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The pandemic has introduced many scientific concepts to the public, but there is some frustration with the way science appears to work, or perhaps appears to not work. So as both a scientist and teacher, I’d like to share a little about the science involved.
Let me start with COVID-19 testing, as that will be crucial to our return to public life. There are two classes of tests, one to detect virus, as when you have an active infection, and one to detect whether you have already had a COVID-19 infection. Most of the latter type tests depend on detecting antibodies in your blood that react with the virus. Let’s talk about how that works first, and where some of the challenges lie.
Antibodies work by recognizing specific parts of the virus and when they do so, they enable your body to target the virus for destruction. They are produced by your immune system, but it generally takes more than a week to really get a strong response. From your perspective, an antibody has the advantage that it is specific for the virus and it can be fired up quickly in the future should you be exposed to the same virus later; this is the rationale behind vaccines.
To look for such antibodies, we have to know what specific part(s) of the virus are recognized by your immune system, produce that viral part, and incorporate it into a test that can recognize those antibodies and only those antibodies. We use that viral part as a ‘fish hook’ to pull the specific antibodies out of your blood so that we can detect them.
The COVID -19 piece has to be distinct from parts of other viruses, and particularly other coronaviruses, such as those that cause the common cold. If not, this can cause “false positives” – test results that say you have antibodies, but these are not really the ones we’re interested in.
The viral part that we use in the test also has to be one that your body produces antibodies to. If not, then you may have antibodies but the test wouldn’t see them and would incorrectly suggest that you have not had COVID-19. Also, if you are tested too soon after infection, you may not have made any antibody yet, and this too would lead to an incorrect negative result.
Finally, most of the tests currently in use are qualitative – they tell us whether you have antibody, but not how much, nor how effective those antibodies are at enabling your body to destroy the virus. So that’s part of why it is hard to say, even if the antibody test is accurately positive, we can’t say whether you are immune from future infections.
Unlike antibodies, which are present in blood, with COVID-19, there is little or no virus found there. Consequently, for viral testing, a sample is collected differently – with a swab in your nasal cavity, for example, or possibly using saliva.
The virus that causes COVID-19 is a coronavirus and is named SARS-CoV-2. Coronaviruses are RNA viruses, meaning that their genetic material is RNA rather than DNA. Most tests for the virus are designed to detect a portion of viral RNA, which as for the antibody test, must be specific to SARS-CoV-2.
Usually there is such a small amount of viral material, RNA or otherwise, that we can’t detect it directly, so we need a way to amplify the signal. The way to do that most often employs a technology called PCR, polymerase chain reaction (see sidebar). What this does is make a DNA copy of a portion of the RNA, and then goes through cycles of copying the DNA so that eventually there is enough to measure. This process earned a Nobel prize for a California scientist and surfer dude named Kary Mullis (https://en.wikipedia.org/wiki/Kary_Mullis).
These repeated cycles require not only specialized equipment, enzymes and materials, but also time to go through repeated cycles, which is why there is both a delay in getting the results of the test and difficulty in cranking up the number of tests that can be performed. The materials needed to collect the samples are also specialized and have been in short supply, likewise slowing our ability to test as many people as is needed.
In summary, both kinds of tests will be needed to enable us to move forward. We clearly need to know who is currently sick and infectious. But we also need to know who has recovered. Those people may not only serve as a source of a treatment (their plasma does contain antibodies that could help destroy the virus), but also as an indicator of who may be able to work in certain places and, when we’ve had enough exposure as a society, to provide herd immunity.
Russell Kohnken holds a Ph.D. in biochemistry. He was involved in biomedical research for about 25 years before becoming a teacher at Evanston Township, where was known as Doc K.
Polymerase Chain: Copying DNA
To make a copy of DNA, we use an enzyme called DNA polymerase.
As you may know, DNA has two strands, and in order to make copies, we have to separate the strands.
This is done by heating, and then making copies of each of these strands at a cooler temperature. Each time the copying cycle is performed, the number of DNA molecules doubles.
As you can see, the cycle involves repeated heating and cooling, which usually destroys enzymes, and so was not practical until utilizing enzymes from thermophilic bacteria. Thermophilic means ‘heat loving’, and the bacterium used was Thermus aquaticus (Taq, https://en.wikipedia.org/wiki/Thermus_aquaticus) originally found in the hot springs of Yellowstone National Park.
More for entertainment than information, check out this song from a manufacturer of a device that performs PCR (https://video.search.yahoo.com/search/video?fr=yfp-t-s&p=bio+rad+pcr+machine+songs#id=51&vid=7d89ad99d68595d25e6f538f045a2889&action=click