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Testing for SARS-CoV-2 has two main goals.
The first is diagnostic testing in patients with acute symptoms. The question being asked here is: Are the symptoms in this patient due to COVID-19 or something else? This is the most important question in the early stages of this pandemic.
The second type of testing is designed to answer the question: Has this person been exposed to SARS-CoV-2 and developed an immune response? Can they be removed from isolation and permitted to go back to work/school etc? Is the community developing herd immunity? These questions are becoming increasingly important as we move to the next phase of the pandemic. And there is a pressing need for answers.
Stage 1: Diagnostic testing
RT-PCR – the reverse-transcriptase polymerase chain reaction.
In Australia, and around the world, the main type of test being used to detect the coronavirus that causes COVID-19 is called RT-PCR – the reverse-transcriptase polymerase chain reaction.
This type of testing for the genetic material of viruses and other microbes has come into common use only in recent years. Tests for a wide variety of pathogens are available.
Laboratories around Australia use a number of different RT-PCR testing platforms. However, they require sophisticated instruments and highly trained staff and so are only available in larger labs with the expertise to perform them. They are relatively expensive and take several hours to produce a result.
A significant advantage of RT-PCR tests is that they can be multiplexed – designed to test for several respiratory pathogens at the same time. Typically, these tests use several sets of probes to amplify several different parts of the viral genome and include a positive control set of probes to ensure the sample is adequate and the test performed to specification.
The tests vary in specificity and some require confirmation of positive results by a second more specific test. Very recent data from China suggest that RT-PCR may have a higher fase-negative rate than currently thought mainly due to difficulty in obtaining adequate specimens from the right anatomical sites. When serological tests (see below) become widely available we will be able to see if this is correct.
A new version of RT-PCR test called the Cepheid Xpert® Xpress SARS-CoV-2 has been approved and is being rolled out in sites in Australia. This is both simpler and faster than most other RT-PCR tests and can be used outside main laboratory settings.
There are other types of test that can also be used for diagnostic purposes in people with acute symptoms of COVID-19 but none of these are available in Australia yet.
RT-LAMP – reverse transcriptase loop-mediated isothermal amplification.
One of the most advanced of these is another type of amplification technology called RT-LAMP – reverse transcriptase loop-mediated isothermal amplification.
The Abbott ID NOW™ COVID-19 test has been approved for use in the US and some laboratories in Australia already have the ID NOW instruments and are using them for testing for other respiratory pathogens such as influenza and RSV.
These instruments are small, simple to operate and give very rapid test results e.g. COVID-19 positive test results in less than 10 minutes. However, they are not easily multiplexed so they can only assay for one pathogen at a time.
A problem for Australia is going to be that demand for the instruments and test kits in the US will be very high and Abbott may not be able to produce enough to export them at this stage of the pandemic.
Furthermore, the Abbott ID NOW COVID-19 test is not yet on the TGA list of approved tests. Other companies are also developing RT-LAMP tests for COVID-19 but none are available yet for use in Australia.
Other new diagnostic tests on the way
Other types of diagnostic tests are in development. Two companies are in an advanced stage of development of tests that have adapted the CRISPR gene-editing technology to make rapid diagnostic tests that may be suitable for point-of-care use when commercially released.
Another company is developing a rapid antigen test that will identify a unique SARS-CoV-2 protein. We don’t know yet how long it will take to finish development of these tests and get them approved and available in Australia.
Stage 2: Exposure testing
Exposure testing relies on standard serology looking for IgM, IgG and possible IgA anti SARS-CoV-2 antibodies. Several point-of-care serology tests have been approved by the TGA for use in Australia. Since people may not develop a measurable antibody response for 10 or even more days post symptom onset, these rapid point of care tests are unsuitable for diagnosis of acutely symptomatic patients. They are more suited to answering the second type of question posed earlier; Has this person been exposed to SARS-CoV-2 and developed an immune response? Can they be removed from isolation and permitted to go back to work/school etc?
However, the test kits have not yet arrived in volume so at present they are relatively inaccessible, but this should change soon.
The approved tests are all simple plastic cassettes that use lateral flow of the sample by diffusion. These tests can typically give a result in 10-20 minutes and they use a fingerprick or venous blood. They can detect the presence of both IgM and IgG separately by the development of coloured lines in the reading window on the cassette.
They also have a control line that must develop to show that the test has worked properly. These tests have not yet been thoroughly characterised.
However, data supplied by the manufacturers show they vary in their sensitivity. One test claims around 96% sensitivity at five days post-symptom onset and another 81% sensitivity at 4-10 days and 100% sensitivity at 11 days.
They also claim good specificity with close to 100% negative results in unaffected people. This is somewhat surprising since there are a number of other, less dangerous coronaviruses, in circulation in Australia and around the world and many, if not most people will have been exposed to one or more of these. The manufacturers’ figures will need to be confirmed once the tests are in widespread use.
Pathology laboratories will require automated high-volume tests and until these arrive and are approved for use, it will not be possible to get a handle on the real epidemiology of COVID-19 in our communities. It is likely that high-volume serological tests will become available soon. Once pathology laboratories have access to these serological tests and results are notifiable to state health departments, it will be possible to address another pressing question; Is the community developing herd immunity?
For further information
Nature Biotechnology https://www.nature.com/articles/d41587-020-00010-2
Last Review Date: September 2, 2020