Our Newly Developed RT-PCR Test – Identifying OMICRON Directly from RT-PCR

Testing for COVID-19 has gone up significantly in the last month, and consequently positive cases have risen as well and more Omicron variants were identified at our laboratory.
Given the high cost of sequencing, we have adopted a strategy where we developed a RT PCR test with which we can distinguish samples with the unique mutations of the Omicron variant directly from the RT PCR.
With the currently available RT-PCR test, for example, from 1,000 individuals tested, if 5% positive cases were detected (50 cases) but the number of Omicron cases could not be determined, you would normally need to sequence them all, which is costly. That is why in the State of Texas the government plan is to only sequence 25% positive samples randomly, which would leave 75% of cases unidentified.
Here at Ayass Bioscience, LLC Laboratory, using our newly developed RT-PCR test, we are able to distinguish the positive cases that carry Omicron-specific mutations and then sequence them, reducing the chance of missing any Omicron samples down to zero.
We are proud to be the only laboratory that took the necessary scientific steps to quickly identify samples with the Omicron variant directly from our new RT PCR test, and then confirm it with NGS (Next Generation Sequencing).

MOHAMAD AMMAR AYASS, M.D.

Ayass BioScience, LLC has detected cases of the OMICRON variant in the DFW Metroplex using Next Generation Sequencing (NGS). This is a part of our continued efforts to provide the best laboratory services in the area and help our communities.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Omicron has 60 mutations (with 30 on the spike protein), reportedly enhancing its ability to infect people.

Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage. (According to WHO)

Scientist who helped identify omicron: ‘It’s more of a Frankenstein than others’

Scientists currently working to determine effects on people who have been immunized.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021. (WHO)

Sub-lineage of: B.1.1. Countries circulating: Botswana (3 genomes), Hong Kong ex S. Africa (1 genome, partial). Currently only 4 sequences so would recommend monitoring for now. Export to Asia implies this might be more widespread than sequences alone would imply. Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies).

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage. (WHO)

Conserved Spike mutations – A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F.

Conserved non-Spike mutations – NSP3 – K38R, V1069I, Δ1265/L1266I, A1892T; NSP4 – T492I; NSP5 – P132H; NSP6 – Δ105-107, A189V; NSP12 – P323L; NSP14 – I42V; E – T9I; M – D3G, Q19E, A63T; N – P13L, Δ31-33, R203K, G204R.

Genomes:
EPI_ISL_6590608 (partial RBD Sanger sequencing from Hong Kong)
EPI_ISL_6640916
EPI_ISL_6640919
EPI_ISL_6640917

Transmissability: Increased risk of reinfection. It is not yet clear whether Omicron is more transmissible (e.g., more easily spread from person to person) compared to other variants, including Delta. The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of Omicron or other factors. (According to WHO)
Virulence: It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta. Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of specific infection with Omicron. There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants. Initial reported infections were among university students—younger individuals who tend to have more mild disease—but understanding the level of severity of the Omicron variant will take days to several weeks. All variants of COVID-19, including the Delta variant that is dominant worldwide, can cause severe disease or death, in particular for the most vulnerable people, and thus prevention is always key. (According to WHO)
Antigenicity: Increase in transmissibility or detrimental change in COVID-19 epidemiology; increase in virulence or change in clinical disease presentation; decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics (monoclonal antibodies).
Effectiveness of current tests: The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any impact on other types of tests, including rapid antigen detection tests.
Spread: South_Africa 73.0%, Botswana 11.0%, Hong_Kong 3.0%, Australia 2.0%, Italy 2.0%.

Global Positive Samples Sequenced: 7,456,294

B.1.1.529 Sequenced: 3,205

% of Global Samples Sequenced: 0.04%

Omicron (Combined Lineages) Sequenced: 528,572

Most common countries:

B.1.1.529: United States of America 62.0%, Turkey 15.0%, India 3.0%, Germany 3.0%, Italy 3.0%

BA.1: United Kingdom 44.0%, United States of America 32.0%, Denmark 5.0%, Canada 3.0%, Germany 2.0%

BA.2: Denmark 79.0%, United Kingdom 6.0%, India 5.0%, Sweden 2.0%, Singapore 2.0%

BA.3: Poland 42.0%, South_Africa 40.0%, United Kingdom 10.0%, Germany 3.0%, Belgium 1.0%

Summary of B.1.1.529 Data

Summary for Omicron (Combined Lineages) Data

Global Samples Sequencing Data

Updated January 2022

Urgent Question

Urgent questions remain regarding whether Omicron is also able to evade vaccine-induced immunity and the potential implications of reduced immunity to infection on protection against severe disease and death. Vaccine makers are monitoring emerging variants that can potentially escape protection from their vaccines.

Ayass BioScience, LLC are sequencing positive COVID-19 cases to find new mutations:

Evidence strongly suggests that the Omicron variant poses the most significant risk to unvaccinated populations. If you are worried about Omicron or other variants, get vaccinated now at our location: