As SARS-CoV-2 changes over time, the FYR Pandemic Response Taskforce will continue to provide information on emerging Variants of Concern (VOC), with the goal of disseminating the most up to date, scientifically sound information. FYR maintains close contact with state and federal officials and actively collaborates with the Montana Department of Public Health and Human Services.
Where is Omicron (B.1.1.529)? Has Omicron been detected in Montana?
Since FYR’s last December 1st update, Omicron has been detected in over 85 countries and in 38 states. Omicron has not been detected in Montana yet.
Omicron currently accounts for 3% of cases in the United States, where the Delta variant still predominates. However, Omicron quickly overtook Delta in South Africa, where data indicates that Omicron spread there with a doubling time of between 3-4 days. In the UK, early numbers suggest Omicron is spreading with a doubling time of between 2-3 days, and in the city of London, Omicron is already the dominant variant. The doubling time is the amount of time it takes for the number of identified Omicron cases to double. This epidemiological data, along with predictions based on the molecular changes in the spike protein, indicate that the Omicron variant is more transmissible than previous variants, including Delta. However, more data are needed to define just how much more transmissible Omicron is than Delta, and why. It is apparent that Omicron has the ability to overtake Delta, even in countries boasting high rates of vaccination. Therefore, we can expect Omicron to become the dominant variant in the US.
Updates about Omicron classification and lineages
The World Health Organization (WHO) designated the Omicron variant, Pango lineage B.1.1.529, as a VOC on November 26, 2021. Omicron contains 45-52 amino acid changes, with more than half of these changes occurring in the viral S-gene region that codes for the spike protein. The spike protein mediates viral entry into host cells and is the primary immunogen used in COVID-19 vaccines to induce protection against SARS-CoV-2 infection. Due to the unprecedented number of mutations in Omicron, there has been considerable concern and uncertainty regarding the impact of these changes on immune evasion, vaccine-mediated protection, transmissibility, and disease severity.
As more scientists around the world are submitting sequencing data describing B.1.1.529, it is clear that our definition of Omicron and its closest relatives, called sublineages, will continue to evolve. The original B.1.1.529 VOC has multiple sublineages already, with BA.1 as the primary sublineage with the most amount of cases. However, other sublineages are beginning to emerge, such as BA.2 and BA.3. The BA.2 sublineage has a consensus panel of mutations that includes many of the same mutations of BA.1, with some important differences. BA.2 lacks one of the primary mutations that is exploited to screen for potential Omicron positive samples during PCR testing, which complicates BA.2 tracking and surveillance efforts.
Updates about current PCR and antigen testing
Due to the large number of mutations in Omicron, some molecular diagnostics tests have become ineffective or less effective at detecting infection with the Omicron variant. However, these instances of test failure are limited to a few tests that only detect a single viral genome target. It is more common that multi-target tests that detect multiple regions of the SARS-CoV-2 genome, may have failure or drop out of a single testing target, called S gene target failure, or SGTF. These tests, unlike single target tests, still accurately diagnose SARS-CoV-2 infection, because they detect multiple regions of the viral genome.
The FDA has provided an online resource listing tests for which performance may be impacted by viral mutations (source below). Some labs have utilized tests that are susceptible to SGTF to identify which positive samples might be Omicron to prioritize those samples for sequencing; however, the newly identified sublineage of Omicron, BA.2, does NOT have the mutation that causes SGTF, and therefore SGTF will not be as reliable for identifying presumptive Omicron samples for all sublineages. FYR’s PCR-based variant screening method, unlike SGTF, can detect both sublineages of Omicron.
At this time, it is believed that most widely used rapid antigen tests will remain effective at detecting Omicron, but studies are ongoing to determine whether the mutations in Omicron impact the sensitivity or specificity of these tests. While rapid antigen tests are a convenient tool to quickly diagnose SARS-CoV-2 in symptomatic individuals, most of these tests do not allow for downstream PCR or sequencing based variant surveillance.
Updates about vaccine efficacy against Omicron
South African researchers have reported an increased risk of reinfection associated with the Omicron variant when compared with other variants, which suggests that the mutations in Omicron may allow the virus to evade the immune response mounted by individuals who have been previously exposed to SARS-CoV-2. Preliminary laboratory studies are beginning to support that notion, indicating that Omicron partially escapes recognition by neutralizing antibodies conferred by prior infection and vaccination. However, these early studies have largely looked at one facet of immunity, called neutralizing antibodies. There are other prongs of the immune system, like T-cell mediated immunity, that determine how our bodies respond to infection, and early data there are more encouraging.
Pfizer and BioNTech released data showing that while a two-dose course of the Pfizer-BioNTech COVID-19 Vaccine (BTN162b2) was less effective at antibody-mediated neutralization of Omicron when compared with other variants, the vast majority of epitopes recognized by T-cells are still present in Omicron. Laboratory data are beginning to corroborate the robustness of the T-cell response against Omicron.
These preliminary data suggest that vaccination and prior infection offer some level of protection against Omicron, but that breakthrough infections and reinfections may be more likely with Omicron. However, laboratory and real-world data will continue to better our understanding of this topic in the coming weeks. FYR defers to the CDC and WHO for guidance related to vaccines.
Updates on how FYR is responding to Omicron and other emerging Variants of Concern
The team uses advanced next generation sequencing (NGS) technology to monitor variants of concern from confirmed COVID-positive samples. To more rapidly detect Omicron in positive COVID samples, FYR is using its PCR-based variant screening methodology to quickly identify potential Omicron samples to prioritize for sequencing. Since the current guidance is to sequence approximately 10-15% of eligible positive COVID samples, FYR can use the pre-sequencing screening method to screen 100% of positives to ensure that samples that are likely Omicron are represented in the 10-15% that can be sequenced.
SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests. https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests#omicron.
WHO Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests#omicron variant-ofconcern.
European Centre for Disease Prevention and Control. Threat Assessment Brief: Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA. https://www.ecdc.europa.eu/en/publications-data/threat-assessment-brief-emergence-sars-cov-2-variant-b.1.1.529.
Reduced Neutralization of SARS-CoV-2 Omicron Variant by Vaccine Sera and monoclonal antibodies. https://www.medrxiv.org/content/10.1101/2021.12.07.21267432v2.full.pdf.
Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2.full.pdf.
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. https://www.medrxiv.org/content/10.1101/2021.12.08.21267417v1.full.pdf.
Updates to Omicron lineage B.1.1.529. https://www.pango.network/updates-to-omicron-lineage-b-1-1-529/.
Centers for Disease Control and Prevention COVID Data Tracker. https://covid.cdc.gov/covid-data-tracker/#variant-proportions.
Omicron strain spreads with the doubling time of 3.2—3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant. https://www.medrxiv.org/content/10.1101/2021.12.08.21267494v1
Gov.UK Investigation of SARS-CoV-2 variants of concern: technical briefings. https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings
Epidemiological Update: Omicron variant of concern (VOC). https://www.ecdc.europa.eu/en/news-events/epidemiological-update-omicron-data-16-december.
SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests. https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests?utm_medium=email&utm_source=govdelivery
Background on FYR Diagnostics
FYR (pronounced “Fire”) Diagnostics is a Montana-based company focused on developing and commercializing novel technology for diagnostics and testing in human health, life sciences, and agriculture. FYR Diagnostics is currently developing diagnostic solutions for cancers, neurological disorders, agricultural diseases, and neonatal-associated syndromes.
Thanks to support from the State of Montana, FYR’s partnership with the State Lab has increased statewide COVID-19 testing capacity and reduced the time patients must wait to receive results. For more information, visit fyrdiagnostics.com.
FYR Diagnostics does not make any representation or warranties with respect to the accuracy, applicability, fitness, or completeness of the above content and/or any associated materials, collectively (“Materials”). FYR Diagnostics assumes no responsibility for errors or omissions in the contents of the Materials. FYR Diagnostics hereby disclaims any and all liability to any party for any direct, indirect, implied, punitive, special, incidental, or other consequential damages arising directly or indirectly from any use of the Materials, which is provided as is, and without warranties. Please seek advice from your healthcare provider regarding your personal healthcare questions.