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Journal article Open Access

Development of accurate SARS-CoV-2 RT-PCR with Omicron/stealth/Delta diagnosis

Jung Moon

Recently (November 24, 2021), a new concern mutant, Omicron Corona 19 virus(BA.1) was reported in South Africa, which has 32 mutations with more mutations than Delta in the spike protein is becoming Omicron mutation is rapidly spreading to 54 countries within two weeks, and the number of confirmed cases in Korea has reached 36. Even stealth-type omicron mutations (BA.2) have been reported. There is an urgent need for a test that can quickly diagnose Omicron in large numbers in the field, but the reality is that they are still stuck on a high-cost and time-consuming sequencing method.

“Development of accurate SARS-CoV-2 RT-PCR with Omicron/stealth/Delta diagnosis

In late November 2021, the World Health Organization designated the SARS-CoV-2 Omicron variant (B.1.1.529, BA 1) as a “variant of concern.” The highly transmissible (three to five times as Delta) Omicron variant has been connected to sharp surges in cases globally raced around the globe and been reported in 89 countries. The Netherlands went into lockdown on Sunday and the possibility of more COVID-19 restrictions are imposed ahead of the holidays in European countries as the Omicron variant spreads rapidly. In the US, NIAID Director Dr. Anthony Fauci “urged people travelling to visit loves ones to get booster shots and always wear masks in crowded public spaces.” The risk of reinfection with the Omicron coronavirus variant is more than five times higher and it has shown no sign of being milder than Delta, according to the results of the study by “Imperial College London.” Preliminary research suggests only most other Covid vaccines have reduced protection against Omicron infections and some protection against serious illness.

Before Omicron, variants of SARS-CoV-2/COVID-19 were analogous to “antigenic drift,” e.g., D614G and the four previous WHO-designated variants of concern: Alpha, Beta, Gamma and Delta. With Omicron comes the first “antigenic shift” and a new pandemic virus. While influenza antigenic shift requires new pandemic influenza-specific vaccines, the effect of the accumulation of a large number of mutations in SARS-CoV-2 Omicron S in COVID-19 vaccines remains to be established.

The Biden administration has warned COVID-19 test makers and labs that demand for tests could soon double or even triple. HHS “Testing and Diagnostic Working Group” shared an internal model with the diagnostic industry showing “3 million to 5 million daily tests needed by January or February, an estimate that makes the assumption the Omicron variant is three to five times more transmissible than Delta and becomes the dominant variant in four weeks. However, 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. N-gene and S-gene “drop outs” (false negative) in molecular testing of SARS-CoV-2 are typically not observed in the delta variant but may be observed in omicron variants and cause a problem in routine COVID-19 testing.

To control the spread of Omicron in the setting of Delta predominance, accurate diagnosis of SARS-CoV-2 as well as differentiation of Delta and Omicron variants is crucial. This is why Cellgenemedix (https://cellgenemedix.com/) developed a test to accurately diagnose presence of COVID-19 infection and identification of “WHO delta-type and related variant” as well as “omicron/omicron stealth-type variant of interest”.

This “GG COVID-19 Omicron and Delta kit” is a one step, single tube, multiplex real time reverse transcription PCR assay utilizing hydrolysis probes (Taqman probes) and primers for N protein as well as 3 hot spot mutations of spike protein which are key markers of VOCs and allow discrimination of each type. This is the first test of its kind known to diagnose SARS CoV-2 as well as identification of “WHO delta-type and its related variant of SARS-CoV-2” as well as “omicron” and “omicron stealth-type variant of interest” with high sensitivity and specificity (> 90%). It was developed based on CE mark-acquired and US-patented technology.

Time to results are 90 minutes and the associated software converts the results to COVID-19 Positive (Omicron/Delta/non-Omicron, non-Delta type) versus negative for COVID-19.  2 lab personnel may test 400-1600 patient specimens per day using any of the most common Real time RT-PCR machines (CFX96/Rotorgene/ABI 7500). Thus, this reagent kit has the capacity to test hundreds of thousands of patient specimens per day.

Jung Moon M.D. (licensed US and Korean MD, Clinical Pathologist) says “Accurate diagnosis of SARS-CoV-2 as well as differentiation of Delta and Omicron variants is crucial in the next 4 weeks in which Omicron is expected to replace Delta variant in the United States. This is why Cellgenmedix developed a test to accurately diagnose presence of COVID-19 infection and identification of “WHO delta-type and related variant” as well as “omicron/omicron stealth-type variant of interest”. GG COVID-19 Omicron and Delta kit is a cost effective diagnostic tool optimized for rapid diagnosis of Omicron, Delta, and SARS CoV-2 infection, and is expected to be a useful tool in the control and surveillance as well as accurate diagnosis of SARS-CoV-2 in the new, antigen shift era of COVID-19 pandemic” The cost of this test is known to be similar to or slightly more expensive than (less than 10$/test) the previous GG Quadplex Real Time RT-PCR test for diagnosis of COVID-19.

Dr Moon also added that “The Omicron variant differs from previous variants of SARS CoV-2 in the increased number (~30) of mutations present in the spike protein and these mutations may have implications for the performance of certain molecular tests targeting the spike protein gene, as well as for transmissibility and neutralization by monoclonal antibodies from COVID-19 vaccination or SARS-CoV-2 natural infection. Thus, Omicron seems to be a variant that will signify a new era of COVID-19 in many ways and needs to be dealt with utmost seriousness and correct diagnostic tools such as the GG COVID-19 Omicron and Delta kit (Investigational use only, not for use in USA yet).

Disclaimer: this technology is patent pending and this communication with its contents may contain confidential and/or legally privileged information. It is solely for the use of the intended recipient(s). Unauthorized interception, review, use or disclosure is prohibited and may violate applicable laws including the Electronic Communications Privacy Act. If you are not the intended recipient, please contact the sender and destroy all copies of the communication. Contents and any attached file are intellectual property of Cellgenemedix.

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