comes out is a compressed data file that is processed to reveal the sequences of every 250 character strand from all 96 patients.
These 250-character strands, comprised of the letters A, T, C, and G, are then reassembled into the original 30,000 nucleotide long strand in a process Blankenship likened to assembling a jigsaw puzzle without any idea of what the final picture is supposed to look like.
Once the entire SARS-CoV-2 genome is reconstructed, it is compared to known variants to identify the variant in the sample. The sequence is also uploaded to international databases for further tracking.
Why isn’t every positive test sequenced?
Because sequencing takes roughly five days from the time the sample arrives at the lab, there is essentially no practical value to sequencing every positive test.
However, continuous random sampling is essential to monitor the pandemic to identify trends in the dominance of certain variants.
Since the pandemic’s start, the MDHHS lab has sequenced 26,300 COVID samples.
Related: Michigan reports 7,725 new COVID cases, 81 deaths over past week