COVID-19 Test Makers Confirm Their Assays Spot Omicron Variant
By Sam Brusco, Associate Editor | 12.01.21
Over 30 mutations to the virus' spike protein raise concerns about diagnostic testing accuracy and efficacy.
Initially identified in South Africa and subsequently in a number of African, European, and North American countries, the Omicron variant (B.1.1.529) of the SARS-CoV-2 virus contains about 30 mutations in its spike protein alone. As a result, there has been some concern that currently available diagnostic tests may be less effective in spotting the Omicron variant.
The WHO reported preliminary evidence suggests Omicron has an increased transmission risk compared to other variants of concern. This designation and information are leading to renewed travel restrictions and research to examine the variant's impact on existing vaccine and test accuracy.
Firms specializing in diagnostic tests for COVID-19 are working quickly to confirm their tests are still effective. Following are those that have confirmed via internal studies. (This list will be updated as more results come to light.)
The company conducted an assessment of Omicron and confirmed its rapid and PCR COVID-19 tests can detect the virus. According to Abbott, although the spike protein is mutated, the tests do not rely on the spike gene to spot the virus. Abbott’s Pandemic Defense Coalition— network of research, academic, and public health collaborators strategically placed around the globe—is actively sequencing viruses to look for COVID variants. The group is actively engaged with its partner in South Africa on Omicron.
“We also have an entire team of Abbott scientists dedicated to monitoring COVID-19 variants,” the company announced on its website. “To date, we have carefully analyzed over 1.4 million sequences from 63 different variants and none have impacted the ability of our diagnostic tests to detect the virus. And as soon as the Omicron sequence was made available, our scientists worked non-stop to evaluate it and determined the mutations would not impact the ability of our rapid and PCR tests to detect it."
The company released a statement on Tuesday regarding testing for the Omicron variant. Dave Hickey, BD’s president of Life Sciences, told the press:
"Our analysis of the Omicron variant was conducted using all available genome sequences deposited in the GISAID EpiCoV database as of Nov. 29. When live viral samples are made available, BD will perform additional rigorous testing in the laboratory. BD actively monitors all sequenced SARS-CoV-2 isolates worldwide. Our team has evaluated over 3.5 million genomes to monitor for emerging variants. Variants of concern have been tested by BD and our partners and no undetectable variants have been identified. "Reliable and widely available testing remains one of the most important measures to mitigate the spread of COVID-19. BD will continue to monitor and verify the performance of its COVID-19 tests to serve its mission of advancing the world of health."
According to the company, its portfolio of BioGX SARS-CoV-2 products that target the nucleocapsid (N-gene) and envelope (E-gene) will spot Omicron. Analysis conducted by BioGX confirmed the BioGX portfolio of COVID-19 tests maintain detection coverage for all variants of interest and variants of concern.
Hologic’s three SARS-CoV-2 tests—the Aptima SARS-CoV-2 Assay, Aptima SARS-CoV-2/Flu Assay, and Panther Fusion SARS-CoV-2 Assay—all detect the recently emerged variant, according to the company. Hologic analyzed genetic sequences from over 175 Omicron-infected samples to determine that none of the new mutations occur in the genome regions these tests target.
“We fully expect that SARS-CoV-2 will continue to evolve, as that is the natural path for viruses,” Kevin Thornal, Hologic’s Diagnostic Solutions Division president told the press. “We designed our assays with this in mind, and as a result, we are confident that the Omicron variant will not impact the performance of our assays.”
The company’s Lucira Check-It (OTC) and All-In-One (Rx) test kits have been confirmed by the company to detect Omicron. The company’s evaluation determined its COVID-19 assay can spot 100 percent of genome sequences of the Omicron variant available in the GISAID database as of November 26.
"While there is still a lot to learn about the Omicron variant, the ability to detect circulating strains is fundamental to help slow the virus spread," Debkishore Mitra, Ph.D., chief technology officer and co-founder of Lucira Health told the press. "This is why our team is relentlessly assessing newly available genetic sequences against our test."
The company has reported its SARS-CoV RT-PCR tests are not impacted by Omicron’s emergence. The over 30 mutations occur in its S gene, and the company’s assays don’t target the S gene for SARS-CoV-2 detection. In silico assessment against variant databases such as GISAID confirm that none of the mutations associated with Omicron variant impact PerkinElmer’s PCR based diagnostic kits.
“Omicron contains a large number of mutations in the S gene, adding to concerns about transmissibility, immune system evasion, and vaccine resistance. It is critical to ensure that the diagnostic accuracy of SARS-CoV-2 detection assays is not compromised due to Omicron and other variants,” Arvind Kothandaraman, managing director of specialty diagnostics at PerkinElmer told the press.
The company’s PCR tests remain accurate and effective, according to an announcement made on November 26. This includes the artus SARS-CoV-2 Prep&Amp UM Kit, QIAstat-Dx syndromic testing system, NeuMoDx 96 and 288 integrated PCR testing systems, QIAcuity digital PCR solution, and QIAprep& Viral RNA kit.
The assessment was made against data available in the GISAID and GenBank public databases.
“We are pleased to report that the emergence of this new variant of concerns, as has been the case with other variants, has had no impact on the effectiveness of our SARS-CoV-2 PCR tests,” QIAGEN chief medical officer Dr. Davide Manissero told the press. “Further genomic sequencing of SARS-CoV-2 samples worldwide will vastly increase transparency and help us identify and respond to potentially dangerous mutations of the virus, while at the same time broadening the database we can use to verify if vaccines and tests continue to be effective.”
The company announced its Rheonix COVID-19 MDx assay will detect the newly emerging variant. Assessments indicated the assay spots all SARS-CoV-2 variants of concern.
“Rheonix continually assesses the potential impact of variants on assay performance by conducting in silico analysis of publicly available SARS-CoV-2 sequence data as well as laboratory testing of prevalent variants,” Gwendolyn Spizz, Ph.D., chief scientist at Rheonix told the press. “The robust design of the Rheonix COVID-19 MDx Assay has allowed for the detection of all designated variants of concern to date, including the delta variant. Based on our analysis, we are highly confident in our ability to detect the omicron variant, and we will continue to rigorously monitor the public genome databases.”
The company's Allplex SARS-CoV-2 Master Assay was deemed capable of detecting Omicron's unique pattern of mutations. The test simultaneously detects four wild-type SARS-CoV-2 genes (E gene, RdRP gene, N gene, and S gene) and five notable S-gene mutations: HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H. Since the latest variant Omicron contains HV69/70 deletion, N501Y, and P681H mutations, this test can detect Omicron.
“In order to contain the further spread of Omicron, it is extremely important to preemptively detect the Omicron variant at the primary screening stage,” Dr. Jong-Yoon Chun, Seegene founder and CEO told the press. “To that end, we will fully support countries in need of our tests to enable more rapid detection of the latest variant. Along with strengthening surveillance testing, the implementation of relevant quarantine measures will give more time for countries around the world to contain the rising Omicron infections and protect their citizens.”
The company’s TaqPath COVID-19 Combo Kit and TaqPath COVID-19 CE-IVD RT-PCR Kit accuracy has not been impacted. According to the company, The TaqPath COVID-19 assays detect infections by identifying the presence of three gene targets from the orf1a/b, S, and N regions of the virus. By surveying across multiple genes, the test can report accurate results even when one of the targets is impacted by a mutation.
In addition to the original tests, the firm has developed the TaqPath COVID-19 2.0 tests to compensate for emerging mutations. The assays detect SARS-CoV-2 by utilizing eight gene targets across the orf1a/b and N regions of the virus. These were also assessed against sequences in the GISAID public database and confirmed in silico to detect all B.1.1.529 mutations with no loss in sensitivity.
Specific genotyping assays to detect Omicron are being developed for the company’s TaqMan Mutation Panel. It is currently used for research purposes and already has a menu of over 50 assays to assess confirmed COVID-19 cases for the presence of known variants and mutations.
"Like all viruses, we have always known that SARS-CoV-2 would continue to mutate, and that effective testing strategies are a key to curbing the pandemic," said Mark Stevenson, exec. VP and COO of Thermo Fisher Scientific. "That is why we developed assays with additional built-in checks and balances, to ensure that clinicians, researchers and public health officials would have effective tools to accurately test for COVID-19 even as the genetic makeup of the virus evolved."
The WHO reported preliminary evidence suggests Omicron has an increased transmission risk compared to other variants of concern. This designation and information are leading to renewed travel restrictions and research to examine the variant's impact on existing vaccine and test accuracy.
Firms specializing in diagnostic tests for COVID-19 are working quickly to confirm their tests are still effective. Following are those that have confirmed via internal studies. (This list will be updated as more results come to light.)
Abbott Laboratories
The company conducted an assessment of Omicron and confirmed its rapid and PCR COVID-19 tests can detect the virus. According to Abbott, although the spike protein is mutated, the tests do not rely on the spike gene to spot the virus. Abbott’s Pandemic Defense Coalition— network of research, academic, and public health collaborators strategically placed around the globe—is actively sequencing viruses to look for COVID variants. The group is actively engaged with its partner in South Africa on Omicron.
“We also have an entire team of Abbott scientists dedicated to monitoring COVID-19 variants,” the company announced on its website. “To date, we have carefully analyzed over 1.4 million sequences from 63 different variants and none have impacted the ability of our diagnostic tests to detect the virus. And as soon as the Omicron sequence was made available, our scientists worked non-stop to evaluate it and determined the mutations would not impact the ability of our rapid and PCR tests to detect it."
Becton Dickinson
The company released a statement on Tuesday regarding testing for the Omicron variant. Dave Hickey, BD’s president of Life Sciences, told the press:
"Our analysis of the Omicron variant was conducted using all available genome sequences deposited in the GISAID EpiCoV database as of Nov. 29. When live viral samples are made available, BD will perform additional rigorous testing in the laboratory. BD actively monitors all sequenced SARS-CoV-2 isolates worldwide. Our team has evaluated over 3.5 million genomes to monitor for emerging variants. Variants of concern have been tested by BD and our partners and no undetectable variants have been identified. "Reliable and widely available testing remains one of the most important measures to mitigate the spread of COVID-19. BD will continue to monitor and verify the performance of its COVID-19 tests to serve its mission of advancing the world of health."
BioGX
According to the company, its portfolio of BioGX SARS-CoV-2 products that target the nucleocapsid (N-gene) and envelope (E-gene) will spot Omicron. Analysis conducted by BioGX confirmed the BioGX portfolio of COVID-19 tests maintain detection coverage for all variants of interest and variants of concern.
Hologic
Hologic’s three SARS-CoV-2 tests—the Aptima SARS-CoV-2 Assay, Aptima SARS-CoV-2/Flu Assay, and Panther Fusion SARS-CoV-2 Assay—all detect the recently emerged variant, according to the company. Hologic analyzed genetic sequences from over 175 Omicron-infected samples to determine that none of the new mutations occur in the genome regions these tests target.
“We fully expect that SARS-CoV-2 will continue to evolve, as that is the natural path for viruses,” Kevin Thornal, Hologic’s Diagnostic Solutions Division president told the press. “We designed our assays with this in mind, and as a result, we are confident that the Omicron variant will not impact the performance of our assays.”
Lucira
The company’s Lucira Check-It (OTC) and All-In-One (Rx) test kits have been confirmed by the company to detect Omicron. The company’s evaluation determined its COVID-19 assay can spot 100 percent of genome sequences of the Omicron variant available in the GISAID database as of November 26.
"While there is still a lot to learn about the Omicron variant, the ability to detect circulating strains is fundamental to help slow the virus spread," Debkishore Mitra, Ph.D., chief technology officer and co-founder of Lucira Health told the press. "This is why our team is relentlessly assessing newly available genetic sequences against our test."
PerkinElmer
The company has reported its SARS-CoV RT-PCR tests are not impacted by Omicron’s emergence. The over 30 mutations occur in its S gene, and the company’s assays don’t target the S gene for SARS-CoV-2 detection. In silico assessment against variant databases such as GISAID confirm that none of the mutations associated with Omicron variant impact PerkinElmer’s PCR based diagnostic kits.
“Omicron contains a large number of mutations in the S gene, adding to concerns about transmissibility, immune system evasion, and vaccine resistance. It is critical to ensure that the diagnostic accuracy of SARS-CoV-2 detection assays is not compromised due to Omicron and other variants,” Arvind Kothandaraman, managing director of specialty diagnostics at PerkinElmer told the press.
QIAGEN
The company’s PCR tests remain accurate and effective, according to an announcement made on November 26. This includes the artus SARS-CoV-2 Prep&Amp UM Kit, QIAstat-Dx syndromic testing system, NeuMoDx 96 and 288 integrated PCR testing systems, QIAcuity digital PCR solution, and QIAprep& Viral RNA kit.
The assessment was made against data available in the GISAID and GenBank public databases.
“We are pleased to report that the emergence of this new variant of concerns, as has been the case with other variants, has had no impact on the effectiveness of our SARS-CoV-2 PCR tests,” QIAGEN chief medical officer Dr. Davide Manissero told the press. “Further genomic sequencing of SARS-CoV-2 samples worldwide will vastly increase transparency and help us identify and respond to potentially dangerous mutations of the virus, while at the same time broadening the database we can use to verify if vaccines and tests continue to be effective.”
Rheonix
The company announced its Rheonix COVID-19 MDx assay will detect the newly emerging variant. Assessments indicated the assay spots all SARS-CoV-2 variants of concern.
“Rheonix continually assesses the potential impact of variants on assay performance by conducting in silico analysis of publicly available SARS-CoV-2 sequence data as well as laboratory testing of prevalent variants,” Gwendolyn Spizz, Ph.D., chief scientist at Rheonix told the press. “The robust design of the Rheonix COVID-19 MDx Assay has allowed for the detection of all designated variants of concern to date, including the delta variant. Based on our analysis, we are highly confident in our ability to detect the omicron variant, and we will continue to rigorously monitor the public genome databases.”
Seegene
The company's Allplex SARS-CoV-2 Master Assay was deemed capable of detecting Omicron's unique pattern of mutations. The test simultaneously detects four wild-type SARS-CoV-2 genes (E gene, RdRP gene, N gene, and S gene) and five notable S-gene mutations: HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H. Since the latest variant Omicron contains HV69/70 deletion, N501Y, and P681H mutations, this test can detect Omicron.
“In order to contain the further spread of Omicron, it is extremely important to preemptively detect the Omicron variant at the primary screening stage,” Dr. Jong-Yoon Chun, Seegene founder and CEO told the press. “To that end, we will fully support countries in need of our tests to enable more rapid detection of the latest variant. Along with strengthening surveillance testing, the implementation of relevant quarantine measures will give more time for countries around the world to contain the rising Omicron infections and protect their citizens.”
Thermo Fisher Scientific
The company’s TaqPath COVID-19 Combo Kit and TaqPath COVID-19 CE-IVD RT-PCR Kit accuracy has not been impacted. According to the company, The TaqPath COVID-19 assays detect infections by identifying the presence of three gene targets from the orf1a/b, S, and N regions of the virus. By surveying across multiple genes, the test can report accurate results even when one of the targets is impacted by a mutation.
In addition to the original tests, the firm has developed the TaqPath COVID-19 2.0 tests to compensate for emerging mutations. The assays detect SARS-CoV-2 by utilizing eight gene targets across the orf1a/b and N regions of the virus. These were also assessed against sequences in the GISAID public database and confirmed in silico to detect all B.1.1.529 mutations with no loss in sensitivity.
Specific genotyping assays to detect Omicron are being developed for the company’s TaqMan Mutation Panel. It is currently used for research purposes and already has a menu of over 50 assays to assess confirmed COVID-19 cases for the presence of known variants and mutations.
"Like all viruses, we have always known that SARS-CoV-2 would continue to mutate, and that effective testing strategies are a key to curbing the pandemic," said Mark Stevenson, exec. VP and COO of Thermo Fisher Scientific. "That is why we developed assays with additional built-in checks and balances, to ensure that clinicians, researchers and public health officials would have effective tools to accurately test for COVID-19 even as the genetic makeup of the virus evolved."
Tests Expected to Fail
Due to the inability of these tests to detect the Omicron variant, the FDA recommends the following tests should not be used until the issue is resolved:- Meridian Bioscience, Inc. Revogene SARS-CoV-2
- Tide Laboratories DTPM COVID-19 RT-PCR Test
- Applied DNA Science Linea COVID-19 Assay Kit
