Omicron enters the COVID-19 battle

Dec. 22, 2021

As 2022 dawns, a world weary from battling SARS-CoV-2 faces a new variant of the virus: Omicron (B.1.1.529).

The World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) have classified Omicron as a variant of concern (VOC). It has a large number of mutations, including 26-32 in the spike protein.

The good news is that most diagnostic RT-PCR and antigen tests do not appear to be impacted by Omicron, according to the WHO. The issue is whether a diagnostic test will produce accurate results if a mutation occurs in the genetic target that the test is designed to detect.

If a test detects multiple targets, it will still detect the presence of SARS-CoV-2, via the other targets, and produce accurate test results. Since many of the widely used tests do, in fact, use multiple targets to detect the presence of SARS-CoV-2 in a specimen, they should continue to produce accurate results, according to the U.S. Food and Drug Administration (FDA), which has been assessing the performance of various tests based on the mutations present in Omicron. The agency also has been posting the results of its assessments online, so clinical labs have the information they need to provide diagnostic testing services.

Most of the sequences of Omicron that labs have performed show a deletion in the S gene. That is why vendors whose tests target the S gene (in addition to other targets) have suggested that their tests could be used to flag specimens that may contain Omicron. Those specimens could then be prioritized for sequencing to confirm the presence of the variant. Sequencing is necessary to make an official determination on the presence of Omicron because the S-gene deletion can also be found in Alpha and subsets of Gamma and Delta, according to the WHO.

Sequencing specimens to track the activity of various SARS-CoV-2 variants is also a central component of surveillance efforts.

As of early December, the WHO said Omicron already had been identified in 63 countries. The WHO also predicts that Omicron will spread more rapidly than Delta did. “It is spreading faster than the Delta variant in South Africa where Delta circulation was low, but also appears to spread more quickly than the Delta variant in other countries where the incidence of Delta is high, such as in the United Kingdom. Whether Omicron’s observed rapid growth rate, in countries with high levels of population immunity, is related to immune evasion, intrinsic increased transmissibility, or a combination of both remains uncertain. However, given the current available data, it is likely that Omicron will outpace the Delta variant where community transmission occurs,” the WHO said.

The WHO also said the overall risk presented by Omicron is very high. “Preliminary evidence suggests potential humoral immune escape against infection and high transmission rates, which could lead to further surges with severe consequences.”

What all of this means for clinical laboratorians is clear: They are likely to spend a lot of their time in 2022, as they did in 2020 and 2021: testing specimens for evidence of SARS-CoV-2.

I welcome your comments, questions, and opinions – please send them to me at [email protected].