- The emergence of a new COVID-19 variant, named Omicron (B.1.1.529), is putting pressure on diagnostics manufacturers who test for the presence of SARS-CoV-2 to ensure its results are not impacted. Thermo Fisher Scientific, Qiagen and Lucira Health were quick to claim their tests can detect the emerging variant.
- Omicron has been designated a "variant of concern" by the World Health Organization which reported that preliminary evidence suggests an increased risk of transmission compared to other variants. While scientists are still trying to better understand the new variant discovered in South Africa that may allow it to spread quickly, even among the vaccinated, test makers are trying to reassure the public that its COVID-19 diagnostics are effective in detecting omicron.
- Thermo Fisher on Monday confirmed that its polymerase chain reaction TaqPath COVID-19 testing kits provide accurate test results and are able to detect SARS-CoV-2 in samples containing the omicron variant. Qiagen has also evaluated its PCR tests against the genetic mutations of the variant, finding that their diagnostics remain accurate and effective in light of the emergence of B.1.1.529. Lucira's evaluation of omicron also showed that its COVID-19 at-home molecular tests can detect 100% of variant genome sequences analyzed.
Omicron has now been reported in at least a dozen countries in Africa, Europe, the Eastern Mediterranean and Western Pacific regions, according to WHO. The designation of omicron as a variant of concern by WHO is reserved for dangerous variants that may spread quickly, cause severe disease or decrease the effectiveness of vaccines and treatments. The last coronavirus variant to receive this WHO label was the delta variant, which currently accounts for virtually all COVID-19 cases in the United States.
While FDA has been monitoring SARS-CoV-2 viral mutations and potential impacts on testing throughout the pandemic, the agency has yet to provide guidance on the emerging omicron variant of concern which has more than 30 mutations in the spike protein alone.
FDA has previously warned clinical laboratory staff and healthcare providers about the potential impact of viral mutations on authorized COVID-19 molecular tests and that false negative results can occur with any such test for the detection of SARS-CoV-2 if a mutation occurs in the part of the virus's genome assessed by that test.
In January, FDA first reported PCR tests from Applied DNA Sciences, Mesa Biotech and Thermo Fisher may be affected by variants but said the impact does not appear to be significant, later adding Cepheid products to the agency's list.
However, Thermo Fisher pointed out in its Monday announcement that WHO and the European Centers for Disease Control have both reported that using S-gene target failure (SGTF) of the PCR assays as a proxy for the variant helped to identify omicron.
The omicron variant has been found to include the 69-70del mutation of the S gene, first identified as a mutation in the alpha variant, which causes a "dropout" of the S-gene target in results from Thermo Fisher's TaqPath test and is suggestive of the presence of the new variant.
"The Thermo Fisher test allowed us to detect cases that may contain the new variant by identifying samples exhibiting S-gene dropout," Tulio de Oliveira, director of South Africa's Centre for Epidemic Response and Innovation, Stellenbosch University and UKZN, said in a statement in Thermo Fisher's announcement. "This early identification is very important in helping us track and understand the spread of the B.1.1.529 variant to South Africa and the world."
WHO on Sunday stated that several labs "have indicated that for one widely used PCR test (ThermoFisher TaqPath), one of the three target genes is not detected (called S gene dropout or S gene target failure, SGTF) and this test can therefore be used as marker for this variant, pending sequencing confirmation."
FDA in September revised the EUAs of certain authorized molecular, antigen and serological tests to establish additional Conditions of Authorization in response to the continued emergence of new variants of SARS-CoV-2. The additional conditions require test developers to update their authorized labeling and evaluate the impact of viral mutations on their test’s performance, among other things.
Qiagen on Monday said it has been closely monitoring the performance of its PCR tests as new variants emerge, including for omicron and that surveillance of genetic variations will continue on a biweekly basis.
Lucira also said it is performing ongoing surveillance of emerging SARS-CoV-2 strains by assessing reactivity against genome sequence databases, adding that the company's recent finding that its COVID-19 assay can detect 100% of genome sequences of the omicron variant is consistent with previously identified variants including alpha, beta, delta and gamma.