COVID-19 test kits
A run-down of various kit types out there
I decided to wade through news from the past few months and get an overview of the various types of COVID-19 test kits on the market or at least in advanced development. It’s a rabbit hole! I hope you’ll find the article as informative as I did researching and writing it.
It seems that after an initial frenzy at the start of the COVID-19 pandemic, when seemingly almost any old test could somehow make it on the market (check out the April news review for comments on quality issues), we’ve seen not just quality tests but also kits with added features appear from summer 2020. More and more COVID-19 tests have been developed and gained regulatory authorisations since I last covered them in my newsletter. It's time to sort through the news to get and idea of the types of kits out there.
Molecular tests aka PCR tests
Polymerase chain reaction (PCR)-based tests were the first to make it on the market as far as I can tell. We saw a surge of PCR kit releases from March 2020 onwards. They are considered the gold standard for testing because they can detect extremely low viral loads. These tests tell us whether a person is currently infected, which is important for quarantine and treatment decisions.
PCR kits detect genetic material from the virus in a sample (often a nose or throat swab). The reaction mix in those tests amplifies the available genetic viral material (RNA). This multiplication step reduces the need for large amounts of material being present in the original sample and, consequently, creates the high test sensitivity. Major drawbacks of the traditional PCR tests are that they take a long time to yield results with people being informed several hours after testing, require a professional lab and trained staff.
However, some organisations have simplified and sped up the process since the release of the early test kits. E&O Laboratories set out to make the manual process flow safer and more streamlined with its VPSS (Viral PCR Sample Solution), which simplifies and accelerates sample handling. Fluidigm has increased through-put per sample batch using microfluidics technology on saliva samples. DnaNudge's portable system yields test results from swab or saliva samples in just over an hour. These can be sent directly to a clinician via an integrated app.
As time went on, new PCR tests were released that didn't only detect the COVID-19 virus SARS-CoV-2 in a sample but also other viruses that can cause similar symptoms. Eurobio Scientific, QIAGEN, Thermo Fisher Scientific and BGI Genomics have released multiplex PCR tests that distinguish in a single run between main viruses responsible for flu-like symptoms. After having already released portable COVID-19 PCR test kits that yields results in under two hours, Oxford Nanopore Technologies has also begun developing a multiplex assay for respiratory viruses. Being able to distinguish between different viruses helps medical professionals give relevant advice to patients and supports our understanding of the dynamics between those infectious agents.
Rutgers researchers have developed a PCR test that can detect the three currently most notorious coronavirus variants in just over an hour and shared their method online. Seegene's assay takes this further, as it is designed to identify each coronavirus variant. Besides influencing potential treatment decisions, this is also important for monitoring the spread of such variants between populations and geographies.
There has been a drive towards home-testing kits, as this avoids the need for travel and potential spread of the virus by an infected person; it is also safer and reduces the need for healthcare staff. This in turn means that medical professionals, who would otherwise be seconded to COVID-19 testing, can take up their usual or other needed roles to cater for the plethora of other healthcare services, some of which had been put on hold due to the pandemic.
Alveo Technologies, GetMyDNA and LetsGetChecked have released home PCR sampling kits using nasal swabs. However, there is a risk that unsupervised swabbing is not done correctly or that the sample does not stem from the right person. Other companies went one step further and developed kits using saliva samples. This is intended to be more comfortable and reliable than self-swabbing. According to my radar, the first at-home saliva tests came from RUCDR Infinite Biologics and MicroGen DX.
Isothermal amplification-based tests
Isothermal amplification is a novel molecular technology that also uses amplification of genetic material but differs in various aspects from PCR. The mechanism is simpler, quicker and more cost-effective. Thanks to their relative simplicity, these novel kits require only minimal training of technicians.
Isothermal amplification is employed in MicrosensDx' and Abbott's portable point-of-care kits, which yield results in under 30 min. OptiGene has attracted some controversy when its loop-mediated isothermal amplification (LAMP)-based test missed about half of the positive cases in a Manchester trial, whereas other trials showed high sensitivity dependent on viral load in the sample.
Illumina has released a next-generation sequencing (NGS)-based test for swab samples. NGS is like PCR on steroids. In terms of routine COVID-19 testing, the main advantage of NGS is the higher through-put. Thus, it could scale up testing capacities quickly. For lower through-put PCR appears to be more economical. That said, the Sanger Institute is developing a cost-effective NGS test for saliva and swab samples with a view to making it suitable for rapid point-of-care and home testing.
Antigen tests detect virus proteins usually in nose swab samples. Hence, like PCR tests, they tell us whether a person is currently infected. However, there is no amplification step for proteins as there is for genetic material. This means that enough of those proteins must be build in the body after virus infection before they can be reliably detected. This reveals one inherent disadvantage of antigen tests compared to PCR tests: lower sensitivity. These tests require a higher level of viral load to return a positive result. Consequently, there is a higher risk of false negatives, i.e. an infected person gets a negative test result. If there is doubt over the result, it may well be required to run a PCR test in addition.
One of the advantages of antigen tests is that they are usually easy-to-use rapid tests. Commonly, tests deliver results in 10-15 minutes and use lateral flow technology similar to pregnancy tests. Mondialab was early out of the starting blocks with its blood sample-based point-of-care kit. The test strips are machine-read to avoid human error and instantly create a digital record. Other tests generally use nasopharyngeal swabs sampled by professionals or under supervision, such as kits released by Siemens Healthineers, SD-Biosensor, Roche and Humasis/Celltrion . Abbott released its Panbio COVID-19 Ag kit for professional use and took it a few steps further with its BinaxNOW™ COVID-19 Ag Card. It comes as a professional use or telehealth-facilitated home test. The kit allows the transfer of results from a test card to a mobile app that provides people who test negative with a temporary encrypted digital health pass. A low-cost telehealth-facilitated home test kit is offered by LABx Corp. Pelican Diagnostics' saliva kit is super fast (results in 30 sec) with a sensitivity rivalling PCR tests thanks to nanosensor technology. It is suitable for home and professional use and can be hooked up to a mobile app to store and share results.
Serological tests aka antibody tests
Antibodies are produced by white blood cells, called B cells, that are part of our adaptive immune system. Serological tests detect antibodies against SARS-CoV-2 usually in blood samples. This tells us whether the person has ever been infected because antibodies are part of our immune defence and persist for some time even when the virus is gone. Generally, they take about 1-2 weeks to appear in the body at detectable levels because our immune system needs time to generate an anti-viral response. Thus, a newly-infected person does not yet have antibodies but will have genetic virus material. In contrast, a person who has overcome the infection, may not have detectable genetic material anymore but will probably have antibodies. Hence, correct timing of these different tests is crucial to avoid false negatives.
Results from antibody tests are informative in several ways:
They help epidemiologists understand how many people in a population have been infected. Since not everybody experiences symptoms or gets a PCR test when feeling unwell, it is impossible to have reliable estimates. Without such information, fatality rates (how many deaths per infected number of people) cannot be reliably calculated. This means that we cannot know how serious the infectious disease really is. This, in turn, makes it difficult to set effective and efficient healthcare policies.
Knowing how many people have had the virus, and how it is spreading also informs vaccination programmes.
They are a tool to assess how effective a vaccine is because a vaccine is supposed to stimulate an antibody-mediated immune response.
They can also help assess for how long immunisation by vaccination or natural infection lasts.
Identifying people with a strong antibody-mediated immune response helps find potential convalescent plasma donors whose antibodies may save patient lives.
Knowing which healthcare staff is considered immune, i.e. tests positive for antibodies, can help allocate frontline care tasks, such as intubating an infected patient.
Soon after PCR kits, more and more serological kits started appearing on the market. Following concerns about the quality of early kits, the FDA tightened its enforcement, issued a ‘removed’ list, and later tests have been promising sensitivity and specificity at or near 100%. In addition to 'basic' serological tests, some interesting ones have been developed. Researchers from the University of Illinois created a rapid low-cost COVID-19 antibody test chip that does not require diagnostic laboratories. The University of Exeter spin-out Attomarker has developed a multiplex point-of-care Triple Antibody Test that can be connected to mobile devices. This test detects 3 classes of antibodies (IgM/G/A) against 3 virus proteins. Many serological tests seem to simply detect any virus-specific antibody. This only really tells us that the person has been infected previously. Duke-NUS Medical School has developed a test that specifically detects neutralising antibodies. These are the antibodies that inactivate the virus and can give us some idea of antibody-mediated immunity, which is more informative for the choice of convalescent plasma donors for example. Microfluidics-facilitated portable rapid kits might also be an option for rapid COVID-19 antibody testing in very small sample volumes.
Researchers at NTU Singapore have developed a rapid COVID-19 test that can detect even mutated virus variants in nasopharyngeal swab samples using the gene-editing tool CRISPR. This is important because SARS-CoV-2 is highly mutable and tests must keep up with mutations to avoid false negatives. Briefly, the test uses molecular 'scissors' that recognise specifically defined and conserved (i.e. low mutation risk) parts of the viral genetic material. The scissors only get activated in the presence of the virus RNA and, at the same time as cutting the virus material, also cleave a detection reagent that starts to glow as a result. This light emission signals the virus detection when analysed by a reader in the lab version of the test. In addition, there is an easy-to-use paper strip version (think pregnancy test) and a mobile app that assists in interpreting the paper strip detection bands. TATA Sons have already gained approval in India for their point-of-care CRISPR paper strip kit. An original protocol had been published by US researchers through the COVID-19 Technology Access Framework.
Breathonix is developing a one-minute breath test detecting exhaled Volatile Organic Compounds (VOC), which can indicate changes in a person’s breath profile due to disease. The analyser uses machine learning algorithms. Scientists from Vancouver's BC Cancer Research Institute are working on a similar project. Breathomix has also developed a rapid breath analyser and launched an initial roll-out in Amsterdam, NL in Feb 21. It is expected to be reliable for negative results. However, positive reads must be backed up by PCR test until more usage data are available to confirm whether the kit can distinguish between different virus infections.
T cell assays
T cells are white blood cells and part of our adaptive immune system. They do not produce antibodies but are critical in the activation cascade that simulates B cells to produce antibodies. Information on the behaviour of T cells can be used to determine whether a person has had the virus previously or is harbouring a latent infection. Further applications are ongoing immune monitoring and determination of the strength and longevity of the immune response to natural infection or vaccination. Improved understanding of the different phases of the immune response can inform medical decision-making and further research into diagnostic, prevention and treatment strategies of COVID-19.
Hence, some companies have laid their eyes on testing T cell activity to complement other tests mentioned above. Oxford Immunotec's assay measures the T cell-mediated immune response to SARS-CoV-2 using blood samples. It has gained regulatory approval in different countries for research use only. Sysmex and Kobe University have released data on their joint research, which shows that the test measures virus-specific T cell activity. BD's multi-colour test kit identifies and enumerates T cell subtypes. It has been approved for clinical application in Europe. Adaptive's FDA-authorised NGS kit uses Microsoft's artificial intelligence (AI) for genetic analysis of T cells to determine past infection and immunological 'memory'. Note that the virus NGS tests mentioned earlier target virus RNA, whilst Adaptive's kit analyses T cell DNA. NGS technology can be used with genetic material from various sources.
Machine learning & AI
Vertebrate Antibodies is developing a COVID-19 antibody test suitable for mass screening using AI to identify virus components that trigger an immune reaction. These are then used to capture antibodies in the sample to yield a positive result should the relevant antibodies be present.
Now that test accuracy is not a major concern anymore because of the high quality of existing kits, speed has increasingly become a key discriminator. iAbra's 20-second test could be a complete game changer. After a trial at Heathrow airport, iAbra is now eyeing up proper roll-out. The start-up is backed by Dell and Intel. The technology takes a novel diagnostic approach based on AI-driven microscopic holographic imaging. A digital camera feeds data from saliva samples under a microscope to the trained AI, which identifies the infection.
Blockchain isn't just a buzzword anymore, and its uses go way beyond cryptocurrency. Kahala Biosciences & Rymedi collaborated early on in the pandemic to bring us a rapid point-of-care antibody test (IgG/M) that is connected to a blockchain-enabled mobile app to provide a tamper-proof record of kit provenance, test results and symptom tracking. Since then, more organisations have been looking to leverage blockchain technology for authentication of test kits and results; latterly these include healthcare provider Innova Medical in collaboration with Quantum Materials Corp, Singapore's government, Emirates airline and lab service Arion Genetica in collaboration with tech start-up Genobank.io.
The organisations mentioned are simply examples I have spotted in the news. This article does not aim to offer a comprehensive list of relevant organisations or test kits.