Audience: Laboratories Performing COVID-19 Testing

Level: Laboratory Alert

On November 30, 2021, the SARS-CoV-2 Interagency Group (SIG) classified the new SARS-CoV-2 variant (B.1.1.529, also called Omicron) as a Variant of Concern, which matches the designation used by the World Health Organization (WHO). South Africa was the first to report this variant to the WHO. By December 1, the Omicron variant had been detected in at least 20 countries in addition to those in Southern Africa, including the United States, Israel, Hong Kong, Nigeria, Saudi Arabia, South Korea, Australia, Canada, the United Kingdom, and several European countries.

CDC has issued a Health Alert Notification (HAN) to inform physicians about this situation and provide recommendations for public health departments, testing laboratories, healthcare providers, and the general public.

What Laboratories Should Know: 

-There are no authorized, cleared, or approved diagnostic tests to specifically detect SARS-CoV-2 variants (Omicron or other variants). Currently, COVID-19 tests are designed and authorized to check broadly for the SARS-CoV-2 virus, not for specific variants.

-The Omicron variant has a deletion in the spike (S) gene (Δ69-70). Some molecular tests with multiple genetic targets include a target covering the portion of the S gene where the deletion occurs. The presence of this mutation can result in an S-gene target failure (SGTF, also referred to as an S-gene drop out). The S-gene target will fail (return as negative) while other targets are expected to remain positive in the presence of this virus. SGTF can signal the need for sequencing to characterize the variant in a specimen.

-SGTF has been observed in other variants and thus is not specific to the Omicron variant. SGTF has also been observed without the presence of a mutation in the S gene, due to the sensitivity of the S-gene target. Therefore, these tests cannot be used as a diagnostic tool or specific identifier of the Omicron variant.

-SGTF is not typically observed in the Delta variant. Since Delta is the primary variant circulating in the United States, specimens with an SGTF profile may be potentially Omicron variants and should be prioritized for sequencing confirmation.

-The U.S. Food and Drug Administration (FDA) updated the SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests web page to identify currently authorized tests that may be affected by the Omicron variant, including those with SGTF. These tests are identified based on initial bioinformatics analyses and may have not yet been evaluated against the Omicron variant in the laboratory.

-If you are using a test that may have SGTF, it can potentially be used for public health surveillance efforts for identifying a case with a potential Omicron variant. Laboratories should reach out to their state health departments (SHDs) or local public health laboratory for information about their notification protocols and to potentially provide specimens for sequencing.

-Results regarding the presence of the Omicron variant, or any other variant, should not be reported back to patients or providers and cannot be used for diagnostic purposes.