COVID-19 strains – what are they and why do they matter? A Q&A with Dr Michael Risley – 28 January 2021

      The COVID-19 pandemic, also known as the coronavirus pandemic, is an ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the beginning of the global COVID-19 outbreak, the diagnostic and research community has undertaken an unprecedented effort to understand how best to manage, eradicate and prevent the disease. In recent months we have seen the rollout of ambitious vaccination schedules worldwide, as well as the strengthening of viral test and trace programmes. However, we have also seen the emergence of new viral strains around the world, such as the B1.1.7 strain first found in the UK, or the newer South Africa variant. The evolution of these new strains raises questions and concerns around the ability to diagnose SARS-CoV-2, as well as the efficacy of the vaccines.In the below interview Yourgene Health’s Chief Development Officer, Dr Michael (Mike) Risley addresses common questions about COVID-19 testing and it’s continued role in managing the worldwide pandemic. He also discusses the evolution of new viral strains and what this means for diagnostic efforts worldwide.

Mike has extensive experience in the molecular diagnostics industry with a track record of delivering high quality products. He oversees Product Development activities at Yourgene Health, utilising innovative solutions and a range of technologies to deliver products that meet customer needs, while ensuring compliance to quality and regulatory standards.

Prior to joining Yourgene Health, Mike successfully led the product design and development of QIAGEN companion diagnostic systems from project inception through to FDA approval. He also played a key role in mapping the product development process for a diagnostic assay then utilising this to make improvements to processes and projects.

Mike has a PhD in Cell Biology from University of Manchester, where he also spent two years as a Post-Doctoral Research Associate, and a BSc (Hons) in Human Genetics from the University of Nottingham.

How can COVID-19 be tested for?
The presence of the virus that causes Covid-19, named “SARS-CoV-2”, can be tested for by using two different methods, known as antigen and PCR tests.

What is the difference between a COVID-19 antigen and antibody test?
An antigen test detects the presence of the virus in a person at that time, with the result used to understand if a person is infected or not. The virus infection leads to an immune response in individuals, including the production of antibodies which are created to kill the virus. After the virus has been removed from an individual’s body, the antibodies remain in that person and usually for a long period of time. The COVID-19 antibody tests detect the antibodies specific for killing the SARS-CoV-2 virus and are used to understand if someone was infected at some point in the past.

Which test is best for COVID-19?
If you want to know whether you have the infection there and then, you need to take an antigen or PCR test. Of the two types, PCR tests are much more sensitive and will be more likely to detect the virus, therefore can be considered as the gold standard. Antigen tests can be much quicker and useful in certain situations, however have a higher risk of false negative results.
If you want to know whether you might have been infected at some point in the past, perhaps asymptomatically or earlier in the pandemic when mass testing was not available, then an antibody test is the best type to use.

What is qPCR?
PCR is a well-established methodology that has been used reliably for many diagnostic tests over recent decades. It stands for Polymerase Chain Reaction and is a method use to amplify, or increase the amount of, genetic material in a sample. It does this by using ‘primers’ and ‘probes’ that match the genetic sequence in a small region of the target of interest and creating many copies of that sequence. In the case of COVID-19 tests, the target is a region of the virus RNA. The amplification allows tiny amounts of genetic material to be converted into much larger amounts, which can then be detected using a specialized instrument. In qPCR, the q stands for “quantitative” and is a sensitive PCR technique that also allows the measurement of the amount of genetic material in a sample.

Can qPCR-based COVID-19 tests detect all the strains of the virus?
In theory yes, this should be possible, however it is not always the case. Test primers and probes are designed to detect specific regions of the virus, which is essential to allow PCR to work effectively. This design involves creating primers and probes with sequences that exactly match the virus sequence, though this isn’t always essential. Different strains of the virus arise due to mutations, which are changes in virus RNA sequence. If any of these changes are present in the area the primers and probes are designed to attach to, then it may prevent the test from working. We have seen this with competitor tests, where the recent VUI 202012/01, aka lineage B.1.1.7 strain has caused tests to no longer function or perform as intended.

Are we likely to see more COVID-19 strains emerge?
Without a doubt, we will do so. However, this is normal for any virus and not new to COVID-19.

How do manufacturers ensure their test remains accurate in light of the rate of new strains emerging?
Manufacturers need to closely monitor the emergence of new strains, typically using online databases that contain the RNA sequences of such strains. Doing so allows the identification of where new mutations are found in the sequence and whether they are in a location that could impact test performance, such as in the primer and probe regions. If a mutation is found under a primer or probe, then laboratory testing is required to determine whether the test can be expected to remain accurate. For instance, during monitoring of new strains it became clear that one mutation in the VUI 202012/01, aka lineage B.1.1.7, strain had a single mutation in a primer region of the Clarigene SARS-CoV-2 test. The mutation was in an area of a primer that is not critical for binding to the target, proven by laboratory testing that showed Clarigene can detect this strain of the virus as effectively as the original strain.

Yourgene Health are committed to delivering the high quality products our customers expect and deserve. The company have in place already an ongoing rigorous internal surveillance programme to ensure continued monitoring for the development of new viral strains. This includes database monitoring for SARS-CoV-2 variants with mutations in the N and the E gene which fall around the assay primers and probes, as well as impact assessment on these mutations on assay performance, evaluated by in silico analysis and wet lab confirmation. This process allows us to be confident that so far the performance of the Clarigene assay is not impacted by any strains circulating at high levels in the population. Click here to find out how Yourgene Health can support your organisation in delivering COVID testing. The Clarigene assay is also available for use in your own laboratory to deliver a high quality, rapid testing.

Clarigene - SARS-CoV-2 Test