Many of the mutations were found at sites on the spike protein where antibodies bind, which may explain why the Omicron variant is more infectious than previous variants
Scientists at the University of Missouri (UM) now have a better understanding of why the SARS-CoV-2 Omicron variant is more infectious than previous variants and that knowledge may lead to improved antivirals and clinical laboratory tests for COVID-19.
As the Omicron variant of the coronavirus spread across the globe, scientists noted it appeared to be more contagious than previous variants and seemed resistant to the existing vaccines. As time went by it also appeared to increase risk for reinfection.
The UM researchers wanted to know why. They began by examining the Omicron variant’s mutation distribution, its evolutionary relationship to previous COVID-19 variants, and the structural impact of its mutations on antibody binding. They then analyzed protein sequences of Omicron variant samples collected from around the world.
“We know that viruses evolve over time and acquire mutations, so when we first heard of the new Omicron variant, we wanted to identify the mutations specific to this variant,” said Kamlendra Singh, PhD, Associate Research Professor, Department of Veterinary Pathobiology at UM’s College of Veterinary Medicine (CVM), in a UM press release.
In their paper, the UM team wrote, “Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. … The structural analyses showed that several mutations are localized to the region of the S protein [coronavirus spike protein] that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.”
There are a total of 46 highly prevalent mutations throughout the Omicron variant.
Twenty-three of the 46 mutations belong to the S protein (more than any previous variant).
Twenty-three of 46 is a markedly higher number of S protein mutations than reported for any SARS-CoV-2 variant.
A significant number of Omicron mutations are at the antibody binding surface of the S protein.
“Mutation is change in the genome that results in a different type of protein,” Singh told NBC affiliate KOMU. “Once you have different kinds of protein after the virus and the virus attacks the cell, our antibodies do not recognize that, because it has already been mutated.”
Omicron Mutations Interfere with Antibody Binding
Of the 46 Omicron variant mutations discovered by the UM researchers, some were found in areas of the coronavirus’ spike protein where antibodies normally bind to prevent infection or reinfection.
“The purpose of antibodies is to recognize the virus and stop the binding, which prevents infection,” Singh explained. “However, we found many of the mutations in the Omicron variant are located right where the antibodies are supposed to bind, so we are showing how the virus continues to evolve in a way that it can potentially escape or evade the existing antibodies, and therefore continue to infect so many people.”
These findings explain how the Omicron variant bypasses pre-existing antibodies in a person’s blood to cause initial infection as well as reinfection.
The UM team hopes their research will help other scientists better understand how the SARS-CoV-2 coronavirus has evolved and lead to future clinical laboratory antiviral treatments.
“The first step toward solving a problem is getting a better understanding of the specific problem in the first place,” Singh said. “It feels good to be contributing to research that is helping out with the pandemic situation, which has obviously been affecting people all over the world.”
Singh and his team have developed a supplement called CoroQuil-Zn designed to reduce a patient’s viral load after being infected with the SARS-CoV-2 coronavirus. The drug is currently being used in parts of India and is awaiting approval from the US Food and Drug Administration (FDA).
New discoveries about SARS-CoV-2 and its variants continue to further understanding of the coronavirus. Research such as that performed at the University of Missouri may lead to new clinical laboratory tests, more effective treatments, and improved vaccines that could save thousands of lives worldwide.
Like Holmes, Balwani faces 12 counts of fraud and conspiracy to commit wire fraud for allegedly misleading investors, patients, and others about blood-testing startup’s technology
Clinical laboratory managers and pathologists are buckling up as the next installment of the Theranos story gets underway, this time for the criminal fraud trial of ex-Theranos President and COO Ramesh “Sunny” Balwani.
In one text to Holmes, Balwani wrote, “I am responsible for everything at Theranos,” NBC Bay Area reported.
Partners in Everything, including Crime, Prosecutors Allege
According to the Wall Street Journal (WSJ), prosecutors are following the Holmes trial playbook. They focused their opening arguments on the personal and working relationships between the pair, tying Balwani to Holmes’ crimes at the Silicon Valley blood-testing startup.
As second in command at Theranos, Balwani helped run the company from 2009 to 2016. He also invested $5 million in Theranos stock, while also underwriting a $13 million corporate loan.
“They were partners in everything, including their crimes,” Assistant US Attorney Robert Leach told jurors, the Mercury News reported. “The defendant and Holmes knew the rosy falsehoods that they were telling investors were contrary to the reality within Theranos.”
Leach maintained that Balwani was responsible for the phony financial projections Theranos gave investors in 2015 predicting $990 million in revenue when the company had less than $2 million in sales.
“This is a case about fraud. About lying and cheating to obtain money and property,” Leach added. Balwani “did this to get money from investors, and he did this to get money and business from paying patients who were counting on Theranos to deliver accurate and reliable blood tests so that they could make important medical decisions,” the WSJ reported.
Defense attorneys downplayed Balwani’s decision-making role within Theranos, pointing out that he did not join the start-up until six years after Holmes founded the company with the goal of revolutionizing blood testing by developing a device capable of performing blood tests using a finger-prick of blood.
“Sunny Balwani did not start Theranos. He did not control Theranos. Elizabeth Holmes, not Sunny, founded Theranos and built Theranos,” defense attorney Stephen Cazares, JD of San Francisco-based Orrick, said in his opening argument, the WSJ reported.
The trial was expected to begin in January but was delayed by the unexpected length of the Holmes trial. It was then pushed out to March when COVID-19 Omicron cases spiked in California during the winter.
Balwani’s trial is being held in the same San Jose courthouse where Holmes was convicted. Balwani, 56, is facing identical charges as Holmes, which include two counts of conspiracy to commit wire fraud and 10 counts of wire fraud. He has pleaded not guilty.
Holmes, who is currently free on a $500,000 bond, will be sentenced on Sept. 26, Dark Daily reported in January.
Judge Excludes Jurors for Watching Hulu’s ‘The Dropout’
During jury selection in March, some jurors acknowledged they were familiar with the case, causing delays in impaneling the 12-member jury and six alternates. US District Court Judge Edward Davila excluded two potential jurors because they had watched “The Dropout,” Hulu’s miniseries about Holmes and Theranos. Multiple other jurors were dropped because they had followed the Holmes trial in the news, Law360 reported.
When testimony began, prosecutors had a familiar name take the stand—whistleblower and former Theranos lab tech Erika Cheung, who provided key testimony in the Holmes trial. During her testimony, Cheung said she revealed to authorities what she saw at Theranos because “Theranos had gone to extreme lengths to [cover up] what was happening in the lab,” KRON4 in San Francisco reported.
“It was important to report the truth,” she added. “I felt that despite the risk—and I knew there could be consequences—people really need to see the truth of what was happening behind closed doors.”
Nevada State Public Health Laboratory (NSPHL) Director Mark Pandori, PhD, who served as Theranos’ lab director from December 2013 to May 2014, was the prosecution’s second witness. Pandori testified that receiving accurate results for some tests run through Theranos’ Edison blood testing machine was like “flipping a coin.”
“When you are working in a place like Theranos, you’re developing something new. And you want it to work. Quality control remained a problem for the duration of my time at the company. There was never a solution to poor performance,” Pandori testified, according to KRON4.
While the defense team has downplayed Balwani’s decision-making role—calling him a “shareholder”—Aron Solomon, JD, a legal analyst with Esquire Digital, maintains they may have a hard time convincing the jury that Balwani wasn’t a key player.
“There’s no way the defense is going to be successful in painting Sunny Balwani in the light simply as a shareholder,” he told NBC Bay Area. “We know that, literally, Sunny Balwani was intimately involved with Theranos, because he was intimately involved with Elizabeth Holmes,” Solomon added.
Little Media Buzz for Balwani, Unlike Holmes Trial
While the Holmes trial hogged the media spotlight and drew daily onlookers outside the courthouse, reporters covering Balwani’s court appearances describe a much different atmosphere.
“The sparse crowd and quiet atmosphere at US District Court in San Jose, Calif., felt nothing like the circus frenzy that engulfed the same sidewalk months earlier when his alleged co-conspirator and former girlfriend, Elizabeth Holmes, stood trial on the same charges,” The New York Times noted in its coverage of the Balwani trial.
The Balwani trial may not reach the same headline-producing fervor as the Holmes legal battle. However, clinical laboratory directors and pathologists who follow these proceedings will no doubt come away with important insights into how Theranos went so terribly wrong and how lab directors must act under the Clinical Laboratory Improvement Amendments of 1988 (CLIA).
New nanotechnology device is significantly faster than typical rapid detection clinical laboratory tests and can be manufactured to identify not just COVID-19 at point of care, but other viruses as well
Researchers at the University of Central Florida (UCF) announced the development of an optical sensor that uses nanotechnology to identify viruses in blood samples in seconds with an impressive 95% accuracy. This breakthrough underscores the value of continued research into technologies that create novel diagnostic tests which offer increased accuracy, faster speed to answer, and lower cost than currently available clinical laboratory testing methods.
The innovative UCF device uses nanoscale patterns of gold that reflect the signature of a virus from a blood sample. UCF researchers claim the device can determine if an individual has a specific virus with a 95% accuracy rate. Different viruses can be identified by using their DNA sequences to selectively target each virus.
According to a UCF Today article, the University of Central Florida research team’s device closely matches the accuracy of widely-used polymerase chain reaction (PCR) tests. Additionally, the UCF device provides nearly instantaneous results and has an accuracy rate that’s a marked improvement over typical rapid antigen detection tests (RADT).
“The sensitive optical sensor, along with the rapid fabrication approach used in this work, promises the translation of this promising technology to any virus detection, including COVID-19 and its mutations, with high degree of specificity and accuracy,” Debashis Chanda, PhD, told UCF Today. Chanda is professor of physics at the NanoScience Technology Center at UCF and one of the authors of the study. “Here, we demonstrated a credible technique which combines PCR-like genetic coding and optics on a chip for accurate virus detection directly from blood.”
The team tested their device using samples of the Dengue virus that causes Dengue fever, a tropical disease spread by mosquitoes. The device can detect viruses directly from blood samples without the need for sample preparation or purification. This feature enables the testing to be timely and precise, which is critical for early detection and treatment of viruses. The chip’s capability also can help reduce the spread of viruses.
No Pre-processing or Sample Preparation Needed for Multi-virus Testing
The scientists confirmed their device’s effectiveness with multiple tests using varying virus concentration levels and solution environments, including environments with the presence of non-target virus biomarkers.
“A vast majority of biosensors demonstrations in the literature utilize buffer solutions as the test matrix to contain the target analyte,” Chanda told UCF Today. “However, these approaches are not practical in real-life applications because complex biological fluids, such as blood, containing the target biomarkers are the main source for sensing and at the same time the main source of protein fouling leading to sensor failure.”
The researchers believe their device can be easily adapted to detect other viruses and are optimistic about the future of the technology.
“Although there have been previous optical biosensing demonstrations in human serum, they still require off-line complex and dedicated sample preparation performed by skilled personnel—a commodity not available in typical point-of-care applications,” said Abraham Vazquez-Guardado, PhD, a Postdoctoral Fellow at Northwestern University who worked on the study, in the UCS Today article. “This work demonstrated for the first time an integrated device which separated plasma from the blood and detects the target virus without any pre-processing with potential for near future practical usages.”
More research and additional studies are needed to develop the University of Central Florida scientists’ technology and prove its efficacy. However, should the new chip prove viable for point-of-care testing, it would give clinical laboratories and microbiologists an ability to test blood samples without any advanced preparation. Combined with the claims for the device’s remarkable accuracy, that could be a boon not only for COVID-19 testing, but for testing other types of viruses as well.
Supplychain shortages involving clinical laboratory products may not ease up any time soon, as China’s largest shipping province is once again in COVID-19 lockdown
Following two years of extremely high demand, pathology laboratories as well as non-medical labs in the United Kingdom (UK) and Europe are experiencing significant shortages of laboratory resources as well as rising costs. That’s according to a recently released survey by Starlab Group, a European supplier of lab products.
In its latest annual “mood barometer” survey of around 200 lab professionals in the UK, Germany, Austria, Italy, and France, Starlab Group received reports of “empty warehouses” and a current shortage of much needed lab equipment, reportedly as a result of rising costs, high demand, and stockpiling of critical materials needed by pathology laboratories during the COVID-19 pandemic, according to Laboratory News.
The survey respondents, who represented both medical laboratories and research labs, noted experiencing more pressure from staff shortages and insufficient supplies required to meet testing demands in 2021 as compared to 2020. For example, only 23% of respondents said they had enough liquid handling materials—such as protective gloves and pipettes—in 2021, down from 39% who responded to the same question in 2020.
“The entire laboratory industry has been in a vicious circle for two years. While more and more materials are needed, there’s a lack of supplies. At the same time, laboratories want to stockpile material, putting additional pressure on demand, suppliers, and prices,” Denise Fane de Salis, Starlab’s UK Managing Director and Area Head for Northern Europe, told Process Engineering. “Institutes that perform important basic work cannot keep up with the price competition triggered by COVID-19 and are particularly suffering from this situation,” she added.
Lab Supply Shortages Worsen in 2021
With a UK office in Milton Keynes, Starlab’s network of distributors specialize in liquid handling products including pipette tips, multi-channel pipettes, and cell culture tubes, as well as PCR test consumables and nitrile and latex gloves.
According to Laboratory News, Starlab’s 2021 annual survey, released in March 2022, found that:
64% cited late deliveries contributing to supply woes.
58% noted medical labs getting preference over research labs, up from 46% in 2020.
57% said demand for liquid handling products was the same as 2020.
30% of respondents said material requirements were up 50% in 2021, compared to 2020.
76% reported dealing with rising prices in lab operations.
29% expect their need for materials to increase by 25% in 2022, and 3% said the increase may go as high as 50%.
17% of respondents said they foresee challenges stemming from staff shortages, with 8% fearing employee burnout.
UK-European Medical Laboratories on Waiting Lists for Supplies
Could import of lab equipment and consumables from Asia and other areas outside UK have contributed to the shortages?
“A substantial portion of the world’s clinical laboratory automation, analyzers, instruments, and test kits are manufactured outside UK. Thus, UK labs may face a more acute shortage of lab equipment, tests, and consumables because governments in countries that manufacture these products are taking ‘first dibs’ on production, leaving less to ship to other countries,” said Robert Michel, Editor-in-Chief of Dark Daily and our sister publication The Dark Report.
Indeed, a statement on Starlab’s website describes challenges the company faces meeting customers’ requests for supplies.
“The pandemic also has an impact on our products that are manufactured in other countries. This particularly affects goods that we ship from the Asian region to Europe by sea freight. Due to the capacity restrictions on the ships, we expect additional costs for the transport of goods at any time. Unfortunately, the situation is not expected to ease for the time-being,” Starlab said.
Furthermore, economists are forecasting probable ongoing supply chain effects from a new SARS-CoV-2 outbreak in China.
Lockdown of China’s Largest Shipping Province Threatens Supply Chains Worldwide
According to Bloomberg News, “Shenzhen’s 17.5 million residents [were] put into lockdown on [March 13] for at least a week. The city is located in Guangdong, the manufacturing powerhouse province, which has a gross domestic product of $1.96 trillion—around that of Spain and South Korea—and which accounts for 11% of China’s economy … Guangdong’s $795 billion worth of exports in 2021 accounted for 23% of China’s shipments that year, the most of any province.”
Bloomberg noted that “restrictions in Shenzhen could inflict the heaviest coronavirus-related blow to growth since a nationwide lockdown in 2020, with the additional threat of sending supply shocks rippling around the world.”
“Given that China is a major global manufacturing hub and one of the most important links in global supply chains, the country’s COVID policy can have notably spillovers to its trading partners’ activity and the global economy,” Tuuli McCully, Head of Asia-Pacific Economies, Scotiabank, told Bloomberg News.
Wise medical laboratory leaders will remain apprised of supply chain developments and possible lockdowns in Asia while also locating and possibly securing new sources for test materials and laboratory equipment in anticipation of future supply shortages.
The technology is similar to the concept of a liquid biopsy, which uses blood specimens to identify cancer by capturing tumor cells circulating in the blood.
According to the American Cancer Society, lung cancer is responsible for approximately 25% of cancer deaths in the US and is the leading cause of cancer deaths in both men and women. The ACS estimates there will be about 236,740 new cases of lung cancer diagnosed in the US this year, and about 130,180 deaths due to the disease.
Early-stage lung cancer is typically asymptomatic which leads to later stage diagnoses and lowers survival rates, largely due to a lack of early disease detection tools. The current method used to detect early lung cancer lesions is low-dose spiral CT imaging, which is costly and can be risky due to the radiation hazards of repeated screenings, the news release noted.
MGH’s newly developed diagnostic tool detects lung cancer from alterations in blood metabolites and may lead to clinical laboratory tests that could dramatically improve survival rates of the deadly disease, the MGH scientist noted in a news release.
Detecting Lung Cancer in Blood Metabolomic Profiles
The MGH scientists created their lung-cancer predictive model based on magnetic resonance spectroscopy which can detect the presence of lung cancer from alterations in blood metabolites.
The researchers screened tens of thousands of stored blood specimens and found 25 patients who had been diagnosed with non-small-cell lung carcinoma (NSCLC), and who had blood specimens collected both at the time of their diagnosis and at least six months prior to the diagnosis. They then matched these individuals with 25 healthy controls.
The scientists first trained their statistical model to recognize lung cancer by measuring metabolomic profiles in the blood samples obtained from the patients when they were first diagnosed with lung cancer. They then compared those samples to those of the healthy controls and validated their model by comparing the samples that had been obtained from the same patients prior to the lung cancer diagnosis.
The predictive model yielded values between the healthy controls and the patients at the time of their diagnoses.
“This was very encouraging, because screening for early disease should detect changes in blood metabolomic profiles that are intermediate between healthy and disease states,” Cheng noted.
The MGH scientists then tested their model with a different group of 54 patients who had been diagnosed with NSCLC using blood samples collected before their diagnosis. The second test confirmed the accuracy of their model.
Predicting Five-Year Survival Rates for Lung Cancer Patients
Values derived from the MGH predictive model measured from blood samples obtained prior to a lung cancer diagnosis also could enable oncologists to predict five-year survival rates for patients. This discovery could prove to be useful in determining clinical strategies and personalized treatment decisions.
The researchers plan to analyze the metabolomic profiles of the clinical characteristics of lung cancer to understand the entire metabolic spectrum of the disease. They hope to create similar models for other illnesses and have already created a model that can distinguish aggressive prostate cancer by measuring the metabolomics profiles of more than 400 patients with that disease.
In addition, they are working on a similar model to screen for Alzheimer’s disease using blood samples and cerebrospinal fluid.
More research and clinical studies are needed to validate the utilization of blood metabolomics models as early screening tools in clinical practice. However, this technology might provide pathologists and clinical laboratories with diagnostic tests for the screening of early-stage lung cancer that could save thousands of lives each year.
Researchers say their method can trace ancestry back 100,000 years and could lay groundwork for identifying new genetic markers for diseases that could be used in clinical laboratory tests
Cheaper, faster, and more accurate genomic sequencing technologies are deepening scientific knowledge of the human genome. Now, UK researchers at the University of Oxford have used this genomic data to create the largest-ever human family tree, enabling individuals to trace their ancestry back 100,000 years. And, they say, it could lead to new methods for predicting disease.
This new database also will enable genealogists and medical laboratory scientists to track when, where, and in what populations specific genetic mutations emerged that may be involved in different diseases and health conditions.
New Genetic Markers That Could Be Used for Clinical Laboratory Testing
As this happens, it may be possible to identify new diagnostic biomarkers and genetic indicators associated with specific health conditions that could be incorporated into clinical laboratory tests and precision medicine treatments for chronic diseases.
“We have basically built a huge family tree—a genealogy for all of humanity—that models as exactly as we can the history that generated all the genetic variation we find in humans today,” said Yan Wong, DPhil, an evolutionary geneticist at the Big Data Institute (BDI) at the University of Oxford, in a news release. “This genealogy allows us to see how every person’s genetic sequence relates to every other, along all the points of the genome.”
Researchers from University of Oxford’s BDI in London, in collaboration with scientists from the Broad Institute of MIT and Harvard; Harvard University, and University of Vienna, Austria, developed algorithms for combining different databases and scaling to accommodate millions of gene sequences from both ancient and modern genomes.
The BDI team overcame the major obstacle to tracing the origins of human genetic diversity when they developed algorithms to handle the massive amount of data created when combining genome sequences from many different databases. In total, they compiled the genomic sequences of 3,601 modern and eight high-coverage ancient people from 215 populations in eight datasets.
The ancient genomes included three Neanderthal genomes, a Denisovan genome, and a family of four people who lived in Siberia around 4,600 years ago.
The University of Oxford researchers noted in their news release that their method could be scaled to “accommodate millions of genome sequences.”
“This structure is a lossless and compact representation of 27 million ancestral haplotype fragments and 231 million ancestral lineages linking genomes from these datasets back in time. The tree sequence also benefits from the use of an additional 3,589 ancient samples compiled from more than 100 publications to constrain and date relationships,” the researchers wrote in their published study.
Wong believes his research team has laid the groundwork for the next generation of DNA sequencing.
“As the quality of genome sequences from modern and ancient DNA samples improves, the tree will become even more accurate and we will eventually be able to generate a single, unified map that explains the descent of all the human genetic variation we see today,” he said in the news release.
Developing New Clinical Laboratory Biomarkers for Modern Diagnostics
In a video illustrating the study’s findings, evolutionary geneticist Yan Wong, DPhil, a member of the BDI team, said, “If you wanted to know why some people have some sort of medical conditions, or are more predisposed to heart attacks or, for example, are more susceptible to coronavirus, then there’s a huge amount of that described by their ancestry because they’ve inherited their DNA from other people.”
Wohns agrees that the significance of their tree-recording methods extends beyond simply a better understanding of human evolution.
“[This study] could be particularly beneficial in medical genetics, in separating out true associations between genetic regions and diseases from spurious connections arising from our shared ancestral history,” he said.
The underlying methods developed by Wohns’ team could have widespread applications in medical research and lay the groundwork for identifying genetic predictors of disease risk, including future pandemics.
Clinical laboratory scientists will also note that those genetic indicators may become new biomarkers for clinical laboratory diagnostics for all sorts of diseases currently plaguing mankind.