SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests
The SARS-CoV-2 virus has mutated over time, resulting in genetic variation in the population of circulating viral strains over the course of the COVID-19 pandemic. Molecular, antigen, and serology tests are affected by viral mutations differently due to the inherent design differences of each test.
This page provides information about the impact of viral mutations on COVID-19 tests, recommendations for clinical laboratory staff and health care providers, and information about certain tests for which the FDA has identified potential impacts on performance due to SARS-CoV-2 genetic mutations. The FDA will list tests on this page as the FDA's analyses identify tests for which performance may be impacted for known SARS-CoV-2 variants. For consumer information on COVID-19 testing and SARS-CoV-2 variants, visit Coronavirus Disease 2019 Testing Basics.
The FDA will update this page as significant new information becomes available.
On this page:
- Genetic Variations: Background and Considerations
- General Information for Clinical Laboratory Staff and Health Care Providers
- Omicron Variant: Background
- Omicron Variant: Impact on Antigen Diagnostic Tests
- Omicron Variant: Impact on Molecular Tests
- Other Variants: Molecular Tests that May Be Impacted
- Resources
Genetic Variations: Background and Considerations
A mutation (also referred to as viral mutation or genetic mutation) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is a change in the genetic sequence of the SARS-CoV-2 virus when compared with a reference sequence such as Wuhan-Hu1 (the first genetic sequence identified) or USA-WA1/2020 (the first identified in the United States). A new variant (virus variant or genetic variant) or sub-lineage of SARS-CoV-2 may have one or more mutations that differentiate it from the reference sequences or predominant virus variants already circulating in the population. Variants of SARS-CoV-2 can have different characteristics. For example, some may spread more easily or show signs of resistance to existing treatment options and some may have no impact when compared with previous and currently circulating virus.
The presence of mutations in the SARS-CoV-2 virus in a patient sample can potentially impact test performance. The impact of mutations on a test's performance is influenced by several factors, including the sequence of the variant, the design of the test, and the prevalence of the variant in the population.
The FDA has collaborated with stakeholders to better understand the public health impact of new SARS-CoV-2 variants and their impact on test performance, has been routinely monitoring publicly available databases, and has coordinated efforts to evaluate the impact of new virus variants on tests that have received Emergency Use Authorization (EUA).
In February 2021, the FDA issued the Policy for Evaluating Impact of Viral Mutations on COVID-19 Tests to provide a policy and recommendations on evaluating the potential impact of emerging and future viral mutations of SARS-CoV-2 on COVID-19 tests for the duration of the COVID-19 public health emergency, including considerations for test designs to minimize the impact of viral mutations and recommendations for ongoing monitoring.
On September 23, 2021, the FDA revised the EUAs of certain authorized molecular, antigen, and serology tests to establish additional Conditions of Authorization in response to the continued emergence of new variants of SARS-CoV-2. These conditions have also been included in other EUAs, such that all EUAs previously issued for COVID-19 molecular, antigen, and serology tests include these conditions, and they continue to be included in new EUAs. These conditions require test developers to update their authorized labeling and evaluate the impact of SARS-CoV-2 viral mutations on their test's performance, among other things.
The FDA will update this page as significant new information becomes available, including the information provided by EUA holders in their authorized labeling.
General Information for Clinical Laboratory Staff and Health Care Providers (As of 12/22/2021)
Clinical laboratory staff and health care providers should be aware that false negative results may occur with any molecular test for the detection of SARS-CoV-2, particularly if a mutation occurs in the part of the virus' genome assessed by that test.
Changes in the viral genome can result in changes to viral proteins and, therefore, can also impact the performance of an antigen or serology test.
The FDA recommends clinical laboratory staff and health care providers who use SARS-CoV-2 tests note the following:
- Genetic variants of SARS-CoV-2 arise regularly, and false negative test results can occur.
- Consider negative results in combination with clinical observations, patient history, and epidemiological information.
- Consider repeat testing with a different EUA authorized or FDA cleared molecular diagnostic test (with different genetic targets) if COVID-19 is still suspected after receiving a negative test result.
- Test performance may be impacted by certain variants.
- Tests with single targets are more susceptible to changes in performance due to viral mutations, meaning they are more likely to fail to detect new variants.
- Tests with multiple targets are more likely to continue to perform as described in the test's labeling as new variants emerge. Multiple targets means that a molecular test is designed to detect more than one section of the SARS-CoV-2 genome or, for antigen tests, more than one section of the proteins that make up SARS-CoV-2.
In addition to these general recommendations, the FDA is providing information related to specific variants and recommendations for the use of specific tests that may be impacted by genetic variation in the sections below.
Omicron Variant: Background (As of 12/22/2021)
The omicron variant, B.1.1.529, of SARS-CoV-2, was designated by the United States as a Variant of Concern (VOC) on November 30, 2021. The first confirmed case of omicron in the United States was identified on December 1, 2021.
The omicron variant has significantly more mutations than previous SARS-CoV-2 variants, particularly in its S-gene, the gene that encodes the virus's spike protein.
The FDA is working with our government partners and test developers to evaluate the impact of the omicron variant on SARS-CoV-2 diagnostic tests.
Omicron Variant: Impact on Antigen Diagnostic Tests (As of 12/28/2021)
Throughout the ongoing COVID-19 pandemic, the FDA has been monitoring and evaluating the potential impact of genetic variants on antigen tests.
The FDA is collaborating with the National Institutes of Health's (NIH) RADx program to study the performance of antigen tests with patient samples that have the omicron variant. RADx recently performed preliminary studies evaluating the performance of some antigen tests using patient samples containing live virus, which represents the best way to evaluate true test performance in the short-term. Early data suggests that antigen tests do detect the omicron variant but may have reduced sensitivity.
Prior to completing these live virus tests, RADx conducted initial laboratory tests using heat-inactivated samples for some of the currently available antigen tests, which were able to detect the omicron variant, with similar performance when detecting other variants. Heat-inactivated samples are patient samples with omicron variant that have been heat-treated so that the virus is no longer live. Heat-inactivated samples are the best available option when patient samples with live virus are not available.
It is important to note that these laboratory data are not a replacement for clinical study evaluations using patient samples with live virus, which are ongoing. The FDA and RADx are continuing to further evaluate the performance of antigen tests using patient samples with live virus.
The FDA continues to authorize the use of these tests as directed in the authorized labeling and individuals should continue to use them in accordance with the instructions included with the tests. Antigen tests are generally less sensitive and less likely to pick up very early infections compared to molecular tests. In following the FDA's long-standing rapid test recommendations, if a person tests negative with an antigen test but is suspected of having COVID-19, such as experiencing symptoms or have a high likelihood of infection due to exposure, follow-up molecular testing is important for determining a COVID-19 infection. If a person tests positive with an antigen test, they should self-isolate and seek follow-up care with a health care provider to determine the next steps.
The FDA, our partners, and test developers continue to evaluate test sensitivity, when tests should be performed, and the frequency of testing. The agency is also coordinating with our international regulatory counterparts who are also evaluating the impact of omicron on antigen tests used in their countries.
The agency will provide updated information and any needed recommendations to the public should they become available.
Omicron Variant: Impact on Molecular Tests (As of 12/22/2021)
The FDA's analysis to date has identified certain EUA-authorized molecular tests whose performance may be impacted by mutations in the SARS-CoV-2 omicron variant. These tests fall into two categories, as described below: those that are expected to fail to detect the SARS-CoV-2 omicron variant, and those that are expected to detect the SARS-CoV-2 omicron variant with a specific gene drop out detection pattern.
Tests Expected to Fail to Detect the SARS-CoV-2 Omicron Variant (As of 12/27/2021)
Due to the inability of these tests to detect the SARS-CoV-2 omicron variant, the FDA recommends that these tests should not be used until this issue of these tests' inability to detect the omicron variant is resolved.
- Test Name (Link to EUA): Revogene SARS-CoV-2
- Manufacturer: Meridian Bioscience, Inc.
- The FDA's Analysis: This test is expected to fail to detect the SARS-CoV-2 omicron variant (B.1.1.529) due to a nine-nucleotide deletion in the N-gene, spanning positions 28370-28362. The single genetic target of this test covers the portion of the N-gene where the deletions occur.
- Potential Impact: Since this is a single target test, the test is expected to fail to detect the SARS-CoV-2 omicron variant, resulting in false negative results in patients with the omicron variant. This nine-nucleotide deletion appears to be specific to the omicron variant; therefore, based on initial bioinformatics analysis, the performance of the test is not expected to be impacted for other known SARS-CoV-2 variants.
- Notes: The FDA understands that Meridian Biosciences has not yet distributed this test and does not intend to distribute this test, within or outside the United States, until this issue is resolved. The FDA continues to gather additional information and work with the manufacturer to address this issue.
- Test Name: Linea COVID-19 Assay Kit
- Manufacturer: Applied DNA Sciences
- The FDA's Analysis: This test is expected to fail to detect the SARS-CoV-2 omicron variant (B.1.1.529) due to deletions at amino acid positions 69-70 and mutations at nucleotide positions 23599 (T to G) and 23604 (C to A). The two viral targets of this test cover the portions of the S-gene where these mutations occur.
- Potential Impact: This test has two viral targets on the SARS-CoV-2 genome, and both of the targets will fail to detect the SARS-CoV-2 omicron variant (B.1.1.529), resulting in false negative results in patients with the omicron variant.
- Notes: The FDA continues to gather additional information and work with the manufacturer to address this issue.
Issue Resolved: Tests Previously Expected to Fail to Detect the SARS-CoV-2 Omicron Variant (As of 12/27/2021)
These tests have been modified or otherwise have addressed the issue of their inability to detect the omicron variant.
- Test Name (Link to EUA): DTPM COVID-19 RT-PCR test
- Manufacturer: Tide Laboratories, LLC
- The FDA's Analysis:This test is now expected to detect the SARS-CoV-2 omicron variant (B.1.1.529). The original test was a single target test that was expected to fail to detect the SARS-CoV-2 omicron variant (B.1.1.529) due to a nine-nucleotide deletion in the N-gene, spanning positions 28370-28362, which is within the portion of the N-gene that the single target covered. The test has been modified and is now a multiplex test with an added reverse primer to detect the omicron variant.
- Potential Impact: This test as modified is now expected to detect the SARS-CoV-2 omicron variant (B.1.1.529).
- Notes: Bioinformatics analysis demonstrated a 100% match with omicron variant sequences as well as delta variant sequences. Initial laboratory testing also demonstrates the ability to detect the omicron variant. Additional laboratory testing is ongoing as a condition of the EUA, reissued on December 22, 2021.
Tests with Detection Patterns that May Be Associated with the SARS-CoV-2 Omicron Variant (As of 12/22/2021)
These tests are expected to detect the SARS-CoV-2 omicron variant. Due to mutations found in the SARS-CoV-2 omicron variant, these tests may be useful in identifying samples where omicron may be present so that sequencing can be considered to characterize the variant.
- The FDA's Analysis: Certain mutations in the SARS-CoV-2 omicron variant (B.1.1.529) lead to significantly reduced sensitivity in an N-gene or S-gene genetic target that covers the portion of the gene where the mutation occurs. In tests that are designed to detect multiple genetic targets, where only one genetic target has reduced sensitivity due to a mutation, the tests are still expected to detect the SARS-CoV-2 omicron variant. The detection pattern, showing the drop out, or failure of the affected target, may help to signal the presence of the omicron variant in a patient sample with a positive result so that sequencing can be considered to characterize the variant.
- Potential Impact: Since these tests are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted. The pattern of SARS-CoV-2 detection with one gene drop out may provide a signal that the omicron variant may be present so that sequencing can be considered to characterize the variant. However, testing positive for SARS-CoV-2 with one of these tests does not mean an individual is infected with the omicron variant. Further, not all patient samples with the omicron variant display a mutation that leads to a gene drop out. Therefore, the omicron variant may still be present without a gene drop out detection pattern.
- Notes: These tests are identified based on initial bioinformatics analyses and may not yet have been evaluated against the omicron variant in the laboratory.
Recommendations for Clinical Laboratory Staff and Health Care Providers Using These Tests
- Be aware that the target failure or gene drop out pattern of detection (reduced sensitivity with the one genetic target) when using these tests is consistent with certain mutations, including those in some samples of the omicron variant. If a laboratory reports a gene drop out detection pattern when providing test results, we encourage laboratories to explain what the pattern may or may not mean.
- A gene drop out may occur due to different mutations in other variants and may not be specific to the omicron variant. A gene drop out may also be observed without the presence of a mutation in the target area, due to the sensitivity of the genetic target. Therefore, the presence of a gene drop out detection pattern is not a definitive confirmation of the presence of the omicron variant.
- The presence of a gene drop out detection pattern can signal that sequencing should be considered to characterize the variant in that specimen.
- N-gene and S-gene drop outs are typically not observed in the delta variant. Specimens with a gene drop out detection pattern may be omicron variants and should be prioritized for sequencing confirmation.
- If local or state clinical laboratories have access to quick turnaround whole genome sequencing services, these labs should consider further characterizing the specimen with genetic sequencing when this pattern is identified. If such services are not readily available, local or state clinical laboratories should consider reaching out to the Centers for Disease Control and Prevention at EOCevent177@cdc.gov for additional information.
Tests with N-Gene Drop Out - SARS-CoV-2 Detection Should Not Be Significantly Impacted
For each of the tests listed in the below table, one genetic target is expected to have significantly reduced sensitivity due to a mutation in the SARS-CoV-2 omicron variant (B.1.1.529). A nine-nucleotide deletion in the N-gene, spanning positions 28370-28362, results in an N-gene drop out, also referred to as an N-gene target failure (NGTF), where the genetic target that covers the portion of the N-gene where the deletion occurs fails to detect the virus. Since these tests are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted.
Test Developers | Test Name |
---|---|
DxTerity Diagnostics, Inc. | DxTerity SARS-CoV-2 RT PCR CE Test |
Vela Diagnostics USA, Inc. | ViroKey SARS-CoV-2 RT-PCR Test v2.0 |
Tests with S-Gene Drop Out - SARS-CoV-2 Detection Should Not Be Significantly Impacted
For each of the tests listed in the below table, one genetic target is expected to have significantly reduced sensitivity due to a mutation in the SARS-CoV-2 omicron variant (B.1.1.529). A specific deletion in the spike (S) gene (Δ69-70) results in an S-gene drop out, also referred to as an S-gene target failure (SGTF), where the genetic target that covers the portion of the S-gene where the deletion occurs fails to detect the virus.
Since these tests are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted.
* The TaqPath COVID-19, FluA, FluB Combo Kit is expected to have an S-gene drop out due to the presence of a mutation in the S-gene, without a significant impact to overall test sensitivity. However, due to the design of the test, there will not be a distinct S-gene detection pattern to signal the potential presence of the omicron variant.
Other Variants: Impact on Diagnostic Tests (As of 12/15/2021)
Several variants have been in circulation in the United States at various times during the pandemic. As part of the FDA's analysis of the impact of viral mutations on COVID-19 tests, the FDA has identified certain tests whose performance may be impacted by SARS-CoV-2 viral mutations. Note that the variants discussed in this section may no longer be the predominantly circulating variants in the United States, which are discussed in the above sections of this webpage.
- Test Name (Link to EUA): Accula SARS-CoV-2 Test
- Manufacturer: Mesa Biotech Inc.
- The FDA's Analysis: Performance may be impacted when a SARS-CoV-2 patient sample having certain viral mutations is tested. The FDA previously alerted health care providers about a potential performance impact due to a genetic mutation at positions 28881-28883 (GGG to AAC). In addition, there is potential impact on performance of the test due to a genetic mutation at positions 28877-28878 (AG to TC) in patient samples.
- Potential Impact: While the impact does not appear to be significant, the FDA is providing this information out of an abundance of caution.
- Notes: The FDA's analysis included information provided by the manufacturer.
Recommendations for Clinical Laboratory Staff and Health Care Providers Using This Test
Be aware that the current instructions for use for the Accula SARS-CoV-2 Test include the exact variant location, in silico analysis of the primer binding, and observed performance impact due to genetic mutation at positions 28881-28883 (GGG to AAC) when compared with the perfect match target, but do not yet include specific information about impact from a genetic mutation at positions 28877-28878 (AG to TC).
- Test Name (Link to EUA): Linea COVID-19 Assay Kit
- Manufacturer: Applied DNA Sciences, Inc.
- The FDA's Analysis: One of the two targets of the test has significantly reduced sensitivity due to certain mutations, including one of the mutations in the B.1.1.7 variant (UK VOC-202012/01).
- Potential Impact: Since this test is designed to detect multiple genetic targets, the overall test sensitivity should not be impacted. The pattern of detection when certain mutations are present may help with early identification of new variants in patients to reduce further spread of infection.
- Notes: The FDA's analysis included information provided by the manufacturer.
Recommendations for Clinical Laboratory Staff and Health Care Providers Using This Test
Be aware that one positive target and one negative target showing the S-gene drop out (reduced sensitivity with the S-gene target) when using the Linea COVID-19 Assay Kit is consistent with certain mutations, including those in the B.1.1.7 variant. If local or state clinical laboratories have access to quick turnaround whole genome sequencing services these labs should consider further characterizing the specimen with genetic sequencing when this pattern is identified. If such services are not readily available, local or state clinical laboratories should consider reaching out to the Centers for Disease Control and Prevention at EOCevent177@cdc.gov for additional information.
- Test Name (Link to EUA): TaqPath COVID-19 Combo Kit (may also be labeled as the TaqPath COVID-19 Combo Kit Advanced)
- Manufacturer: Thermo Fisher Scientific, Inc.
- The FDA's Analysis: One of three targets of the test has significantly reduced sensitivity due to certain mutations, including one of the mutations in the B.1.1.7 variant (UK VOC-202012/01).
- Potential Impact: Since this test is designed to detect multiple genetic targets, the overall test sensitivity should not be impacted. The pattern of detection when certain mutations are present may help with early identification of new variants in patients to reduce further spread of infection.
- Notes: The FDA's analysis included information provided by the manufacturer and multiple reports from clinical laboratories.
Recommendations for Clinical Laboratory Staff and Health Care Providers Using This Test
Be aware that two positive targets and one negative target showing the S-gene drop out (reduced sensitivity with the S-gene target) when using the TaqPath COVID-19 Combo Kit is consistent with certain mutations, including those in the B.1.1.7 variant. If local or state clinical laboratories have access to quick turnaround whole genome sequencing services these labs should consider further characterizing the specimen with genetic sequencing when this pattern is identified. If such services are not readily available, local or state clinical laboratories should consider reaching out to the Centers for Disease Control and Prevention at EOCevent177@cdc.gov for additional information.
- Test Name (Link to EUA): Xpert Xpress SARS-CoV-2; Xpert Xpress SARS-CoV-2 DoD; Xpert Omni SARS-CoV-2
- Manufacturer: Cepheid
- The FDA's Analysis: While it is generally unexpected that a single point mutation will impact test performance for most SARS-CoV-2 molecular tests, the FDA's analysis indicates that the Cepheid tests are impacted by a single point mutation in the target area of the test. There are reports noting that two independent single point mutations reduce the test's sensitivity for detecting the N2 target. The E target is still detected when enough virus is present leading to a "presumptive positive" result in the Xpert Xpress SARS-CoV-2 and Xpert Xpress SARS-CoV-2 DoD tests. Detection of the E target without detecting the N2 target will be reported as "positive" in the Xpert Omni SARS-CoV-2
- Potential Impact: Since this test is designed to detect multiple genetic targets, and these mutations do not lead to a false negative patient result (instead reporting as "presumptive positive" or "positive" based on detection of the conserved E gene target), the impact on test performance does not appear to be significant. However, the FDA is providing this information out of an abundance of caution. The FDA's analysis suggests that the impact of a single point mutation on the test performance is associated with the unique chemistry of the Cepheid tests.
- Notes: The FDA continues to gather additional information and work with the manufacturer to address this issue.
Recommendations for Clinical Laboratory Staff and Health Care Providers Using This Test
Be aware of the current instructions for use for each test, especially the "Possible Results" and "Results and Interpretation" tables, which describe when a result is positive, presumptive positive, negative, and invalid, and how to interpret each result. Specifically, "SARS-CoV-2 Presumptive Positive" results may indicate the presence of SARS-CoV-2 nucleic acids, and repeat testing may be indicated; refer to the authorized instructions for use. Clinical laboratory staff and health care providers should contact Cepheid if they have any questions or concerns or suspect an issue with their Cepheid test.
Resources
- Policy for Evaluating Impact of Viral Mutations on COVID-19 Tests
- Revision Concerning Viral Mutation
- Genetic Variants of SARS-CoV-2 May Lead to False Negative Results with Molecular Tests for Detection of SARS-CoV-2 - Letter to Clinical Laboratory Staff and Health Care Providers (January 8, 2021)