Coronavirus testing

I’m getting questions about Covid-19 testing and so another blog post aimed at the non-expert in way of explanation.

Confusion appears to be coming from the fact there are two tests, one already being used and another about to be released. The one that is available at the time of writing tests for the virus, whereas the one about to be released, tests for the antibody to the virus in the bloodstream. The viral test says whether the patient is currently infected, but it will not say if they’ve had Covid-19 once they have recovered because the virus will have gone by then. An antibody test looks for antibodies to the virus in the bloodstream, and these might not have had time to form in the early stages of infection (when the viral test would be positive). But the antibody test will tell if the patient has had Covid-19 in the recent past. Since some people get mild symptoms, it’s possible they may not know they have had the disease, even though they would have been a carrier. A combination of viral and antibody testing will tell us where the virus is and where it’s been and that gives us the best chance to predict where it’s going.

How do these tests work? The two tests work in very different ways but they are both a marvel of modern molecular engineering. The virus test uses a technique called a polymerase chain reaction (PCR) and it looks for the genetic material of SARS-COV-2. All living things have DNA, which contains the genetic code of life. DNA replicates itself, passing from one generation to the next. So if you look at your grandchild and say, she’s got her father’s eyes – it’s all because of DNA. In what’s called the central dogma, DNA makes RNA which makes protein and it’s protein that governs the biochemistry of life. Proteins are hugely complex molecules made from strings of up to 20 distinct types of amino acids. Some proteins contain hundreds or even thousands of individual amino acids; the muscular protein, titin has 30,000 of them. The long strings of amino acids fold like tangled pieces of string but unlike string, the tangles are very precise. Proteins have molecular grooves and pockets where specific biochemical reactions take place. The grooves and pockets are analogous to spanners and wrenches in a biochemical tool kit, each fitting a particular sized nut or bolt in building the machinery of life. The 2015 Nobel Prize winner for physiology or medicine, Yoshinori Ohsumi, summed it up by saying, “Life is an equilibrium between synthesis and degradation of proteins.”

Some viruses have DNA but some have RNA – technically viruses are not actually living because they can only reproduce inside living cells. SARS-COV-2 has RNA as its genetic material and it manufactures proteins from that by highjacking human cells. RNA, like DNA replicates itself, and it’s this replication process that’s used to detect its presence. The biochemistry of replication is essentially put into a test-tube where any SARS-COV-2 RNA multiplies many millions of times, each new stand of RNA being identical to its predecessor. Once enough replicated RNA is available, it’s assayed using a variety of methods. PCR test kits are quick to develop and were first distributed by the World Health Organization last January. PCR is routine but not straightforward, requiring laboratory facilities and 4–6 hours to complete. Add that to the logistics of sample shipment and the turnaround time is typically at least 24-hours. Demand on some components of the PCR test have led to shortages.

The other test doesn’t look for the virus itself, but an antibody to that virus in the blood. When a virus infects the body, we produce antibodies as part of the immune response. Antibodies are Y-shaped proteins (see image) with very specific shapes which latch onto the surface of the virus. Detecting antibodies in the bloodstream in amongst a plethora of other proteins is challenging but in 1971 two Swedish scientists, Eva Engvall and Peter Perlman, solved the problem with the invention of a technique called ELISA (Enzyme-Linked Immunosorbent Assay). This assay uses more antibodies – in fact antibodies to antibodies, and so it gets a little complicated. Let’s start with the antibody to SARS-COV-2 in the blood, we’ll call this viral-antibody. In the laboratory molecular engineering methods are used to make another antibody (we’ll call this antibody-2) which binds onto the viral-antibody. Then another laboratory-made antibody (we’ll call this antibody-3) binds onto antibody-2. Antibody-3 is different however, because it’s fitted with an enzyme, yet another protein, but one that medicates some chemical reaction, typically one which causes a colour change.

By combining antibodies-2 and 3 in a test-kit a spot of blood is taken by finger prick and mixed with antibody-2. If the viral-antibody is present in the blood, antibody-2 will bind to it. Then antibody-3 binds to antibody-2 and its enzyme mediated reaction causes a colour change. The assay is a sort of protein domino effect, one reaction triggering another. All this takes place on a single device and so is conducted in situ outside of a laboratory. It takes perhaps 10-minutes to give an answer – not that much different to a pregnancy test.

It requires some effort to develop an ELISA assay, which is why there’s been a delay in their arrival. Kits are just being issued and after a period of evaluation, they should be widely available. Don’t rush out to buy one just yet, because the evaluation and then scale-up is likely to take a little while.

The pandemic still rages and both infection and mortality rates are increasing, but there is reason for optimism. A combination of tests will pin down where the virus is and where it’s been and with that knowledge we’ll be able to better target our efforts against it.

I’ve outlined the basics in this post but technology is advancing all the time. New techniques for viral and antibody detection are being explored and if one of those comes through, I’ll try and blog on that at a later date.