COVID-19 variants and their impact on testing

Tests using multiple targets on the COVID-19 virus are unlikely to be affected

Recently, the COVID-19 news has been dominated by the arrival in Australia of new variants of the virus, in particular those from the UK and South Africa. This was to be expected. Viruses pick up genetic mutations as they copy themselves inside their host. As cells make new copies of a virus, mistakes occur. As they pass from person to person, these small genetic changes take place, resulting in new variants of the circulating virus.

Scientists who have been monitoring changes in SARS-CoV-2, the virus that causes COVID-19, have observed that it has been changing more slowly than other viruses and it has been regarded as relatively stable especially when compared with viruses such as influenza and HIV.  Nevertheless, thousands of mutations have been recorded, although the majority of these have not affected the virus’s ability to spread or its virulence.

However, these recent new strains of the virus are being shown to be more rapidly transmissible and the UK virus appears to lead to more severe disease, with more people being admitted to hospital.

Major efforts are being undertaken by public health organisations throughout Australia to prevent these new strains getting out into the community and time will tell if these measures remain effective.

Questions are also now being asked about the effectiveness of the vaccines that have been developed.  When developing vaccines, scientists allow for inevitable mutations and they select regions of the virus that are less likely to be affected by them. The general view is that the vaccines we have will continue to be effective.
Another key question surrounds testing. Will the new strains of the virus be detected by the testing methods that are being used by laboratories across Australia?  Most testing for SARS-CoV-2 is performed by molecular genetic tests, designed to recognise specific sequences in the virus’s genome. This is what makes them highly accurate. It is possible for virus mutations to affect the performance of a test if the mutation is in a region of the genome targeted by the test. This has the potential to affect results, especially to produce false negative results in which a person who is infected shows as being negative.

Organisations around the world that are responsible for the quality of laboratory testing have been asking labs to check that the sequences they are using in their tests will not be impacted by the new variant.

The European Centre for Disease Prevention and Control which first identified the new more virulent strain, reported that only one method had been affected and this was not widely used for patient testing. Likewise, the Food and Drug Administration in the Unites States has issued a directive indicating which test methods may also be affected by genetic variants of the virus.

In Australia, almost all laboratories are using SARS-CoV-2 tests that detect more than one genetic sequence on the virus, and therefore they are not likely to be affected by single mutations. This strategy was adopted because it was anticipated that variants of the virus would inevitably evolve and testing methods must be able to cope with that problem.

Any part of the virus’s genome can be a target when designing a test.  Several different gene targets are now being used in SARS-CoV-2 tests, including the E (envelope) gene, RdRp (RNA-dependent RNA polymerase) gene, the N1 and N2 (nucleocapsid) gene, the ORF (Open Reading Frame) and the S gene – taken from the spike on the virus that binds to the ACE receptor; this is also a target for some vaccines.

However as a precautionary exercise the Therapeutic Goods Administration has indicated that it is conducting a review of all testing methods to check for their ability to cope with the present mutations and any possible future ones.  And like other regulatory bodies the TGA also reminds those who are conducting testing to always consider negative results together with the patient’s symptoms and clinical history and if the latter is strongly suggestive of COVID-19, then consider testing by another method.


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