About 50% of South Asians and 16% of Europeans carry gene cluster associated with respiratory failure after SARS-CoV-2 infection and hospitalization
Clinical pathology laboratories and medical laboratory scientists may be intrigued to learn that scientists from two research institutes in Germany and Sweden have determined that a strand of DNA associated with a higher risk of severe COVID-19 in humans is similar to the corresponding DNA sequences of a roughly 50,000-year-old Neanderthal from Croatia.
The researchers concluded that this gene cluster—passed down from Neanderthals to homo sapiens—triples the risk of developing severe COVID-19 respiratory symptoms for some modern day humans.
In a press release, Pääbo said, “It is striking that the genetic heritage from the Neanderthals has such tragic consequences during the current pandemic. Why this is must now be investigated as quickly as possible.”
Might Useful Biomarkers for Clinical Laboratory Tests Be Identified?
Though it is not immediately clear how these findings may alter current approaches to developing treatments and a vaccine for the SARS-CoV-2 coronavirus, it is another example of how increased knowledge of human DNA leads to new understandings about genetic sequences that can spur development of useful biomarkers for clinical laboratory diagnostics tests.
Swedish geneticist Svante Pääbo, PhD (above right), Director of the Max Planck Institute for Evolutionary Anthropology in Germany, is co-author of a recent study that traced a gene cluster linked to a higher risk of severe COVID-19 to 50,000-year-old Neanderthals from Croatia. “It is striking that the genetic heritage from the Neanderthals has such tragic consequences during the current pandemic,” he said. Nevertheless, such discoveries sometimes lead to new biomarkers for clinical laboratory tests and diagnostics. (Photo copyright: Max Planck Institute for Evolutionary Anthropology.)
This latest research reveals that people who inherit a specific six-gene combination on chromosome 3—called a haplotype—are three times more likely to need artificial ventilation if they are infected by the SARS-CoV-2 coronavirus. Yet, the researchers can only speculate as to why the gene cluster confers a higher risk.
“The genes in this region may well have protected the Neanderthals against some other infectious diseases that are not around today. And now, when we are faced with the [SARS-CoV-2] coronavirus, these Neanderthal genes have these tragic consequences,” Pääbo told the Guardian.
According to the study, the gene risk variant is most common in South Asia where about half of the population carries the Neanderthal risk variant. In comparison, one in six Europeans have inherited the gene sequence and the trait is almost nonexistent in Africa and East Asia.
“About 63% of people in Bangladesh have at least one copy of the disease-associated haplotype, and 13% have two copies (one from their mother and one from their father). For them, the Neandertal DNA might be partially responsible for increased mortality from a coronavirus infection. People of Bangladeshi origin living in the United Kingdom, for instance, are twice as likely to die of COVID-19 as the general population,” Science News reported.
Other Research Connecting Genes to Severe COVID-19 Symptoms
The haplotype on chromosome 3 first made headlines in June when the New England Journal of Medicine (NEJM) published the “Genomewide Association Study of Severe COVID-19 with Respiratory Failure,” which analyzed COVID-19 patients in seven hospitals in Italy and Spain. The researchers found an association between the gene cluster on chromosome 3 and severe symptoms of SARS-CoV-2 after infection and hospitalization. The study also pointed to the potential involvement of chromosome 9, which contains the ABO blood-group system gene, indicating that humans with type A blood may have a 45% higher risk of developing severe COVID-19 infections.
However, Mark Maslin, PhD, Professor of Climatology at University College London, cautions against drawing strong conclusions from the initial research tying disease risk to the genetic legacy of Neanderthals, the Guardian reported. He suggested that, while the Neanderthal-derived variant may contribute to COVID-19 risk in certain populations, genes are more likely to be just one of multiple risk factors for COVID-19 that include age, gender, and pre-existing conditions.
“COVID-19 is a complex disease, the severity of which has been linked to age, gender, ethnicity, obesity, health, virus load among other things,” Maslin told the Guardian. “This paper links genes inherited from Neanderthals with a higher risk of COVID-19 hospitalization and severe complications. But as COVID-19 spreads around the world it is clear that lots of different populations are being severely affected, many of which do not have any Neanderthal genes.
“We must avoid simplifying the causes and impact of COVID-19, as ultimately a person’s response to the disease is about contact and then the body’s immunity response, which is influenced by many environmental, health and genetic factors.”
Andre Franke, PhD, Director of the Institute of Clinical Molecular Biology, Kiel University in Germany, agrees with Maslin, the Associated Press reported. In a statement “ahead of the study’s final publication,” he said these latest findings have no immediate impact on the treatment of COVID-19, and he questioned “why that haplotype—unlike most Neanderthal genes—survived until today,” AP reported.
All of this deepens the mystery of the SARS-CoV-2 coronavirus. Genomics research continues to add new insights into what is known about COVID-19 and may ultimately provide answers on why some people contract the disease and remain asymptomatic—or have mild symptoms—while others become seriously ill or die. Understanding why and how certain genes increase the risk of severe COVID-19 could give rise to targeted clinical laboratory tests and therapies to fight the disease.
Clinical laboratory managers may want to follow the debate that surfaced shortly after publication of the study in a peer-reviewed journal, when editors of the journal issued concerns over the researchers’ claims
Virologists and medical laboratory scientists continue to investigate ways the SARS-CoV-2 coronavirus can be defeated using the body’s own defenses in conjunction with medical treatments and a possible vaccine. Now, researchers at the Boston University School of Medicine have discovered that higher levels of vitamin D in the blood may improve chances of recovering from a COVID-19 infection.
“This study provides direct evidence that Vitamin D sufficiency can reduce the complications, including the cytokine storm (release of too many proteins into the blood too quickly) and ultimately death from COVID-19,” Michael F. Holick, PhD, MD, Professor of Medicine, Physiology and Biophysics at Boston University School of Medicine and one of the authors of the study, told SciTechDaily.
Holick is well-known in the scientific community for his many published studies on Vitamin D. In 2018, Kaiser Health News and The New York Times published a retrospective on Holick and his advocacy on behalf of Vitamin D, titled, “The Man Who Sold America On Vitamin D—and Profited in the Process.” In that story, Holick acknowledged working as a consultant for several organizations, including Quest Diagnostics in a relationship that dates back to 1979. KHN and NYT noted that Quest Diagnostics performs Vitamin D tests.
The Boston University researchers published their study in PLOS ONE, a peer-reviewed open-access scientific journal published by the Public Library of Science (PLOS). The paper’s apparent conclusions, however, invoked an “expression of concern” from the journal’s editors, which, along with direct responses from the Boston University researchers, can be read on PLOS ONE.
Can Vitamin D Save Lives?
To perform their research, the Boston University researchers examined the Vitamin D levels of 235 patients who had been admitted to a hospital with a SARS-CoV-2 infection. The patients were then tracked for clinical outcomes, including:
Blood samples were also analyzed for the number of lymphocytes and inflammatory markers. The researchers compared the collected data between patients who were sufficient to those who were deficient in Vitamin D levels.
They determined that patients over the age of 40 who were Vitamin D sufficient were 51.5% less likely to die from a COVID-19 infection than those who were deficient in the vitamin.
“Because Vitamin D deficiency and insufficiency is so widespread in children and adults in the United States and worldwide, especially in the winter months, it is prudent for everyone to take a vitamin D supplement to reduce risk of being infected and having complications from COVID-19,” Michael F. Holick, PhD, MD (above), told SciTechDaily. The Boston University School of Medicine professor and study author has been praising the health benefits of Vitamin D for years. He played a role in drafting national guidelines for the vitamin and also authored books that tout the advantages of Vitamin D, the importance of UV rays, and the biologic effects of light. (Photo copyright: Boston Herald.)
How Vitamin D Works and Why It’s So Important
In a fact sheet, the National Institutes of Health (NIH) recommend that adults between the ages of 19 and 70 take 15 micrograms (mcg) or 600 International Units (IU) of Vitamin D per day. Adults over the age of 70 should increase that amount to 20 mcg or 800 IUs per day.
According NBC News, Americans spent $936 million on supplements in 2017, which was nine times more than the previous decade. That article also stated that medical laboratory testing for Vitamin D levels have exponentially increased over the years. More than 10 million tests for Vitamin D levels were ordered for Medicare patients in 2016 at a cost of $365 million, which represents an increase of 547% since 2007. Currently, approximately one in four adults over the age of 60 in the US take Vitamin D supplements.
The NIH fact sheet notes that Vitamin D is a nutrient found in cells throughout the body and is needed for good health and to maintain strong bones. Individuals who are deficient in Vitamin D may develop soft, thin, brittle bones, as well as rickets in children and osteomalacia in adults. Vitamin D also helps the immune system fight off invading bacteria and viruses, helps nerves carry messages between the brain and other body parts, and helps muscles move. It can also play a role in warding off osteoporosis in older adults.
Very few foods naturally contain Vitamin D. The best dietary sources for the vitamin are fatty fish such as salmon, tuna, and mackerel, and foods fortified with Vitamin D, such as milks, some breakfast cereals, and yogurt. Being outside on sunny days is another way to obtain Vitamin D, as the body makes the vitamin when skin is directly exposed to the sun.
The Boston University study outlines the advantages of having sufficient Vitamin D levels, as well as how the vitamin may help ward off and possibly lessen the effects of infections like COVID-19, though those conclusions have been called into question.
Nevertheless, individuals who are deficient in the vitamin may want to take a supplement or get plenty of sunshine, just to be on the safe side. And clinical laboratory managers will want to keep in mind that over the years “the steady increase in physician and patient demand for Vitamin D tests has kept most clinical and pathology laboratories scrambling to maintain turnaround times and quality,” which Dark Daily reported in “Why Vitamin D Continues to Be the World’s Fastest-Growing Clinical Laboratory Test.”
CEOs of NorDx Laboratories, Sonora Quest Laboratories, and HealthPartners/Park Nicollet Laboratories expect demand for SARS-CoV-2 tests to only increase in coming months
The short answer is that large volumes of COVID-19 testing will be needed for the remaining weeks of 2020 and substantial COVID-19 testing will occur throughout 2021 and even into 2022. This has major implications for all clinical laboratories in the United States as they plan budgets for 2021 and attempt to manage their supply chain in coming weeks. The additional challenge in coming months is the surge in respiratory virus testing that is typical of an average influenza season.
Stan Schofield (above center), President of NorDx, a regional laboratory corporation that supports an integrated delivery system at MaineHealth in Portland, Maine.
Rick L. Panning (above right), MBA, MLS(ASCP)CM, retired as of Oct. 2 from the position of Senior Administrative Director of Laboratory Services for HealthPartners and Park Nicollet in Minneapolis-St. Paul, Minnesota.
Each panelist was asked how his parent health system and clinical laboratory was preparing to respond to the COVID-19 pandemic through the end of 2020 and into 2021.
First to answer was Panning, whose laboratory serves the Minneapolis-Saint Paul market.
A distinguishing feature of healthcare in the Twin Cities is that it is at the forefront of operational and clinical integration. Competition among health networks is intense and consumer-focused services are essential if a hospital or physician office is to retain its patients and expand market share.
Panning first explained how the pandemic is intensifying in Minnesota. “Our state has been on a two-week path of rising COVID-19 case numbers,” he said. “That rise is mirrored by increased hospitalizations for COVID-19 and ICU bed utilization is going up dramatically. The number of hospitalized COVID-19 patients has doubled during this time and Minnesota is surrounded by states that are even in worse shape than us.”
These trends are matched by the outpatient/outreach experience. “We are also seeing more patients use virtual visits to our clinics, compared to recent months,” noted Panning. “About 35% of clinical visits are virtual because people do not want to physically go into a clinic or doctor’s office.
“Given these recent developments, we’ve had to expand our network of specimen collection sites because of social distancing requirements,” explained Panning. “Each patient collection requires more space, along with more time to clean and sterilize that space before it can be used for the next patient. Our lab and our parent health system are focused on what we call crisis standards of care.
“For all these reasons, our planning points to an ongoing demand for COVID-19 testing,” he added. “Influenza season is arriving, and the pandemic is accelerating. Given that evidence, and the guidance from state and federal officials, we expect our clinical laboratory will be providing significant numbers of COVID-19 tests for the balance of this year and probably far into 2021.”
COVID-19 Vaccine Could Increase Antibody and Rapid Molecular Testing
Arizona is seeing comparable increases in new daily COVID-19 cases. “There’s been a strong uptick that coincides with the governor’s decision to loosen restrictions that allowed bars and exercise clubs to open,” stated Dexter. “We’ve gone from a 3.8% positivity rate up to 7% as of last night. By the end of this week, we could be a 10% positivity rate.”
Looking at the balance of 2020 and into 2021, Dexter said, “Our lab is in the midst of budget planning. We are budgeting to support an increase in COVID-19 PCR testing in both November and December. Arizona state officials believe that COVID-19 cases will peak at the end of January and we’ll start seeing the downside in February of 2021.”
The possible availability of a SARS-CoV-2 vaccine is another factor in planning at Dexter’s clinical laboratory. “If such a vaccine becomes available, we think there will be a significant increase in antibody testing, probably starting in second quarter and continuing for the balance of 2021. There will also be a need for rapid COVID-19 molecular tests. Today, such tests are simply unavailable. Because of supply chain difficulties, we predict that they won’t be available in sufficient quantities until probably late 2021.”
COVID-19 Testing Supply Shortages Predicted as Demand Increases
At NorDx Laboratories in Portland, Maine, the expectation is that the COVID-19 pandemic will continue even into 2022. “Our team believes that people will be wearing masks for 18 more months and that COVID-19 testing with influenza is going to be the big demand this winter,” observed Schofield. “The demand for both COVID-19 and influenza testing will press all of us up against the wall because there are not enough reagents, plastics, and plates to handle the demand that we see building even now.
“Our hospitals are already preparing for a second surge of COVID-19 cases,” he said.
COVID-19 patients will be concentrated in only three or four hospitals. The other hospitals will handle routine work. Administration does not want to have COVID-19 patients spread out over 12 or 14 hospitals, as happened last March and April.
“Administration of the health system and our clinical laboratory think that the COVID-19 test volume and demand for these tests will be tough on our lab for another 12 months. This will be particularly true for COVID-19 molecular tests.”
As described above, the CEOs of these three major clinical laboratories believe that the demand for COVID-19 testing will continue well into 2021, and possibly also into 2022. A recording of the full session was captured by the virtual Executive War College and, as a public service to the medical laboratory and pathology profession, access to this recording will be provided to any lab professional who contacts info@darkreport.com and provides their email address, name, title, and organization.
Robert L. Michel, Panelist—Publisher, Editor-in-Chief, The Dark Report and Dark Daily, Spicewood, Texas.
Given the importance of sound strategic planning for all clinical laboratories and pathology groups during their fall budget process, the virtual Executive War College is opening this session to all professionals in laboratory medicine, in vitro diagnostics, and lab informatics.
Though gene sequencing is touted as a key component of precision medicine, the medical value of direct-to-consumer testing has yet to show up in improved health outcomes, nor have clinical laboratories benefitted
In a recent example that the market for genetic genealogy testing may have peaked and the days of spectacular growth in the number of direct-to-consumer (DTC) genetic test orders and revenue is over, private-equity firm Blackstone—in a $4.7 billion deal—announced it will acquire a majority stake in Ancestry, which also does some clinical laboratory genetic testing as well.
Blackstone (NYSE:BX) acquired Ancestry of Lehi, Utah, one of the two largest genealogy testing companies (the other being 23andMe of Sunnyvale, Calif.), from a group of equity holders led by investment firms Silver Lake, GIC, Spectrum Equity, and Permira, noted a press release. GIC will retain a “significant minority stake” in Ancestry.
“We are very excited to partner with Ancestry and its management team. We believe Ancestry has significant runway for further growth as people of all ages and backgrounds become increasingly interested in learning more about their family histories and themselves,” David Kestnbaum, a Senior Managing Director at Blackstone, said in the press release. “We look forward to investing behind further data, functionality, and product development across Ancestry’s market leading platform to continue to provide a differentiated service.”
Is Genetic Testing for Genealogy Still a Growth Industry?
Ancestry is the global leader in digital family history services, operating in more than 30 countries with more than three million paying subscribers across its Ancestry online properties and more than $1 billion in annual revenue.
However, some experts say the road ahead may not be smooth for Ancestry or its major competitor, 23andMe.
“The business landscape fell off a cliff last year,” Laura Hercher, Director of Human Genetics Research at Sarah Lawrence College in New York, told STAT. “Fads pass,” she added.
Hercher points out that Ancestry has “this enormous database, which inherently has a lot of value hidden in it—potential energy. But they have not figured out how to get that information out in the way 23andMe has.”
23andMe’s pivot into medical research gained steam in 2018 when pharmaceutical giant GlaxoSmithKline (NYSE:GSK) purchased a $300 million stake in the company with the aim of using 23andMe’s resources to develop new medicines. That collaboration began bearing fruit earlier this year when GlaxoSmithKline started human trials of the first medicine (a cancer drug) to emerge from the partnership, STAT reported.
The public’s declining interest in at-home genealogy, however, has caused both companies to reduce staffing. 23andMe began the year by laying off about 100 employees—an estimated 14% of its workers—and Ancestry followed suit in February, letting go a similar number of employees, representing roughly 6% of its workforce.
According to MIT Technology Review, direct-to-consumer genetic genealogy testing reached its zenith in 2018 when consumers purchased as many DNA tests in one year as they had in all previous years combined, propelling total sales from Ancestry, 21andMe, and other DTC gene testing companies to roughly $26 million.
In 2019, CNBC reported that, market-wide, roughly 30 million tests had been sold across the globe. However, in recent years, sales have fallen short of expectations as the number of people willing to pay $99 to learn about their ancestry has dwindled. “I suspect those that are curious about this information are thinning out and there’s less people to go around to grow,” Greg Yap (above), Partner at Menlo Ventures, told CNBC. “I think there’s a broader issue, which is that the ultimate medical value is still really unproven,” Yap added. “There’s lots of research being done, but value for mass market consumer isn’t there yet, so it keeps a ceiling on the size of that market.” (Photo copyright: VentureBeat.)
Privacy Still a Concern
Ancestry has begun to insert itself into the genetic testing healthcare arena. In a press release, the company announced the launch of AncestryHealth, a $179 DNA testing kit that uses next generation sequencing (aka, high-throughput or massive parallel sequencing), aimed at providing adult consumers information on their inherited health risks.
However, as MedCity News points out, the sale to Blackstone has increased privacy concerns around the direct-to-consumer DNA testing market. Ancestry’s consumer privacy and data protections remain unchanged under the new ownership, but Alan Butler, Interim Executive Director at Electronic Privacy Information Center (EPIC), told MedCity News, “This is one example of a very troubling trend. It’s something regulatory agencies are not up to date to deal with. It’s one of the reasons we need comprehensive privacy law in the US.”
As genealogy companies such as 23andMe and Ancestry shift their focus from providing genetic histories to improving consumers’ health through genetic testing, clinical laboratories should be mindful of the logical next step, which is predicted to be genetic tests where the consumer collects the sample at home and the test is used to aid in diagnosing and treating patients.
This fourth edition of the annual event will be held virtually with free registration for pathologists and clinical laboratory professionals
In its fourth year, stakeholders in the clinical laboratory community have promoted thought leadership around the Lab Industry at the Project Santa Fe Foundation’s Clinical Lab 2.0 Workshop. Clinical Lab 2.0 (CL 2.0) which identifies new opportunities for medical labs to add value as the healthcare industry transitions from fee-for-service to value-based delivery models. But how does this concept apply during the era of COVID-19? That’s a key question participants will discuss at the 2020 Clinical Lab 2.0 Workshop, a virtual event scheduled for Oct. 26-27 with a focus on Population Health.
“This workshop will help all clinical laboratory leaders and pathologists to better understand, ‘How do we manage a pandemic, identifying high risk pool, where are the care gaps, and how do we better manage in the future proactively?’” said Khosrow Shotorbani, MBA, MT (ASCP), co-founder of the CL2.0 initiative and a regular speaker at the Executive War College, in an exclusive interview with Dark Daily. He is President and Executive Director of the Project Santa Fe Foundation, the organization that promotes the Clinical 2.0 Movement.
The coronavirus pandemic has “truly elevated the value of the clinical laboratory and diagnostics as one essential component of the care continuum,” he noted. “The value of the SARS-CoV-2 test became immense, globally, and the mantra became ‘test to trace to treat.’”
Project Santa Fe Foundation’s website defines Clinical Laboratory 2.0 as an effort to demonstrate “the power of longitudinal clinical lab data to proactively augment population health in a value-based healthcare environment.” The “goals are to improve the clinical outcomes of populations, help manage population risk, and reduce the overall cost of delivering healthcare,” the CL 2.0 website states.
“It’s about harnessing lab test results and other data that have predictive value and can help us proactively identify individuals that need care,” explained Shotorbani. “In the context of population health or value-based care, our labs potentially can utilize the power of this data to risk-stratify a population for which we are responsible or we can identify gaps in care.”
Clinical Lab 2.0 and the SARS-CoV-2 Pandemic
In the context of COVID-19, “Clinical Lab 2.0 argues that there is a hidden universe of value that can help augment what happens between COVID-19 testing and COVID-19 tracing to convert this reactive approach—meaning we wait for the person to get ill—versus considering who may be most at risk if they were to become infected so that our clinical laboratories can help caregivers create proactive isolation or quarantine strategies,” he added.
Shotorbani then explained how clinical laboratories have data about comorbidities such as diabetes, asthma, heart disease, and immunosuppression that are associated with more serious cases of COVID-19. “This clinical lab data can be harnessed, associated with demographic and risk data such as age and zip codes to help physicians and others identify patients who would be most at risk from a COVID-19 infection,” he noted.
“Historically, the primary focus of a clinical laboratory was very much on the clinical intervention, contacting the care manager physician, and identifying who’s at risk,” he said. But with COVID-19, Shotorbani sees opportunities to forge relationships with public health specialists to encourage what he describes as “consumer engagement.”
“As medical laboratory professionals, we must evolve to accommodate and support the needs of consumers as they take a more active role in their health,” he continued. “This is moving past simply providing lab test results, but to then be a useful diagnostic and therapeutic resource that helps consumers understand their health conditions and what the best next steps are to manage those conditions.”
Khosrow Shotorbani (above) is President, Executive Director, of the Project Santa Fe Foundation and one of the leaders of the Clinical Laboratory 2.0 movement. He is hopeful that the prominent role of medical laboratories in responding to the coronavirus pandemic will lead to an ongoing “seat at the table” in the higher echelons of healthcare organizations. In normal times, “we reside in basements, and we’re done when we release a result,” he said during an exclusive interview with Dark Daily. “COVID-19 was a kick in the rear to get us upstairs to the C-suite, because healthcare CEOs are under the gun to demonstrate more SARS-CoV-2 testing capacity.” Looking ahead, “we want to make sure that our clinical laboratories stay in that seat and design a future delivery model above and beyond COVID-19, maybe even help health systems, hospitals, and other providers drive their strategies.” (Photo copyright: Albuquerque Business First.)
“None of these are pathologists or come from the lab,” Shotorbani said. “They represent the C-suite and higher organization constituents. These are the healthcare executives who are dealing with their organization’s pain points. As clinical labs, we want to align ourselves to those organizational objectives.”
Pathologist Mark Fung, MD, PhD, will then present a CL 2.0 model for managing COVID-19 or other infectious disease pandemics, followed by a response from the other panelists. Fung is Vice Chair for Population Health in the Department of Pathology and Laboratory Medicine at the Larner College of Medicine at the University of Vermont. He is also on the Project Santa Fe Foundation (PSFF) board of directors.
“Lab 2.0 is a thought leadership organization,” Shotorbani said. “We are developing a template and abstract of this model of clinical laboratory services that other labs can follow while applying some of their own intuition as they make it operational.”
Day Two to the CL 2.0 workshop will feature case studies from the Henry Ford Health System in Detroit and Geisinger Health in Danville, Pa., followed by a discussion with eight PSFF directors. Then, Beth Bailey of TriCore Reference Laboratories in Albuquerque, N.M., will preside over a crowdsourcing session with participation from audience members.
Free Registration for Clinical Laboratories
This will be the first Clinical Lab 2.0 Workshop to be held virtually and registration this year will be free for members of the clinical laboratory community, Shotorbani said. In the past “there has been a hefty tuition to get into this because it’s a very high-touch workshop, especially for senior leaders. But given the critical topic that we’re facing, we felt it was important to waive the cost.”
The Fourth Annual Clinical Lab 2.0 Workshop is partnering this year with the American Society for Clinical Pathology (ASCP), which will provide the software platform for hosting the event, he said. In addition to the live conference sessions, registrants will have access to prerecorded presentations from past workshops. Content will be viewable for six months following the event.
Register for this critical event by clicking here, or by placing this URL in your browser (https://projectsantafefoundation.regfox.com/clinical-lab-20-workshop).
