TESTING FOR THE COVID 19 VIRUS
April 2, 2020 – Allan Maynard, MSc.
This is a topic of great interest to me because my career was in the field of measurement science – in my case measurements for environmental contaminants. Reliable measurements are required for many aspects of our lives from ensuring safety of foods, medicines, infrastructure, water supplies and of course to the monitoring of our health. Now testing is critical for the CoVid 19 pandemic.
It has become increasingly evident that reliable, wide spread testing is one of the key strategies to slow down the rate of infection from the CoVid -19 virus. Germany is one of the best examples of this. Germany’s preparedness was helped in part by an early recognition that coronavirus was likely to become a global problem. Lacking a gene sequence for the new virus, the German team designed their first test kit based on SARS and other known coronaviruses. The protocol was published by WHO (World Health Organization) on January 17, even before the Chinese had a test. By the end of February, the Germans were producing 1.5 million test kits per week. Globally – Germany is among the lowest in infection and mortality rates.
Another of the earliest tests was developed in mainland China by the Chinese Centre for Disease Control, and details of it were posted on the World Health Organization website on January 24, just after the Wuhan lockdown was announced. Fortunately, we are seeing unprecedented speed in CoVid research thanks in large part to early Chinese efforts to sequence the genetic material of the virus that causes Covid-19. China shared that sequence in early January, allowing research groups around the world to grow the live virus. Having this viral material has resulted in research groups around the world to work on developing tests.
HOW DOES THE CURRENT TEST WORK? – A short biochemistry lesson.
The shorts version – a swab is used to collect viral material from the back of the nose, the swab is sent to a lab that isolates the genetic component. The genetic material is rapidly grown (replicated) and then detected by very specific dyes.
A more complete description – For a patient, the process of being tested for the virus is easy and can potentially be done anywhere. It is the same basic protocol used to test for other viral infections. It typically involves taking a swab from deep in a patient’s nasal cavity to collect cells from the back of the nose. The sample is then sent to a lab, where it will be tested to determine if the patient’s cells are infected with the virus.
The swabs are then tested in specialized labs that are able to look for genetic material. The genetic material in the CoVid 19 virus is called RNA – (Ribonucleic Acid). RNA and DNA (Deoxyribonucleic Acid) are nucleic acids and, along with lipids, proteins, and carbohydrates constitute the macromolecules essential for all life.
In the test – the RNA must be converted to DNA. The DNA then replicates itself millions upon millions of times until there is enough genetic material for detection. The method is referred to as “polymerase chain reaction” or PCR. The PCR test was developed by Kary Mullis from California who was awarded the Nobel Prize in 1993 for this important discovery.
The resulting genetic material during the PCR chain reaction binds with a special fluorescent dyes. During the test the fluorescence increases and the genetic material amplifies. There are variations of this test in terms of the way the chain reaction is carried out and in the manner by which the genetic material (DNA – from the RNA) is detected.
The turn around time for this standard test (as is the case for most other viral tests) usually 24 to 72 hours – mainly because of the need to transport the samples to special labs and high volume in these labs. This is clearly has not been adequate and more rapid tests are in development – see below.
WHAT HAPPENED IN THE USA?
As mentioned, China developed its own test. The WHO first adopted a test from German researchers in mid-January. These 2 protocols were basically adopted by other countries in order to produce their own tests. Some countries simply used tests provided by WHO.
The CDC (Center for Disease Control) made the decision to develop its own test towards the end of January with the intention of being the conduit for testing in the US. But there were warnings that the CDC would struggle to keep up with the volume of screening and should focus on working with private industry to develop easy-to-use, rapid diagnostic tests that can be made available to providers. Unfortunately, the CDC did the opposite. When it became clear that testing had to be ramped up, the CDC created tests kits for distribution to state labs. It soon became evident that the test kits sent were not reliable (faulty reagents). This meant that only the CDC could carry out the initial test work. As such the testing had to be restricted to only ‘high-risk patients’ who had recently travelled from China. CDC was ‘back to the drawing board and valuable weeks were lost.
This was a significant set back for the US and is one of the reasons the US has one of the highest rates of infection in the world. Fortunately, this is rapidly changing with more widespread testing now occurring.
TESTING NOW GREATLY ENHANCED AROUND THE WORLD
The short version – due to the urgency of this crisis government incentives were rapidly in place for research organizations and the private sector to develop more rapid and portable test methods. There are a number of these methods now coming on-line. It is encouraging.
A more complete version – Human ingenuity can be amazing when we face a crisis. The research efforts pertaining the CoVid virus around the world has been more than impressive. Now testing protocols have been developed in many countries with 2 main objectives in mind – 1) much more rapid and 2) being portable for use in multi-locations. For the most part – the technology is the same in that the tests focus on identifying viral genetic material. It’s the overall process that has improved in a major way. Here are just 2 examples but needless to say, there are many more.
Abbot Labs – USA – Recently (3 days ago), Abbot Labs announced a new test kit. The “ID NOW” machine as it has been dubbed can test samples one at a time. A health care provider would use a swab to take a sample from a sick patient’s nose or throat and then mix the swab into a chemical solution that breaks open the virus and releases its genetic material. The sample is then placed into the ID NOW instrument, which uses a special “isothermal technology” to replicate and amplify, if present in the sample, the small section of the virus’ genetic sequences in order to quickly detect whether a person is positive or negative for COVID-19. Such a test will allow frontline health care workers to see a patient, quickly diagnose them and make immediate decisions regarding treatment and care, thus helping prevent further transmission of the virus to other people.
Simon Fraser University – Simon Fraser University researchers will use their pioneering imaging technology — called ‘Mango’, for its bright colour — to develop coronavirus testing kits. They’re among a small set of Canadian researchers who responded to the rapid funding opportunity recently announced by the Canadian Institutes of Health Research (CIHR) to help address COVID-19. The latest research, involves using special reagents to detect individual molecules of RNA within a living cell. Dubbed the “Mango system’ it consists of an RNA Mango aptamer. Aptamers are short, single-stranded DNA or RNA molecules that can selectively bind to a specific target — in this case a special dye. The aptamer acts like a magnet – targeting and binding those dye molecules. The dye becomes excitable when bound and glows brightly. RNA molecules modified to contain the aptamer ‘magnet’ now stand out from the other parts of the cell, which makes it much easier for researchers to see and study RNA molecules under a microscope.
WHAT ABOUT A BLOOD TEST?
Short version – blood samples can be collected and tested for antibodies that are formed if a person is infected with the virus. The test mainly determines if a person had the disease rather that for use in early detection.
A more complete version – Blood tests can be very rapid and in some ways easier to get a reliable sample. To do a blood test for the CoVid 19 virus would involve analysing for antibodies to the virus. An antibody, also known as an immunoglobulin, is a large, Y-shaped protein produced mainly by plasma cells and used by the immune system to neutralize pathogens such as pathogenic bacteria and viruses.
Antibody tests are different from the typical diagnostic tests used to determine whether someone has COVID-19. As mentioned above, the latter involves taking samples of mucus and saliva and running a test in a lab to see if those samples contain the coronavirus’ genomic sequence. A serological test, on the other hand, can tell whether a person has coronavirus antibodies in 10 to 15 minutes. In some ways the test can be developed along the lines of a home pregnancy test.
To create the test, the researchers began by designing a slightly altered version of the “spike” protein on the CoVid 19 outer coat. They also isolated the short piece of the spike protein called the receptor-binding domain (RBD), which the virus uses to attach to cells it tries to invade. They then used cell lines to produce large quantities of the altered spike proteins and RBDs. Those lab-made molecules provided the basis for the test, in which antibodies in a sample of blood or plasma trigger a color change when they recognize a target protein.
This test is being used extensively in New York. But it’s main objective will be to determine who has had the disease. It will not provide early detection as it takes time for the antibodies to form in the blood stream of an infected patient.
WHAT ABOUT THE RELIABILITY OF THE TESTS
Tests are generally judged in terms of their sensitivity, accuracy (or in this case specificity) and precision (applies to quantitative tests).
The tests are proven to be “sensitive” in laboratory conditions — in this case, a technical measure of the smallest amount of the target virus they can detect. The tests must also be “specific” — for example, ensuring they do not mistake other pathogens, such as the cold coronaviruses, for the new CoVid 19 virus.
The genetic tests being used are typically very sensitive and specific under lab conditions, but in the real world, how the swab was done and the stage of illness the person was in can make a big difference. To complicate the situation, there isn’t one test. Many different tests are now being used by commercial laboratories, hospital labs and governments around the world. The interpretation of the results will therefore depend on not just the test, but other external factors.
The tests have not been around long enough to know precise information about the sensitivity and selectivity of each one. The rule of thumb that seems to becoming adopted is to assume a 5% chance of false negatives. In essence if a sick patient get’s a negative result, they should be tested again. That is acceptable given the urgency of our situation.
It is encouraging to see how quickly researchers have stepped in to enhance testing around the world. It will make a difference.