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.
More than 312 teams applied for the completion and the prize-winning hand-held device uses clinical laboratory assays to diagnose up to 34 different medical conditions
Star Trek fans among clinical laboratory manager and pathologist will be excited to learn that the winners of the Qualcomm Tricorder XPRIZE were announced earlier this year, five years after the contest began. The purpose of the XPRIZE competition was to challenge teams to create a mobile integrated diagnostic device that weighed less than five pounds and had the ability to monitor health metrics and diagnose 13 specific health conditions. The premise for the contest was inspired by the Star Trek medical tricorder that was first conceptualized on the television show “Star Trek” in the 1960s.
In the popular science-fiction show, the tricorder was a multifunctional hand-held device used for sensor scanning, data analysis, and recording data. The name “tricorder” was an abbreviation for the full name of the gadget, “tri-function recorder,” which referred to the three primary functions of the device.
Based in Culver City, Calif, the XPRIZE Foundation is a non-profit organization that creates and oversees prestigious technological competitions for the purpose of prompting innovations that could benefit humanity.
Handheld Device That Can Perform Multiple Clinical Laboratory Assays
The Qualcomm Tricorder XPRIZE competition was launched in January 2012. Participants had until August 2013 to register for the contest. The qualifying round was held the following August. Three hundred and twelve teams entered the competition. Qualifiers had until March 2015 to design and build their prototypes. Consumer testing on the products began in September 2016 and the winners were announced in April 2017.
The top prize of $2.6 million was awarded to Final Frontier Medical Devices, the team led by Basil Harris, MD, an emergency room physician with a PhD in Materials Engineering led the team, along with his network engineer brother, George Harris.
Basil Leaf Technologies, founded by Basil Harris, MD, PhD, FACEP (above center); and his brother George, a Network Engineer (second from left), is a medical technology company headquartered in Paoli, Pa. Their winning entry, called DxtER (pronounced Dexter), is a small FDA-approved group of medical devices that enable consumers to diagnose illnesses at home or remotely and share that data with healthcare providers. (Photo copyright: XPRIZE Foundation.)
The collection of FDA-approved devices that make up the “tricorder” includes sensors designed to gather data about vital signs, body chemistry, and biological functions. The DxtER device walks patients through the self-diagnosis of 34 medical conditions. The instruments include:
· A compact spirometer that calculates lung strength;
DxtER communicates with a tablet and/or smartphone-based app. Since the components are FDA-approved, diagnostic test results can be taken directly to healthcare professionals.
“You can [receive the] results and take them to the ER or to your physician or whoever’s helping you, and they can build off those results,” George Harris explained in an Engadget article. “They don’t have to start back at square one. They can jump off at that point and move on with their healthcare.”
Basil Leaf Technologies’ DxtER “tricorder” (above) enables the user to self-diagnose up to 34 medical conditions. Each individual component is FDA-approved, so hospital physicians can rely on the accuracy of the test results. (Photo copyright: XPRIZE Foundation.)
According to the contest website, “at the heart of DxtER is an artificially intelligent engine that learned to diagnose by integrating years of experience in clinical emergency medicine with data analysis from actual patients having a variety of medical conditions and outcomes.”
“It is very exciting that our vision of mobile, personalized patient-centric healthcare is getting closer to becoming a reality thanks to the great work of the Qualcomm Tricorder XPRIZE teams,” declared Paul E. Jacobs, PhD, Executive Chairman of Qualcomm Incorporated (NASDAQ:QCOM) in an XPRIZE press release. “Creating technology breakthroughs in an industry as complex as healthcare is quite a milestone, and what these teams accomplished is a great stepping stone to making mobile healthcare a viable option across the world.”
DxtER Functions Like a Mobile Medical Laboratory
In addition to the $2.6-million prize, Qualcomm Foundation is giving the Basil Leaf team $3.8 million to further develop the device. This amount includes a:
· $2.5 million proposal grant to the University of California San Diego; and a
· $1.6-million gift from the Roddenberry Foundation to adapt the tricorder for hospital use in the developing world.
The XPRIZE competition required contestants to create a tricorder device that could accurately diagnose 13 health conditions. This included 10 core conditions and a choice of three elective health conditions. The devices also needed to be able to acquire five real-time vital signs:
1. Blood pressure;
2. Heart rate;
3. Oxygen saturation;
4. Respiratory rate; and
5. Temperature.
The 10 core conditions the devices had to be able to identify were:
It is notable that the TriCorder XPRIZE—with its $2.6 million prize—generated entries from 312 teams. Pathologists and clinical laboratory managers can take this high number of entrants as a sign that the ongoing advances in technology are poised to support a new generation of very small medical lab testing devices. Thus, miniaturized diagnostic technologies, when combined with more sophisticated computing chips and software are making it simpler and more feasible to pack multiple diagnostic instruments into a hand-held package.
Improvements in technology are enabling individuals with basic clinical laboratory knowledge to reproduce expensive medical products using low-cost, less complicated methods
Advances in technology made it possible for a group of high school students in Australia to successfully replicate the primary ingredients of a pharmaceutical drug called Pyrimethamine, which is sold under the name Daraprim. It is another demonstration of how today’s sophisticated technologies can be harnessed by individuals with minimal scientific training to produce complex products.
In recent years,Dark Daily has chronicled the successes of high school students in the United States who did the following: (more…)
Clinical laboratory assays on a USB stick could become a powerful tool in the treatment and containment of HIV-1 in low-resource regions, such as sub-Saharan Africa
Imagine a small USB device that plugs into a computer and, using a small sample of blood, is capable of detecting the presence of HIV and measuring its viral load in that individual. Such technology exists and was created by a team of scientists in the United Kingdom (UK). However, it is not yet ready for use by clinical laboratories.
A story published on the mobile technology news blog Quartz pointed out that more than 24-million of the 37-million people worldwide infected with HIV live in sub-Saharan Africa. It is widely recognized that high cost and lack of access to medical care and clinical laboratory services remain a barrier to diagnosis, treatment, and containment of the disease. “[I]mproving diagnostics is now a key part of global strategies to combat [HIV],” wrote the study authors in a paper published in Nature Research journal Scientific Reports. (more…)
Paper-based devices could perform complex, multistep diagnostic tests at a fraction of the cost of traditional medical laboratory analysis
Many research teams are racing to create paper-based devices for medical laboratory tests. Their primary goal is develop a cheap, fast, reliable way to perform diagnostic testing in third world settings, where modern clinical laboratories are few and far between. One development team is working to combine lab-on-a-chip technologies with the low cost of paper-based platforms.
Meanwhile, over the past decade, point-of-care testing (POCT) has revolutionized diagnosis and treatment options for a myriad of conditions. In developing regions or remote areas, low-cost POCT improves accessibility to vital tests for infectious diseases, such as HIV,Malaria, and Ebola, as well as acute medical conditions, such as sepsis.
In the past eight years, Dark Daily has reported many times on the emergence of new POCT devices. From lactic acid screening to the lab-in-a-needle, which is used for detecting liver toxicity, the ability to produce a quick and accurate diagnosis without intensive clinical laboratory testing is growing.
However, one area where many POCT devices face challenges is in surviving extended environmental exposure. This does not pose an issue in major research hospitals or health systems. However, the consequences can be severe when considering the often harsh, resource-limited conditions of developing countries—one area in which POCT stands to offer the greatest value. (more…)
