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.
Microbiologists will want to take note of the CDC’s statement that the illness can masquerade as other diseases
It is the latest example of a bacterium uncommon in the United States that has infected patients in this country—one of whom has died. The three infected patients live in separate states, but genetic analysis indicates their cases may be related.
According to the health alert, “Based on genomic analysis, these three cases (one male, two females; two adults and one child) may share a potential common source of exposure. The first case, identified in March 2021, was fatal. Two other patients were identified in May 2021, one of whom is still hospitalized. One has been discharged to a transitional care unit. None of the patients’ families reported a history of traveling outside of the continental United States.”
The CDC warned, “Symptoms of melioidosis are varied and nonspecific and may include pneumonia, abscess formation, and/or blood infections. Due to its nonspecific symptoms, melioidosis can initially be mistaken for other diseases such as tuberculosis, and proper treatment may be delayed.”
Microbiology Laboratories Should Be on Alert
Melioidosis is typically only seen in subtropical and tropical regions and can be highly fatal. It is unknown how the trio of patients who contracted the illness became infected, but according to the CDC the cases do appear to be connected.
“Testing suggests a common source of infection, but that source has not yet been identified,” a CDC representative told Gizmodo. “CDC is working with states to assess exposures or products these individuals have in common, as well as environmental samples from the states where cases have been identified. Additionally, CDC experts are providing epidemiologic assistance to help investigate the cause of infection,” the CDC added.
“Melioidosis is a serious neglected tropical disease of Southeast Asia, India, and Australia where it is a major cause of pneumonia, abscesses, and sepsis. The fact that it may be gaining a foothold in the US is concerning,” pediatrician Peter Hotez, MD, PhD (above), Dean of the National School of Tropical Medicine, Professor of Pediatrics and Molecular Virology and Microbiology at Baylor College of Medicine, and Director of the Center for Vaccine Development at Texas Children’s Hospital, told Gizmodo. Clinical laboratories and microbiologists will want to monitor these cases for future developments. (Photo copyright: Baylor College of Medicine.)
Melioidosis, also called Whitmore’s disease, was first described by Alfred Whitmore, an English pathologist, in 1912 in what is now present-day Myanmar. The bacterium (Burkholderia pseudomallei) can be found in contaminated soil and water. It is predominately found in tropical climates in Southeast Asia and northern Australia and can affect humans and many species of animals.
Researchers believe the disease may be acquired through the inhalation of contaminated dust particles or water droplets, the ingestion of contaminated water or soil-contaminated food, or other contact with tainted soil, especially through skin abrasions. It is very rare to contract melioidosis from infected individuals.
Melioidosis Masquerades as Other Illnesses
The symptoms of melioidosis are wide-ranging and non-specific and can resemble those of other illnesses. In addition, there are several types of the illness, and they can each act differently depending on where the infection is in the body. The most common symptoms of melioidosis include:
Localized Infection:
Localized pain or swelling
Fever
Ulceration
Abscess
Pulmonary Infection:
Cough
Chest pain
High fever
Headache
Anorexia
Bloodstream Infection:
Fever
Headache
Respiratory distress
Abdominal discomfort
Joint pain
Disorientation
Disseminated Infection:
Fever
Weight loss
Stomach or chest pain
Muscle or joint pain
Headache
Central nervous system/brain infection
Seizures
According to the CDC, the time between an exposure to Burkholderia pseudomallei and the first emergence of Melioidosis symptoms is not clearly defined but could range from one day to many years. However, most infected individuals begin experiencing symptoms of melioidosis within two to four weeks after exposure.
Melioidosis is difficult to diagnose, and some automated bacterial reading instruments can mistake Burkholderia pseudomallei for other bacteria. It is estimated that the disease accounts for 89,000 deaths per year worldwide. Delays in diagnosis and treatment often lead to poor patient outcomes and the mortality rate can exceed 40% in some regions, Nature reported.
The illness is typically treated with appropriate drug therapies including intravenous antimicrobial medications, such as Ceftazidime or Meropenem, followed by an oral antimicrobial therapy such as Trimethoprim-sulfamethoxazole or Amoxicillin/Clavulanic Acid. It may take several months for a patient to be cured of melioidosis, depending on the extent of the infection.
Deadly Bacterium’s Countries of Origin and Spread to the US
According to CDC data, the greatest number of melioidosis cases are reported in Thailand, Malaysia, Singapore, and northern Australia. Cases also have been reported in other Asian countries as well as Mexico and Central America.
Burkholderia pseudomallei does not occur naturally in the US, and cases of melioidosis identified in the US are usually only seen in world travelers and immigrants who come from countries where the disease is widespread. The bacterium has been found in soil in Mexico, so it is possible that it could spread to parts of the US, which has led to concern among microbiologists.
“Due to changes in weather patterns, some pathogens that normally were not present in a particular area might start causing disease,” Alfredo Torres, PhD, Associate Provost, Department of Microbiology and Immunology, University of Texas Medical Branch, told Gizmodo. “Therefore, it is important to make the health professionals aware of this pathogen and the disease that it causes, so quick identification can be done, and treatment is properly used to save lives. Without that, it might be too late for the next melioidosis patient when the proper diagnosis is done.”
The CDC has suggested that healthcare workers consider melioidosis as a possible diagnosis for patients who have compatible symptoms, even if they have not recently traveled outside of the US.
CDC Suggests Rerunning Certain Clinical Laboratory Tests
Because Burkholderia pseudomallei can be mistaken for other bacteria, the CDC also urges the rerunning of clinical laboratory tests using automated identification, especially if another bacterium that is often mistaken for Burkholderia pseudomallei is present, Gizmodo noted.
“CDC encourages healthcare workers to be aware of the potential for more cases and to report cases to their state health departments,” the CDC stated.
The CDC considers the risk of melioidosis to the public in the US to be low, and that the chances of a potential outbreak are unlikely. However, the origins of these three cases remain a mystery and warrant further investigation.
Microbiologists and clinical laboratories should be aware of and remain alert about this potentially fatal illness. It is possible that more cases will arise in the future, especially in the three states where it has already been found.
It’s the latest example of how the ongoing SARS-CoV-2 pandemic is making it possible for new competitors to enter the clinical laboratory marketplace
In response to increasing demand for COVID-19 testing, warehouse retailer Costco (NASDAQ:COST) is seizing the opportunity to sell at-home saliva self-collection test kits to its customers. It makes Costco the latest company to enter the market for SARS-CoV-2 testing and compete against clinical laboratories.
And these non-invasive tests—which are as simple as spitting saliva into a container and mailing it to a medical laboratory—may be more effective at detecting the SARS-CoV-2 coronavirus than uncomfortable nasal swabs.
Costco is selling its COVID-19 Saliva PCR Test Kit for $129.99 ($139.99 with video observation). Included in the price is a self-collection device, a biohazard bag, a sticker for personal data, and a box for shipping the saliva to a medical laboratory.
The test is actually P23 Labs’ TaqPath SARS-CoV-2 assay and will be administered by Azova, a digital health services provider. P23 says their test has a 98% sensitivity and 99% specificity, according to Business Insider.
The Costco P23 test kit above, “uses parts from Thermo Fisher Scientific and works with collection kits made by testing companies Everlywell and OraSure Technologies, according to the FDA and a P23 spokesperson,” Business Insider reported. “Samples are tested in [P23’s] lab in Little Rock, Arkansas.” (Photo copyright: Costco.)
Saliva-Collection Kits Gain Popularity and FDA Emergency Use Authorizations
P23 Labs’ assay is one of 12 COVID-19 home tests that have received US Food and Drug Administration (FDA) Emergency Use Authorization (EUA). Three of which use saliva specimens.
The FDA’s EUA authorization summary for the P23 assay states it is “for use with saliva specimens that are self-collected at home or in a healthcare setting with or without the supervision and/or assistance of [a healthcare provider (HCP)], by individuals using the P23 At-Home COVID-19 Test Collection Kit, when determined to be appropriate by an HCP based on the results of a COVID-19 medical questionnaire. This test is also for use with nasal swab specimens that are self-collected at home or in a healthcare setting with or without the supervision and/or assistance of an HCP by individuals.”
In a news release announcing the first diagnostic test using saliva specimens, oncologist and FDA Commissioner Stephen Hahn, MD, said that “Authorizing additional diagnostic tests with the option of at-home sample collection will continue to increase patient access to testing for COVID-19. This (saliva sample collection) provides an additional option for the easy, safe, and convenient collection of samples required for testing without traveling to a doctor’s office, hospital, or testing site.” That test was manufactured by Clinical Genomics laboratory of Rutgers New Jersey Medical School.
Below is a list from Business Insider for at-home self-collection SARS-CoV-2 coronavirus tests that have received an FDA EUA. Most can be ordered online, and prices range from $109 to $149, which may be covered by insurance depending on the health plan.
Binx Health Home Nasal Swab COVID-19 sample collection kit
Yale Study Indicates Saliva Tests Have Greater Detection Sensitivity over Swab
Should consumers choose COVID-19 saliva tests over nasal cavity swab tests? Maybe.
A study led by the Yale School of Public Health found and “conducted at Yale New Haven Hospital with 44 inpatients and 98 health care workers—found that saliva samples taken from just inside the mouth provided greater detection sensitivity and consistency throughout the course of an infection than the broadly recommended nasopharyngeal (NP) approach. The study also concluded that there was less variability in results with the self-sample collection of saliva,” states a Yale University news release.
Anne Wyllie, PhD, Associate Research Scientist at Yale School of Public Health, told Time magazine, “Saliva itself is a newer diagnostic method, and a lot of people don’t know how to work with it, are scared to work with it, or not sure how to work with it. Just because a protocol is working with swabs doesn’t mean the same protocol will work with saliva.” Nevertheless, public demand for less invasive COVID-19 testing means clinical laboratories may soon be receiving more requests for processing saliva over nasal swabs. (Photo copyright: Yale University.)
Yale received FDA EUA for SalivaDirect, a real-time quantitative polymerase chain reaction (RT-qPCR) for detection of SARS-CoV-2. However, SalivaDirect is not an “at-home” test. It requires saliva samples to be self-collected into a sterile container in the presence of a healthcare professional, and is being provided by Yale to clinical laboratories as an “open source” protocol, the FDA said in a news release.
“We are trying to work with smaller local labs that want to get up and running to support schools, community groups, universities, and colleges,” Wyllie told Time.
In “Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2,” published in the New England Journal of Medicine (NEJM), Wyllie and others suggest saliva can be just as effective in detecting the coronavirus that causes COVID-19. In their study, COVID-19 patients who were tested by healthcare workers using nasopharyngeal swabs were then asked to collect their own saliva samples.
The researchers found that “Collection of saliva samples by patients themselves negates the need for direct interaction between healthcare workers and patients. This interaction is a source of major testing bottlenecks and presents a risk of nosocomial infection. Collection of saliva samples by patients themselves also alleviates demands for supplies of swabs and personal protective equipment. Given the growing need for testing, our findings provide support for the potential of saliva specimens in the diagnosis of SARS-CoV-2 infection.”
The Yale scientists used primer sequences identified by the Centers for Disease Control and Prevention to detect the coronavirus. They found more SARS-CoV-2 RNA in saliva specimens than in the nasopharyngeal swab specimens. Also, 81% of saliva samples were positive one to five days after diagnosis, as compared to 71% of the nasopharyngeal swab specimens.
“The findings suggest saliva specimens and nasopharyngeal swab specimens have at least similar sensitivity in the detection of SARS-CoV-2 during the course of hospitalization,” the researchers wrote in their NEJM paper.
The increasing popularity of at-home COVID-19 testing—along with studies showing that results improve when specimens are self-collected—suggest that medical laboratory managers should closely monitor the rise of COVID-19 home tests, as well as progress being made in saliva for diagnosing the SARS-CoV-2 coronavirus.
Further, it might be a smart strategy for clinical laboratories with the capability to perform this testing to approach retailers in their region and establish relationships where retailers sell the collection kits, and the lab performs the test and reports the results.
Since patients pay cash for the SARS-CoV-2 tests at the time they purchase the kits, clinical labs are guaranteed payment for the tests without the need to submit claims to consumers’ insurance companies. That’s another benefit to these types of arrangements.
Though only in the pilot study phase, results correlate with earlier studies where both dogs and humans were able to “smell” specific diseases in people Man’s best friend has risked life and limb to save humans for centuries. Now, researchers in Germany have discovered that pooches may be useful in the fight against COVID-19 as well, along with the added benefit that such testing would be non-invasive. In fact, some people believe disease-sniffing dogs may give clinical laboratory testing a...
‘Aerosol and Surface Stability’ study shows that the virus can remain infectious in aerosol form for hours and on surfaces for days
By now, clinical laboratory workers, microbiologists, and phlebotomists should be fully aware of the potential for transmission on surfaces of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the novel coronavirus that causes Coronavirus disease 2019 (COVID-19). The CDC’s latest Morbidity and Mortality Weekly Report revealed that the coronavirus “was identified on a variety of surfaces in cabins of both symptomatic and asymptomatic infected passengers up to 17 days after cabins were vacated on the Diamond Princess, but before disinfection procedures had been conducted,” the New York Post reported. That means the virus can survive on surfaces significantly longer than CDC previously believed.
But did you know a recent study published in the New England Journal of Medicine (NEJM) found that SARS-CoV-2 can also survive in the air for many hours, potentially allowing aerosolized transmission of the virus as well?
The NEJM study also showed that the stability of SARS-CoV-2 to survive on surfaces and in aerosolized form mirrors the stability of the SARS coronavirus (SARS-CoV) that caused the severe acute respiratory syndrome (SARS) outbreak of 2003.
This is critically important information for clinical laboratory professionals in open-space laboratories, phlebotomists collecting medical laboratory specimens, and frontline healthcare workers who come in direct contact with potentially infected patients. They should be aware of every potential COVID-19 transmission pathway.
Hospital infection control teams will be particularly
interested in the possibility of airborne transmission, as they often visit
infected patients and are tasked with tracking both the source of the infection
as well as individuals who may be exposed to sick patients.
The NEJM study, titled “Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1” was conducted by scientists at the National Institute of Allergy and Infectious Diseases (NIAID), an agency of the US Department of Health and Human Services (HHS), the Centers for Disease Control and Prevention (CDC), Princeton University, and University of California, Los Angeles. The researchers concluded that SARS-CoV-2 remains in the air “up to three hours post aerosolization.”
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They also found the virus was detectable for up to four
hours on copper and up to 24 hours on cardboard. The scientists concluded SARS-CoV-2
can remain on plastic and stainless-steel surfaces for two to three days,
though the amount of the virus on surfaces decreases over time.
“Our results indicate that aerosol and fomite transmission of SARS-CoV-2 is plausible, since the virus can remain viable and infectious in aerosols for hours and on surfaces up to days,” the study states. “These findings echo those with SARS-CoV-1, in which these forms of transmission were associated with nosocomial spread and super-spreading events, and they provide information for pandemic mitigation efforts.”
But Can COVID-19 Be Caught Through Air?
However, as noted in Wired, the researchers did not clearly state that infected persons can spread COVID-19 to others in the same airspace. Some experts have pointed out that there is a difference between a virus that can exist as an aerosol—defined as a liquid or solid suspended in gas under only limited conditions—and the measles virus, for example, which the CDC estimates “can live for up two hours in an airspace where the infected person has coughed or sneezed.”
“While the researchers tested how long the virus can survive
in aerosols suspended in the air, they didn’t actually sample the air around
infected people,” Wired noted. “Instead, they put the virus into a
nebulizer and puffed it into a rotating drum to keep it airborne. Then, they
tested how long the virus could survive in the air inside the drum.”
Neeltje van Doremalen, PhD, a research fellow at National Institutes of Health (NIH) and researcher at the NIAID’s Rocky Mountain Laboratories in Hamilton, Montana, who coauthored the NEJM study, cautioned against an overreaction to this latest research. On Twitter she wrote, “Important: we experimentally generated [COVID-19] aerosols and kept them afloat in a drum. This is not evidence of aerosol transmission.”
Nonetheless, the World House Organization (WHO) took note of the study’s findings and on March 16, 2020, announced it was considering “airborne precautions” for healthcare workers, CNBC reported in its coverage of a virtual press conference on March 16, 2020, led by Maria Van Kerkhove, MS, PhD, Technical Lead for WHO’s Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Task Force.
Van Kerkhove emphasized that health officials were
monitoring results from other studies investigating how environmental
conditions such as humidity, temperature, and ultraviolet light affect
the disease and its ability to live on different surfaces.
“When you do an aerosol-generating procedure like in a medical care facility, you have the possibility to what we call aerosolize these particles, which means they can stay in the air a little bit longer,” said Maria Van Kerkhove, MS, PhD (above), Technical Lead for WHO’s Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Task Force during a virtual press conference, CNBC reported. “It’s very important that healthcare workers take additional precautions when they’re working on patients and doing these procedures,” she added. [Photo copyright: World Health Organization/YouTube.)
To Be or Not to Be an Airborne Pathogen
Stanley Perlman, MD, PhD, Professor of Microbiology and Immunology at the University of Iowa, believes aerosol transmission ultimately will be found not to play a large role in COVID-19 transmission.
“I think the answer will be, aerosolization occurs rarely, but not never,” Perlman told STAT. “You have to distinguish between what’s possible and what’s actually happening.”
In an NEJM editorial, Perlman expanded on those thoughts. “Although specific anti-coronaviral therapies are still in development, we now know much more about how to control such infections in the community and hospitals, which should alleviate some of this fear,” he wrote. “Transmission of [SARS-CoV-2] probably occurs by means of large droplets and contact and less so by means of aerosols and fomites, on the basis of our experience with SARS-CoV and MERS-CoV. Public health measures, including quarantining in the community as well as timely diagnosis and strict adherence to universal precautions in healthcare settings, were critical in controlling SARS and MERS. Institution of similar measures will be important and, it is hoped, successful in reducing the transmission of [SARS-CoV-2].”
An NIH news release announcing the SARS-CoV-2 stability study highlighted two additional observations:
“If the viability of the two coronaviruses is
similar, why is SARS-CoV-2 resulting in more cases? Emerging evidence suggest
that people infected with SARS-CoV-2 might be spreading virus without
recognizing, or prior to recognizing, symptoms. That would make disease control
measures that were effective against SARS-CoV-1 less effective against its
successor.
In contrast to SARS-CoV-1, most secondary cases
of virus transmission of SARS-CoV-2 appear to be occurring in community
settings rather than healthcare settings. However, healthcare settings are also
vulnerable to the introduction and spread of SARS-CoV-2, and the stability of
SARS-CoV-2 in aerosols and on surfaces likely contributes to transmission of
the virus in healthcare settings.”
Clearly, the scientific community has not agreed on
aerosolization as a definite source of infection. Nevertheless, clinical
laboratory workers in settings where potential exposure to SARS-CoV-2 exists
should take precautions against airborne transmission until scientists can
definitively determine whether this latest coronavirus can be acquired through
the airborne transmission.
