Proof of vaccination, masking, and availability of on-site testing will continue to be measures taken at in-person events for pathologists and medical laboratory professionals
Organizers of in-person clinical laboratory conferences face an interesting dilemma as they plan events in 2022: Where do they draw the line with COVID-19 safety protocols?
On one hand, the surge of cases caused by the SARS-CoV-2 Omicron variant seems to be in its waning stages and large swaths of the population are vaccinated. On the other hand, clinical laboratory and anatomic pathology events want potential registrants to have confidence that it is safe to travel and attend the gatherings.
One lab industry conference producer who happens to be knee-deep in preparing for an in-person meeting this spring is Robert Michel, Editor-in-Chief of The Dark Report and Founder of the 27th Annual Executive War College on Laboratory and Pathology Management. This informative event takes place on April 27-28 in New Orleans and includes COVID-19 protocols to protect attendees.
The CDC chart above shows the daily number of new COVID-19 cases in the US for the six-month period ending Feb. 28, 2022. Clinical laboratory managers should note that the number of new cases is at its lowest level since the Omicron variant showed up early this year.
“It’s important for all those planning to attend this year’s Executive War College to know that screening COVID-19 protocols will be in place to ensure the health and safety of all participants,” Michel noted. “We did a large lab conference in the fall of 2021 that included protocols for COVID-19 and the attendees told us they appreciated the protection provided by those protocols.”
After a significant rise in COVID-19 cases in January 2022 due to the Omicron variant, current daily case levels now are lower than they were six months ago before the new variant hit, according to numbers from the federal Centers for Disease Control and Prevention (CDC).
The in-person 2021 Executive War College, which took place in San Antonio on Nov. 2-3, 2021, followed the CDC’s recommendations:
COVID-19 protocols included a daily set of questions and a temperature check for all speakers and attendees before they were allowed to enter the conference area.
CLIA-complex rapid PCR COVID-19 tests were available for individuals whose temperature and answers to the screening questions indicated the need for such testing.
Attendees used an app to answer the daily screening questions and upload proof of vaccination.
“At last fall’s Executive War College, approximately 400 attendees were screened on each of the three days before entering the conference area and not one rapid COVID-19 test was needed,” Michel said. “Not only is that an outstanding outcome, but a number of attendees also told us they appreciated our efforts to keep them safe and protect their health.”
The 2022 Executive War College will follow the CDC’s updated COVID-19 guidelines, along with any state and local directives in effect as of April 27.
Although 300 attendees were expected at the 2021 Executive War College, 400 registered and participated.
Proof of Vaccination Has Been Required at Other Clinical Lab Industry Events
Organizers of other clinical lab conferences also have dealt with COVID-19 safety protocols. For example, the American Clinical Laboratory Association (ACLA) will hold its annual meeting in Washington, D.C., on March 9. COVID-19-related requirements for attendees will include proof of vaccination uploaded to a vaccine verification vendor and proof of a negative PCR test taken within 72 hours prior to the event.
The annual meeting of the American Society of Clinical Pathology (ASCP) occurs later this year in September in Chicago—too early yet to publish protocols. Last year’s ASCP conference in Boston was a hybrid event, offering both in-person and virtual options. Those who attended in person needed to upload proof of vaccination to a third-party vendor and were required to wear masks. On-site COVID-19 testing was available.
Revived Corporate Travel Could Boost Clinical Laboratory Conferences
The path back to live events across all industries has not been easy given various COVID-19 surges, political divisiveness over masking, frozen corporate travel budgets, and corporate policies banning or limiting employee travel.
Conference organizers throughout the United States universally hope those barriers will lower as 2022 progresses.
“With the fast-spreading Omicron triggering another round of setbacks to start 2022, event planners now are betting on spring to finally mark a turning point for the hard-hit industry,” MarketWatch reported on Feb. 4. “Their hopes hinge on American corporations taking a note from the recovery already under way for domestic air travel for leisure purposes, with the linchpin being a robust revival of trade show attendance and other in-person business gatherings.”
For Michel, offering actionable advice through well-thought-out sessions has been a cornerstone of the content offered each year at the Executive War College. He believes that approach will continue to be the strongest drawing point for clinical laboratory and pathology executives now considering attending the event.
“Our reading of the tea leaves is that across the profession of laboratory medicine, a great many managers, administrators, executives, and pathologists want to return to in-person conferences,” Michel noted. “Registrations for our April event are running ahead of 2019, and people tell us that they recognize the changes in healthcare and the lab marketplace because of the pandemic. They want to understand what’s driving current trends, like greater consumer involvement in lab testing and how to get private payers to reimburse claims for COVID-19 and genetic tests, as well as how a growing number of clinical laboratories are incorporating artificial intelligence solutions in both clinical care settings and lab operations.”
This “Virus Trap” might eventually be manufactured by clinical laboratories for the diagnostic process
Clinical laboratory managers and pathologists will be fascinated by this new treatment coming out of Germany for viral infections. It’s an entirely different technology approach to locating and neutralizing live viruses that may eventually be able to control anti-viral-resistant strains of specific viruses as well.
As virologists and microbiologists are aware, even in our present era of technological and medical advances, viral infections are extremely difficult to treat. There are currently no effective antidotes against most viral infections and antibiotics are only successful in fighting bacterial infections.
Thus, this new technology developed by a research team at the Technical University of Munich (TUM) in Munich, Germany, that uses DNA origami to neutralize and trap viruses and render them harmless is sure to gain swift attention, especially given the world’s battle with the SARS-CoV-2 Omicron variant.
“Bacteria have a metabolism. We can attack them in different ways,” said virologist Ulrike Protzer, MD (above), Director of the Institute of Virology at TUM School of Medicine and one of the authors of the study, in a TUM press release. “Viruses, on the other hand, do not have their own metabolism, which is why antiviral drugs are almost always targeted against a specific enzyme in a single virus. Such a development takes time. If the idea of simply mechanically eliminating viruses can be realized, this would be widely applicable and thus an important breakthrough, especially for newly emerging viruses,” she added. (Photo copyright: Helmholtz Munich.)
Entrapping Viruses within 3D Hollow Structures
DNA origami is the nanoscale folding of DNA to create two- and three-dimensional complex shapes that can be manufactured with a high degree of precision at the nanoscale. Researchers have been working with and enhancing this technique for about 15 years.
However, scientists at TUM wondered if they could create such hollow structures based on the capsules that encompass viruses to entrap those viruses. They developed a method that made it possible to create artificial hollow bodies the size of a virus and explored using those hollow bodies as a type of “virus trap.”
The researchers theorized that if those hollow bodies could be lined on the inside with virus-binding molecules, they could tightly bind the viruses and remove them from circulation. For this method to be successful, however, those hollow bodies had to have large enough openings to ensure the viruses could get into the shells.
“None of the objects that we had built using DNA origami technology at that time would have been able to engulf a whole virus—they were simply too small,” said Hendrik Dietz, PhD, Professor of Physics at TUM and an author of the study in a press release. “Building stable hollow bodies of this size was a huge challenge,” he added.
So, the team of researchers used the icosahedron geometric shape, which is an object comprised of 20 sides. They engineered the hollow bodies for their virus trap from three-dimensional, triangular plates which had to have slightly beveled edges to ensure the binding points would assemble properly to the desired objects.
“In this way, we can now program the shape and size of the desired objects using the exact shape of the triangular plates,” Dietz explained. “We can now produce objects with up to 180 subunits and achieve yields of up to 95%. The route there was, however, quite rocky, with many iterations.”
By varying the binding points on the edges of the triangles, the scientists were able to create closed hollow spheres and spheres with openings or half-shells that could be utilized as virus traps. They successfully tested their virus traps on adeno-associated viruses (AAV) and hepatitis B viruses in cell cultures.
“Even a simple half-shell of the right size shows a measurable reduction in virus activity,” Dietz stated in the press release. “If we put five binding sites for the virus on the inside—for example suitable antibodies—we can already block the virus by 80%. If we incorporate more, we achieve complete blocking.”
The team irradiated their finished building blocks with ultraviolet (UV) light and then treated the outside with polyethylene glycol and oligolysine. This process prevented the DNA particles from being immediately degraded in body fluids. Those particles were stable in mouse serum for 24 hours. The TUM scientists plan to test their building blocks on living mice soon.
“We are very confident that this material will also be well tolerated by the human body,” Dietz said.
Could Clinical Laboratories Manufacture Components of the Virus Traps?
The researchers noted that the starting materials for their virus traps can be mass produced at a very reasonable cost and may have other uses.
“In addition to the proposed application as a virus trap, our programmable system also creates other opportunities,” Dietz said. “It would also be conceivable to use it as a multivalentantigen carrier for vaccinations, as a DNA or RNA carrier for gene therapy, or as a transport vehicle for drugs.”
There is much research yet to be done on this cutting-edge technology. However, for this therapy to be appropriate for a patient, a specimen of the virus will need to be identified and studied. Then, the DNA origami would be tailored to capture that specific virus. Thus, it’s conceivable that clinical laboratories, if used for the diagnostic step, might also be able to then manufacture the virus trap that is customized to locate, surround, and neutralize that specific virus.
Its low cost may advance liquid biopsy cancer testing used by anatomic pathologists and improve outcomes by speeding time to diagnosis and treatment
Researchers in Japan say they have created a circulating tumor cell (CTC) detection solution that is inexpensive and easy to run. Such a device would be of huge interest to investors and companies wishing to develop clinical laboratory tests that use circulating tumor cells in the blood to identify patients with cancer.
In a proof-of-concept study, researchers at Kumamoto University (KU) in Japan have developed and tested a microfilter device they claim can separate and capture CTCs in blood without large equipment, a KU news release reported.
According to Medgadget, the device is an “inexpensive, convenient, and highly sensitive filter that can successfully work in samples containing as few as five tumor cells in one milliliter of blood and does not require expensive equipment or reagents, unlike certain pre-existing cell capture technologies.”
This Technology Could Give Pathologists a Less-Invasive Cancer Test
As medical laboratory scientists and anatomic pathologists know, a CTC test is less invasive than tissue biopsy, which benefits patients. Furthermore, such a CTC test may enable earlier detection of cancer and start of treatment improving odds for success.
Still, there are many pitfalls to overcome when the challenge is to detect cancer cells in a milliliter (about .03 fluid ounce) of blood. As Medgadget put it, “A needle in a haystack doesn’t even come close.”
“Cancer cell count in the blood of cancer patients is extremely low. If these cells are easily detectable, cancer diagnosis may be possible by simply using a blood test, thus reducing patient burden,” the researchers wrote in their paper.
“This work demonstrates that our microfilter device can accurately detect trace amounts of cancer cells in blood,” said study leader Yuta Nakashima, PhD (above), Associate Professor, Department of Mechanical System Engineering at Kumamoto University, in the news release. “We expect it will be adopted for cancer diagnosis and treatment, including for early diagnosis of cancers that cannot be detected by imaging like CT and PET scans, post-operative follow-up, recurrence monitoring, and tailor-made treatments. In the future, we plan to use blood samples donated by cancer patients to verify the practical and clinical application of the method,” he added. Were it to become available, such a CTC test would be a boon for clinical laboratories and anatomic pathologists engaged in cancer diagnostics and treatment. (Photo copyright: Kumamoto University.)
How Does the CTC Filter Device Work?
The KU scientists created a palm-size “cancer detection device using a microfilter and nucleic acid aptamer,” the paper said, adding:
It includes slits to enable a deformation with force of blood pumping through the device.
As blood flows over the microfilter, cancer cells bind to the nucleic acid aptamer.
Force of blood flow opens microfilter slits, pushing away the healthy cells.
Cancer cells are left on the microfilter.
To test the microfilter the researchers used one milliliter of blood that was “spiked with cancer cells,” according to the paper. Findings include:
Detection of five CTCs in one milliliter of blood.
Blood cell removal rate of 98% suggested “no blood cells were absorbed by the microfilter,” the news release said.
The method “showed higher accuracy than the CellSearch System,” the Talanta paper noted.
The KU research team compared their microfluidic device to CellSearch, an FDA-cleared system for detecting CTCs from a blood sample.
CellSearch enables “identification, isolation, and enumeration of CTCs of epithelial origin,” according to Menarini Silicon Biosystems of Castel Maggiore, Italy. It works from a blood sample of 7.5 millimeters with “high level of sensitivity and specificity,” notes the company’s website.
According to Menarini, labs offering CellSearch CTC testing include:
The UK scientists admit that their research needs further study. Nakashima indicated he plans to test blood samples donated by cancer patients in subsequent device trials.
“Although great progress has been made, there is a long way to go before CTC-based liquid biopsy is widely used as a routine test in clinical application,” the authors of that study noted.
Nevertheless, even with more to do, liquid biopsy testing has come a long way, as multiple Dark Daily eBriefs reported over the years.
If the KU scientists succeed in bringing to market a microfilter that can reduce the cost of CTC detection by clinical laboratories while also improving cancer diagnostics, that will have a huge impact on cancer patients and is worthy of clinical laboratory leaders’ attention.
Study conducted on International Space Station found crew’s red blood cells were destroyed 54% faster in space than while on Earth
Hemolysis in blood specimens is something that clinical laboratories deal with every day. Now researchers in Canada have determined that, while astronauts are in space, hemolysis is a causative factor in the condition known as “space anemia.”
Hematologists whose clinical laboratories process a steady volume of complete blood count (CBC) tests to diagnosis anemia will want to take note of this research study, which was conducted at the University of Ottawa and on the International Space Station. Dubbed the “MARROW” study, it may have uncovered not only why astronauts suffer from anemia even a year after returning to Earth, but also how those insights can be applied to treatments for anemia and other blood diseases for Earthbound patients as well.
Anemia is caused by a marked decrease in the number of red blood cells and can lead to weakness, persistent fatigue, and slower brain function, which on Earth is concerning, but in space can be life threatening.
“Space anemia has consistently been reported when astronauts returned to Earth since the first space missions, but we didn’t know why,” said the study’s lead author Guy Trudel, MD, in a University of Ottawa news release.
Trudel is Director of the Bone and Joint Research Laboratory at the Ottawa Hospital Rehabilitation Centre in Canada. He is also a Rehabilitation Physician and Researcher at the Ottawa Hospital and Professor of Medicine at the University of Ottawa, and the principal investigator of the MARROW study, which is investigating the effects of microgravity on bone marrow, according to NASA.
“Our study shows that upon arriving in space, more red blood cells are destroyed, and this continues for the entire duration of the astronaut’s mission,” he added.
Although these scientific findings may not immediately lead to new methodologies for testing human blood for use in clinical laboratories, the insights gleaned from the study could inform future studies designed to learn how to get the body to produce more red blood cells in ways that benefit patients diagnosed with anemia or other blood disorders.
Guy Trudel, MD (above), Rehabilitation Physician and Researcher at the Ottawa Hospital and Professor at the University of Ottawa, is lead author of a Canadian study explaining why astronauts develop “space anemia.” In space, astronauts’ red blood cells are destroyed 54% faster than while on Earth, a finding that could have implications for space tourists and astronauts on longer missions to the moon and Mars, the researchers noted. (Photo copyright: University of Ottawa.)
Effects of Anemia Continue One Year after Returning to Earth
The MARROW research project, which was funded by the Canadian Space Agency (CSA), required the participation of 14 astronauts on the International Space Station.
The researchers began collecting data in October 2015 and completed their final tests in June 2020. They found that astronauts’ bodies destroyed 54% more red blood cells in space than would be normal on Earth, according to the study published in Nature Medicine.
“Thankfully, having fewer red blood cells in space isn’t a problem when your body is weightless,” Trudel said in the news release. “But when landing on Earth, and potentially on other planets or moons, anemia affecting your energy, endurance, and strength can threaten mission objectives. The effects of anemia are felt once you land and must deal with gravity again.”
The MARROW experiment detected the following changes:
During a six-month mission, astronauts’ bodies were destroying 54% more red blood cells than typical preflight rates.
Five of the 13 astronauts who had their blood drawn shortly after landing back on Earth were anemic. Red blood cell levels gradually improved three to four months post-flight.
The rate of red blood cell destruction remained 30% higher one year after landing than before missions to the International Space Station.
“Increased hemolysis as a primary effect of exposure to space constitutes a paradigm shift in our understanding of space anemia … Persistent hemolysis during space missions suggests that the longer the exposure, the worse the anemia,” the study’s authors wrote.
Measurements were made by testing the astronauts’ blood for iron levels and using breath tests to measure exhaled carbon monoxide. One molecule of carbon monoxide is produced every time one molecule of heme, the deep-red pigment in blood cells, is destroyed.
According to the researchers, the discovery that space travel increases red blood cell destruction:
highlights the need to screen astronauts and space tourists for existing blood or health conditions that are affected by anemia;
impacts longer missions to the moon and Mars, which would likely worsen an astronaut’s anemia;
suggests astronauts require an adapted diet; and
shows it is unclear how long the body can maintain this higher rate of destruction and production of red blood cells.
Space Study Could Lead to Better Healthcare on Earth
A 2007 NASA study published in Microgravity Science and Technology blamed space anemia on water loss during space flight decreasing the amount of hemoglobin in red blood cells. The study labeled space anemia a “15-day ailment” because those researchers believed issues resolved within 15 days of crew members returning to Earth.
The MARROW study, however, found much longer-lasting implications for astronauts in space, which could lead to new insights for patients on Earth. The Canadian Space Agency believes the study’s findings could lead to better understanding and monitoring of the effects of physical inactivity on seniors, bedridden patients, and those with reduced mobility or undergoing rehabilitation.
“The findings have implications for understanding the physiological consequences of space flight and anemia in patients on the ground,” Sulekha Anand, PhD, a professor in the Department of Biological Sciences at San Jose State University, told Reuters.
This latest study shows how discoveries in space continue to lead to advancements in scientists’ understanding of how the human body functions. That knowledge may one day provide the foundation for developing new or improved clinical laboratory tests for astronauts as well as everyday earthlings.
Scientists working to sequence all 1.66 million animal species say this is a missed opportunity to better understand our own genetics; such research would identify biomarkers useful for clinical laboratory testing
For 23 years, the world’s genomic scientists have been on a mission to sequence the genomes of all animal species. And they’ve made great progress. However, according to a recent study conducted by researchers at Washington State University (WSU) and Brigham Young University (BYU), only a fraction of the sequences are from invertebrate species. And that, according to the study’s authors, is “overlooking huge swathes of diversity and opportunity.”
The push to sequence the whole genomes of all animals began in 1998 with the sequencing of the Caenorhabditis elegans roundworm, according to a WSU news release. It was the first animal genome sequence, but it was not to be the last. Nearly 25 years later, genomic scientists have sequenced about 3,300 animal genomes. And while that’s a lot of genomic sequences, it’s a drop in bucket of the approximately 1.7 million animal species on the planet.
But here’s where the missed opportunity comes in. According to the WSU news release, “Vertebrates account for 54% of all genome sequencing assemblies, despite representing only 3.9% of animal species. In contrast, the invertebrates of the Arthropoda phylum, which includes insects and spiders, comprise only 34% of current datasets while representing 78.5% of all species.”
“We are interested in ourselves, and that’s not necessarily a bad thing,” said Paul Frandsen, PhD (above), in the news release. Frandsen is Assistant Professor of Genetics, Genomics, and Biotechnology at Brigham Young University and one of the study authors. “But to begin to understand entire ecosystems,” he continued, “we have to start sampling more of the variety of life to gain a clearer picture. Vertebrates are important components of ecosystems, but arguably insects and many other small creatures probably play an even more important role because they’re down at the base of the food web.” (Photo copyright: Brigham Young University.)
The scientists analyzed the best available genome assemblies found in GenBank, the world’s most extensive genetic database. They found that 3,278 unique animal species across 24 phyla, 64 classes, and 258 orders have been sequenced and assembled to date.
They also found that sequencing efforts have focused heavily on species that most resemble humans. The Hominidae, a taxonomic family of primates that includes humans as well as great apes, bonobos, chimpanzees, orangutans, and gorillas, has the most contiguous genome data assembled.
The team discovered that vertebrates account for 54% of the animal genome sequencing that has been performed even though they make up less than four percent of known animal species. By comparison, invertebrates of the Arthropoda phylum, which represent 78.5% of all animal species, comprise only 34% of the completed animal genome sequencing. And yet, the Arthropoda phylum is the largest phylum in the animal kingdom and includes insects, spiders, scorpions, centipedes, millipedes, crabs, crayfish, lobsters, and barnacles.
“With genome assemblies accumulating rapidly, we want to think about where we are putting our efforts. It’s not being spread evenly across the animal tree of life,” said lead author Scott Hotaling, PhD, post-doctoral researcher at WSU, in the news release. “Invertebrates are still very underrepresented, which makes sense given that people seem to care more about vertebrates, the so-called ‘charismatic megafauna.’”
The team discovered that only five arthropod groups: ants, bees, butterflies, fruit flies, and mosquitos, were well represented in genome sequencing. The longest genome sequenced so far belongs to the Australian lungfish, the only surviving member of the family Neoceratodontidae.
1,100 Years to Sequence All Eukaryotic Life
The scientists also discerned that animal genome assemblies have been produced by 52 countries on every continent with permanent inhabitants. The majority of animal genome sequencing (77%) that is being performed is mostly occurring in developed countries located in the Northern Hemisphere, often referred to as the Global North. Nearly 70% of all animal genome assemblies have been produced by just three countries: the United States, China, and Switzerland.
There are geographic differences between regions regarding the types of animals being sequenced and assembled with North America concentrating on mammals and insects, Europe focusing on fish, and birds being the main type of animals sequenced in Asia.
The scientists would like to see more animal genome sequencing happening in countries from the Global South, or Southern Hemisphere, particularly in tropical regions that contain a myriad of diversity among animal species.
“If we want to build a global discipline, we need to include a global people,” Hotaling said. “It’s just basic equity, and from a pure scientific standpoint, the people who live in areas where species are being sequenced have a lot of knowledge about those species and ecosystems. They have a lot to contribute.”
But the WSU/BYU scientists found that many species in GenBank only have low-quality assemblies available. They noted that “the quality of a genome assembly is likely the most important factor dictating its long-term value.”
Fortunately, several animal genome sequencing ventures have been announced in recent years, so the amount of available data is expected to rise exponentially. These projects include:
The Earth BioGenome Project (EBP) which aspires to sequence and catalog the genes of all the eukaryotic species on the planet within ten years.
The Vertebrate Genomes Project which seeks to generate high-quality assemblies for 70,000 extant vertebrate species.
The Bird 10K Project that seeks to generate assemblies for all extant birds.
The i5K Project which plans to produce 5,000 arthropod genome assemblies.
The authors of the PNAS paper noted that there are currently only about four genome assemblies happening each day and, at that rate, the sequencing of all eukaryotic life will not be completed until the year 3130.
So, microbiologists, clinical laboratory professionals, and genomic scientists have plenty of time to get up to speed.
Given the large number of mutations found in the SARS-CoV-2 Omicron variant, experts in South Africa speculate it likely evolved in someone with a compromised immune system
As the SARS-CoV-2 Omicron variant spreads around the United States and the rest of the world, infectious disease experts in South Africa have been investigating how the variant developed so many mutations. One hypothesis is that it evolved over time in the body of an immunosuppressed person, such as a cancer patient, transplant recipient, or someone with uncontrolled human immunodeficiency virus infection (HIV).
One interesting facet in the story of how the Omicron variant was being tracked as it emerged in South Africa is the role of several medical laboratories in the country that reported genetic sequences associated with Omicron. This allowed researchers in South Africa to more quickly identify the growing range of mutations found in different samples of the Omicron virus.
“Normally your immune system would kick a virus out fairly quickly, if fully functional,” Linda-Gail Bekker, PhD, of the Desmond Tutu Health Foundation (formerly the Desmond Tutu HIV Foundation) in Cape Town, South Africa, told the BBC.
“In someone where immunity is suppressed, then we see virus persisting,” she added. “And it doesn’t just sit around, it replicates. And as it replicates it undergoes potential mutations. And in somebody where immunity is suppressed that virus may be able to continue for many months—mutating as it goes.”
Multiple factors can suppress the immune system, experts say, but some are pointing to HIV as a possible culprit given the likelihood that the variant emerged in sub-Saharan Africa, which has a high population of people living with HIV.
Li “was among the first to detail extensive coronavirus mutations in an immunosuppressed patient,” the LA Times reported. “Under attack by HIV, their T cells are not providing vital support that the immune system’s B cells need to clear an infection.”
Linda-Gail Bekker, PhD (above), of the Desmond Tutu Health Foundation cautions that these findings should not further stigmatize people living with HIV. “It’s important to stress that people who are on anti-retroviral medication—that does restore their immunity,” she told the BBC. (Photo copyright: Test Positive Aware Network.)
Omicron Spreads Rapidly in the US
Genomics surveillance Data from the CDC’s SARS-CoV-2 Tracking system indicates that on Dec. 11, 2021, Omicron accounted for about 7% of the SARS-CoV-2 variants in circulation, the agency reported. But by Dec. 25, the number had jumped to nearly 60%. The data is based on sequencing of SARS-CoV-2 by the agency as well as commercial clinical laboratories and academic laboratories.
Experts have pointed to several likely factors behind the variant’s high rate of transmission. The biggest factor, NPR reported, appears to be the large number of mutations on the spike protein, which the virus uses to attach to human cells. This gives the virus an advantage in evading the body’s immune system, even in people who have been vaccinated.
“The playing field for the virus right now is quite different than it was in the early days,” Joshua Schiffer, MD, of the Fred Hutchinson Cancer Research Center, told NPR. “The majority of variants we’ve seen to date couldn’t survive in this immune environment.”
One study from Norway cited by NPR suggests that Omicron has a shorter incubation period than other variants, which would increase the transmission rate. And researchers have found that it multiplies more rapidly than the Delta variant in the upper respiratory tract, which could facilitate spread when people exhale.
Using Genomics Testing to Determine How Omicron Evolved
But how did the Omicron variant accumulate so many mutations? In a story for The Atlantic, virologist Jesse Bloom, PhD, Professor, Basic Sciences Division, at the Fred Hutchinson Cancer Research Center in Seattle, described Omicron as “a huge jump in evolution,” one that researchers expected to happen “over the span of four or five years.”
Hence the speculation that it evolved in an immunosuppressed person, perhaps due to HIV, though that’s not the only theory. Another is “that the virus infected animals of some kind, acquired lots of mutations as it spread among them, and then jumped back to people—a phenomenon known as reverse zoonosis,” New Scientist reported.
Still, experts are pointing to emergence in someone with a weakened immune system as the most likely cause. One of them, the L.A. Times reported, is Tulio de Oliveira, PhD, Affiliate Professor in the Department of Global Health at the University of Washington. Oliveira leads the Centre for Epidemic Response and Innovation at Stellenbosch University in South Africa, as well as the nation’s Network for Genomic Surveillance.
The Network for Genomic Surveillance, he told The New Yorker, consists of multiple facilities around the country. Team members noticed what he described as a “small uptick” in COVID cases in Gauteng, so on Nov. 19 they decided to step up genomic surveillance in the province. One private clinical laboratory in the network submitted “six genomes of a very mutated virus,” he said. “And, when we looked at the genomes, we got quite worried because they discovered a failure of one of the probes in the PCR testing.”
Looking at national data, the scientists saw that the same failure was on the rise in PCR (Polymerase chain reaction) tests, prompting a request for samples from other medical laboratories. “We got over a hundred samples from over thirty clinics in Gauteng, and we started genotyping, and we analyzed the mutation of the virus,” he told The New Yorker. “We linked all the data with the PCR dropout, the increase of cases in South Africa and of the positivity rate, and then we began to see it might be a very suddenly emerging variant.”
Oliveira’s team first reported the emergence of the new variant to the World Health Organization, on Nov. 24. Two days later, the WHO issued a statement that named the newly classified Omicron variant (B.1.1.529) a “SARS-CoV-2 Variant of Concern.”
Microbiologists and clinical laboratory specialists in the US should keep close watch on Omicron research coming out of South Africa. Fortunately, scientists today have tools to understand the genetic makeup of viruses that did not exist at the time of SARS 2003, Swine flu 2008/9, MERS 2013.
