The BA.2 subvariant has been dubbed “stealth omicron” because it is difficult to detect as a mutation by PCR-based testing, the most common testing method for COVID-19. With the original BA.1 strain, scientists could use PCR-based testing to help identify omicron by looking for a S-gene dropout mutation. Once this was found, the scientists could be fairly certain the positive COVID-19 sample was the omicron variant. The stealth omicron subvariant does not have the S-gene dropout characteristic, making it difficult to distinguish BA.2 as the omicron variant vs. other COVID-19 variants by PCR-based testing alone.

In Denmark, BA.2 is now outpacing its predecessor, omicron BA.1, because it is more transmissible than BA.1. A study conducted by Denmark’s Statens Serum Institut (SSI), which analyzed coronavirus cases in over 8,000 Danish households between December and January, found that people infected with the BA.2 subvariant were roughly 33% more likely to infect others, compared to those infected with BA.1.

Throughout the world, the subvariant is currently present in 57 countries as reported to the GISAID database.  With this data, scientists are determining how deadly the strain is and how well it evades the current vaccines. The genetic difference between BA.1 and BA.2 is greater than the difference between the original SARS CoV-2 variant and the alpha variant, according to SSI. These differences could cause increased severity, the SSI also stated. Fortunately, it is expected that COVID-19 vaccines will have an effect in the mitigation of severe illness upon BA.2 infection.

Increasing access to data on these new variants is so important for our overall understanding of the virus and how it will affect the population,” said Kevin Murdock, CEO of Premier Medical Laboratory Services.

As of February 1, 2022, the state of Florida reported two cases of BA.2. Now, PMLS has identified an additional case for the state and will continue to conduct surveillance to help gather vital data on this new omicron subvariant and others.

“As a laboratory, reliability and consistency is key,” said Kevin Murdock, Founder and CEO of PMLS. “We pride ourselves on being able to deliver accurate results as quickly as possible with every sample we receive. We’ve built an infrastructure that allows us to process large numbers of tests rapidly so that we can truly make a meaningful impact. We look forward to working with the state of North Carolina to help keep their state departments and their economy healthy.”

Throughout the pandemic PMLS has served as the choice processing lab for Health and Human Services testing sites and the trusted COVID-19 management partner for professional sports teams, schools, colleges, large corporations, and health departments spanning from coast to coast. Along with their high capacity and fast turnaround times, PMLS is part of a house of brands under Diversified Medical Healthcare which manufactures testing supplies, develops medical data management software, and provides PPE to seamlessly meet the needs of these organizations without delay or disruption.

With a comprehensive approach to providing solutions, PMLS has also implemented one of the largest variant surveillance initiatives in the country, tracking novel variants like Omicron and Delta. They have the capability to perform next generation sequencing on up to 42,000 specimens per week to provide critical data for a better understanding of the virus and how it’s mutating over time.

The United States’ first confirmed case of the Omicron coronavirus variant has been identified in California. In a White House briefing, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said the virus is present in an individual who traveled to California from South Africa, where the variant was first reported. Dr. Fauci said the individual is self-quarantining and is experiencing “mild symptoms, which are improving at this point.”

The California Public Health Departments confirmed the case was caused by the Omicron variant through Next Generation Sequencing (NGS). The sequence was confirmed by the US Centers for Disease Control and Prevention and reported today. They’re also using NGS to answer questions like, how transmissible is it and how severe is the disease it causes? Next Generation Sequencing has allowed us to search for answers throughout the COVID-19 pandemic. That’s why Premier Medical Laboratory Services (PMLS) has implemented one of the largest initiatives for NGS in the US with a capacity to sequence the genomes of 21,000 specimens per week, a capacity that surpasses most laboratories due to PMLS’ implementation of cutting-edge high throughput lab equipment which automates workflow.

Dr. Vidhya Narayanan, the Technical Lab Director of Premier Medical Laboratory Services, who previously served as the Genomics Scientist for the CDC says “not a lot is known about the Omicron variant yet, and even if its transmission rates are found to be higher than the Delta variant, that still doesn’t mean that it’s more deadly. But there is a huge demand right now for COVID labs that are doing PCR testing to also conduct sequencing like we are at PMLS so that we can slow the spread of this variant early on.” She went on to say, “Out of all of the labs that conduct COVID-19 testing, only about 1 out of 100 are also conducting sequencing initiatives. Because of labs like ours, who are conducting NGS, we should know more over the next few days about Omicron.”

The Omicron variant is the quickest to be labeled a “variant of concern” by the World Health Organization (WHO) because of its seemingly fast spread in South Africa. Besides Africa, the Omicron variant has been detected in several counties including Canada, and now the US. The positive test from California was first detected on November 29th. The CDC said the Omicron variant was identified in under 30 hours “from the time of collection to strain confirmation.”

President Biden said Monday “It’s a cause for concern, not a cause for panic.” He also urged Americans, again, to get vaccinated and to get their booster shot, saying it’s the best protection against this new variant, as well as any others. However, scientists now worry the Omicron variant may be able to evade the body’s immune responses, both to vaccination and to natural infection, more than prior versions of the virus. As scientists continue to scramble for data, they believe the current vaccines should work on the variant for now. Still, the makers of the two most effective vaccines, Pfizer-BioNTech and Moderna, are preparing to reformulate their shots if necessary.

A slew of travel bans went into effect after the news of the Omicron variant emerging. For the US, restricted travel from several countries in Southern Africa went into effect Monday, giving the US more time to respond. President Biden said he would put forward a “detailed strategy outlining how we’re going to fight COVID this winter. Not with shutdowns or lockdowns, but with more widespread vaccinations, boosters, testing, and more.”

As COVID-19 variants continue to impact the health of our nation, vaccination and testing mandates are becoming a reality we all have to adjust to. At PMLS, our goal is to make this as easy and effective as possible so that our economy and our population remain healthy and safe. We are teaming up with employers across the country to provide testing solutions and prevention strategies, slow the spread of COVID-19, and provide a mandate compliance framework that will best protect our communities. Click here to read about our COVID management program.

As the first in a series of upcoming scientific panel discussions hosted at Premier Medical Laboratory Services (PMLS), Dr. Brian Krueger, Chief Scientific Officer of PMLS, and Dr. Stewart Holt, Molecular Diagnostic Technical Supervisor, talk about a wide range of COVID-19 topics including variants, masks, and vaccines.

Dr. Krueger currently oversees scientific functions at PMLS and developed the first commercially authorized SARS CoV-2 COVID-19 test. Meanwhile, Dr. Holt holds over 25 years of experience as a genetics and diagnostics scientist.

Both tackle the misconceptions many of us may have encountered across social media. The CDC says misconceptions or misinformation play a big part in many Americans not wearing masks and not getting vaccinated. Dr. Krueger says, “there’s a lot of misinformation about masks out there,” and we should remember “there’s no question that masks are effective in reducing the transmission of the disease.” The CDC recently said this is especially true for kids under 12 who are still not able to get the vaccine. Dr. Holt adds that masks are “their only primary defense right now.”

The good news is, Pfizer says it’s COVID vaccine is now safe and effective for children ages 5 to 11. But as they get ready to submit for emergency use authorization, there’s still vaccine hesitancy among American adults and parents unwilling to get their kids vaccinated. “The most important thing to keep in mind is that when you get vaccinated, you’re not just doing it for yourself. You’re doing it for your community, you’re doing this to protect your children, you’re doing it for your loved ones,” says Dr. Krueger.

Amid the Delta variant, The CDC has been pushing vaccinations even more, leading to a new nationwide vaccine mandate by the President. The Delta variant is more contagious, and Dr. Holt says, “it has the ability to evade the immune system, which is designed to locate and identify bacteria to clear them from system to prevent infections… that being said our vaccines are still effective against the covid variant.”

So, how does the vaccine fight COVID-19? Dr. Krueger says, “the purpose of the vaccination is to train your B cells, a type of white blood cells, to generate antibodies that are then able to bind to the virus and neutralize it, which essentially means that it prevents the virus from binding to your cells and infecting them.” After being vaccinated, people may still get symptoms like arm pain, chills, or even a fever. This is a natural response and Dr. Holt stressed that “it doesn’t mean you’ve been infected with the virus, or something has been transmitted to you. That’s just your immune system working and it’s a good thing.”

Another challenge our scientists discussed is the upcoming flu season. This will be the second year we’ll have COVID-19 during flu season, which starts in October, and although flu cases were at an all-time low last year, our scientists still want us to have our guards up. “We need to keep in mind that the flu and coronavirus are not going to go away and… our best strategy moving forward and protecting us from hospitalization and death is getting vaccinated every year,” stated Dr. Krueger.

But can you get the flu vaccine and COVID vaccine at the same time? You can find the answer by clicking to watch the full panel discussion below, along with much more from our scientists.

Throughout the COVID-19 pandemic, our world was searching for answers. PMLS was more successful than most laboratories because our NGS research created solutions. With NGS capabilities at PMLS, we’ve been able to track SARS-CoV-2 transmission routes and hotspots, detect mutations stopping the spread of new strains, identify viral mutations that mask, or help targeted strains avoid detection from current molecular diagnostic tests, screen targets for possible COVID-19 therapeutics, and identify viral mutations that may affect vaccine potency. (1,2) PMLS utilizes various methods across multiple platforms for SARS-CoV-2 sequencing; therefore, we are uniquely positioned to tailor our approach to LDH’s fluctuating volume and other challenges. 

NGS can be used for prenatal diagnosis. Noninvasive Prenatal Testing (NIPT) offers genetic screening for chromosomal conditions in as early as ten weeks into the pregnancy. The noninvasive method requires only one tube of blood from the mother carrying the fetus. Once the blood sample has been taken, NGS technology analyzes cfDNA fragments across the whole genome for common chromosomal conditions. NIPT provides high detection rates, low false-positive results, and no risk to the mother or baby. 

Finally, NGS enables PMLS to detect inherited germline mutations associated with hereditary cancer risk. The more our researchers learn about genetic mutations, the more we can take preventative measures to reduce the likelihood of developing cancer. NGS methods rapidly sequence known or suspected hereditary cancer risk-related genes. Consequently, many germline mutations and novel germline variants, linked to cancer, can be detected at once. To reduce sequencing costs, targeted sequencing studies use hereditary cancer panels to assess only specific genes with known cancer predisposition. 

In conclusion, NGS has allowed Premier Medical Laboratory Services the ability to grow, develop, and advance our genomic research in COVID-19 sequencing, non-invasive prenatal diagnosis, and cancer screening. Our NGS technology will continue to allow PMLS to act as an industry leader by fulfilling our mission to help physicians provide the best care to their patients. 

References: 

1. https://www.illumina.com/clinical/reproductive-genetic-health/nipt.html

2. https://www.illumina.com/areas-of-interest/cancer/clinical-cancer-research/germline-mutations.html