Lab-Based COVID-19 PCR Tests Fail to Distinguish New ‘Stealth’ Version of Omicron from Other Variants

Scientists claim to have identified a “stealth” version of Omicron that cannot be distinguished from other SARS-CoV-2 variants using PCR tests utilized by public health officials to gain an understanding of its spread globally. The first Omicron (B.1.1.529) case was reported to the World Health Organization (WHO) on November 24. Just two days later, the WHO designated the variant a Variant of Concern (VOC), based on its unusually large number of mutations and early evidence of its spread. Despite a series of rapidly implemented travel bans, it has now been reported in Africa, many European countries, and a few in Asian countries.

The newly-discovered variant of Omicron shares several mutations with the standard Omicron, but lacks a specific genetic change that allows probable cases to be flagged by lab-based PCR tests. Most PCR machines look for three genes in the virus, although Omicron (and the prior variant Alpha) test positive on only two of these machines due to a genetic change called a deletion in the “S” or spike gene in both Omicron and Alpha. As a result of this glitch, PCR tests that display the so-called “S gene target failure” are highly suggestive of Omicron infections. The commonly used tests can still detect the stealth variant of Omicron as coronavirus, and genomic testing can identify it as the Omicron variant, although routine PCR tests that deliver quicker results can fail to flag probable cases.

Following the discovery of the new form of the Omicron variant, researchers have now split the B.1.1.529 lineage into standard Omicron, known as BA.1, and the newer variant, known as BA.2. Some researchers have now termed the new variant as “stealth Omicron” due to its lack of deletion that allows it to be spotted by PCR tests. Despite falling under Omicron, the stealth variant is so genetically distinct that it could qualify as a new VOC if it spreads rapidly. Researchers are worried over the arrival of two variants, BA.1 and BA.2, in quick succession with shared mutations that could indicate public health surveillance “is missing a big piece of the puzzle”.