Can existing RTPCR tests detect Omicron variant of COVID-19? Explained

The Omicron variant of COVID-19 (SARS-CoV2) is being perceived as a major threat, with the World Health Organization (WHO) Sunday assessing the global risk as “very high”. Preliminary data indicates that Omicron could have higher transmissibility compared to other variants detected so far, and also has a greater ability to evade the immune response generated either through prior infection or vaccines.

Health experts in India on Monday claimed that the currently available measures of diagnostics may fail in accurately detecting the Omicron variant of COVID-19. The RT-PCR test is considered to be the ‘gold standard’ for detecting Coronavirus in India. However, with the emergence of the new variant, the focus is on a highly accurate identifier of infection.

Can the RTPCR test detect Omicron?

The Reverse Transcription-Polymerase Chain Reaction, or RT-PCR, test detects the presence of specific genetic material in a pathogen. In the case of the COVID-19, most RT-PCR tests target the genes in its spike protein, which the virus uses to invade human cells.

To conduct an RT-PCR test, short strands of DNA are mixed with the swab sample. These DNA fragments can attach to a target DNA. The novel coronavirus is an RNA virus, so the RT-PCR test first converts the RNA into DNA using specific enzymes, a method called ‘reverse transcription.' The mixture is then placed in a PCR machine, where fluorescent dyes eventually amplify the target DNA in case the infection is present.

To ensure that the test is accurate, two or more spike genes are targeted so that even if a mutation may have changed one of the genes, the other would still get captured in the test. That has proved to be an advantage in detecting an infection with the new Omicron variant since one of its specific mutations is not captured by certain RT-PCR tests.

The World Health Organisation (WHO) said that this phenomenon called 'S gene dropout' or 'S gene target failure'. This means that specific RT-PCR tests can “be used as a marker for this variant, pending sequencing confirmation". The WHO added that “using this approach, this variant has been detected at faster rates than previous surges in infection".

So can Omicron evade RTPCR tests?

No. As mentioned above, only one mutation escapes detection by the RT-PCR test, which uses two or three target genes to track the pathogen. The WHO has clarified that “most diagnostic tests continue to work and can detect" Omicron, although it is being assessed whether rapid antigen tests (RAT) are still effective in confirming positive cases. Meanwhile, amid apprehensions over whether tests can detect Omicron, the Centre maintained that this new variant cannot escape the RT-PCR or RAT test.

First detected in Botswana and South Africa, Omicron has since spread to various countries in Europe, including Belgium, the Netherlands, France, and the UK, in Australia and Canada, among others.

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