Of interest to clinical pathologists is the finding that sequencing the genomes of Humans and Neanderthals revealed a link between severity of COVID-19 infections and Neanderthal DNA
Genetic scientists from the University of California Santa Cruz have learned that just 7%—or less—of our DNA is unique to the human species, with the remainder of our genomes coming from other archaic species, such as Neanderthal and Denisovan.
Why should this matter to pathologists and clinical laboratories? Because a broader knowledge of how DNA evolves may help researchers and healthcare providers better understand how a modern family’s DNA can change over generations. In turn, these insights may lead to precision medicine tools for personalized diagnosis and treatment.
“We find that a low fraction, 1.5 to 7%, of the human genome is uniquely human, with the remainder comprising lineages shared with archaic hominins from either ILS [incomplete lineage sorting] or [genetic] admixture,” wrote the paper’s authors.
To complete their study, the researchers used DNA extracted from fossils of Neanderthals and Denisovans, as well as genetic information from 279 people from various locations around the world.
One goal was to determine what part of a modern human’s genome is truly unique. Though only a small percentage of our entire genome, those portions are important.
“We can tell those regions of the genome are highly enriched for genes that have to do with neural development and brain function,” Richard Green, PhD, Associate Professor of Biomolecular Engineering at the University of California Santa Cruz and co-author of the paper, told the Associated Press (AP).
In addition to highlighting what makes modern humans unique as a species, the study also suggests, “That we’re actually a very young species. Not that long ago, we shared the planet with other human lineages,” said Joshua Akey, PhD, Professor of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics at Princeton University. Akey co-authored the Science Advances research paper.
Human/Neanderthal Genetic Overlap
The genetic research being conducted at the University of California Santa Cruz is just the most recent in a flurry of studies over the past decade investigating the Neanderthal genome. Most of these studies point to the vast similarities between humans and Neanderthals, but also to how similar humans are to each other.
“Humans have more than three billion letter pairs of DNA in their genome: It turns out less than 2% of that spells out around 20,000 specific genes, or sets of instructions that code for the proteins that make our tissues,” wrote zooarcheologist Anna Goldfield, PhD (above), Adjunct Instructor Cosumnes River College in Sacramento, Calif., and at the University of California, Davis, in Sapiens. “All humans share the same basic set of genes (we all have a gene for earwax consistency, for example), but there are subtle variations in the DNA spelling of those genes from individual to individual that result in slightly different proteins (sticky earwax versus dry earwax) … Overall, any given human being is about 99.9% similar, genetically, to any other human being,” she added. It is those variations that could lead to precision medicine treatments, personalized drug therapies, and clinical laboratory tests that inform physicians about relevant genetic variations. (Photo copyright: Boston University.)
Practically Everyone Has Neanderthal DNA
Understanding that humans and Neanderthals are 93-98.5% similar genetically may—or may not—come as a surprise. In delving into those similarities and differences researchers are making interesting and potentially important discoveries.
For example, researchers have studied a gene that occurs in both modern humans and Neanderthal fossils that has to do with how the body responds to carcinogenic hydrocarbons, such as smoke from burning wood. Neanderthals were far more sensitive to the carcinogens, but also had more genetic variants, such as single-nucleotide polymorphisms, that could neutralize their effects.
Most modern humans carry some Neanderthal DNA. For some time, scientists thought that Africans likely did not carry Neanderthal DNA, since ancient people tended to migrate out of Africa and met Neanderthals in Europe. More recent research, however, shows that migration patterns were more complex than previously thought, and that the ancient people migrated back to Africa bringing Neanderthal DNA with them.
“Our results show this history was much more interesting and there were many waves of dispersal out of Africa, some of which led to admixture between modern humans and Neanderthals that we see in the genomes of all living individuals today,” Akey told CNN.
Neanderthal DNA and COVID-19
Researchers have found that having Neanderthal DNA may affect the health of modern people who carry it. Perception of pain, immune system function, and even hair color and sleeping patterns have been associated with having Neanderthal DNA.
Scientists have even found a potential link between severe COVID-19 infection and Neanderthal DNA, CNN reported.
The researchers added, “It turns out that this gene variant was inherited by modern humans from the Neanderthals when they interbred some 60,000 years ago. Today, the people who inherited this gene variant are three times more likely to need artificial ventilation if they are infected by the novel coronavirus SARS-CoV-2.”
Of course, these links and associations are preliminary science. John Capra, PhD, Research Associate Professor of Biological Sciences and Associate Professor of Biomedical Informatics at the University of California, San Francisco says, “We can’t blame Neanderthals for COVID. That’s a damaging response, and that’s why I want to emphasize so much [that] the social and environmental factors are the real things that people should be worrying about,” he told CNN.
“That said,” he continued, “as a geneticist, I think it is important to know the evolutionary history of the genetic variants we find that do have effects on traits. The effects of Neanderthal DNA traits are detectable, but they’re modest.”
Nevertheless, genetic scientists agree that understanding the genetic roots of disorders could lead to breakthroughs that result in new types of clinical laboratory tests designed to guide precision medicine treatments.
‘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.
New advancements in mHealth, though encroaching on testing traditionally performed at clinical laboratories, offer opportunity to expand testing to remote locations
Mobile technology continues to impact clinical laboratories and anatomic pathology groups and is a major driver in precision medicine, as Dark Daily has reported. Most of the mobile-test development which incorporates smartphones as the testing device, however, has been for chemistry and immunoassay types of lab tests. Now, a new developer in Monmouth Junction, NJ, has created a Complete Blood Count (CBC) test that runs on devices attached to smartphones.
Such devices enable doctors to order test panels for patients in remote locations that also may lack resources, such as electricity.
The developer is Essenlix and it calls its new testing device iMOST (instant Mobile Self-Testing). According to the company’s website, which is mostly “Under Construction,” iMOST can provide “accurate blood and other healthcare testing in less than 60 seconds by a smartphone and matchbox-size-attachment, anywhere, anytime, and affordable to everyone.”
Stephen Chou, PhD, Professor of Electrical Engineering at Princeton University founded Essenlix, and told Business Insider that his company is developing something that will basically be “a mobile chemical biological lab in your hand.” (Photo copyright: Essenlix.)
The company description on the Longitude Prize website states that Essenlix “uses multidisciplinary approaches to develop a new innovative platform of simple, fast, ultrasensitive, bio/chemical sensing and imaging for life science, diagnostics, and personal health.
The Longitude Prize competition was established to promote the invention of “an affordable, accurate, fast and easy-to-use test for bacterial infections that will allow health professionals worldwide to administer the right antibiotics at the right time,” the website states.
The Essenlix iMOST mobile-testing device (above) connects to a smartphone (shown right) and enables clinical laboratory technicians to run tests in remote locations from samples taken at time the test. Though still in trials, iMOST, and other similar devices, promise to expand testing to outside of traditional medical laboratory locations and further promote precision medicine. (Photos copyright: Lydia Ramsey/Business Insider.)
Essenlix’s iMOST mobile testing system consists of:
a mobile application (app);
the device attachment, which goes over the phone’s camera; and,
a cartridge that holds a sample of blood.
So far, there have been two trials with a total of 92 participants, comparing traditional CBC testing with the Essenlix test. The results were within the FDA’s requirements for allowable error, prompting Chou to tell Business Insider, “Our error is clearly smaller than the FDA’s requirement, so the data is very, very good.”
Chou and his team are working toward FDA approval.
Other Testing Devices That Attached to Smartphones
Aydogan Ozcan, PhD, Professor of Electrical Engineering and Bioengineering at UCLA, and Mats Nilsson, PhD, Professor and Scientific Director of the Science for Life Laboratory at Stockholm University, have developed an attachment that they say can transform “a phone into a biomolecular analysis and diagnostics microscope,” according to The Pathologist. Dark Daily has published many e-briefings on Ozcan’s innovations over the years.
Their goal, the researchers said, was to create technology that can be used in low- and middle-income areas (LMICs), as well as in more advanced locations, such as Sweden. “I’ve been involved in other projects where we’ve looked at point-of-care diagnostic approaches,” he said, “and it seems to be very important that the devices [do not] rely on wired electricity or networks to serve not only LMICs, but also modern, developed environments. It’s often difficult to find an available power socket in Swedish hospitals.”
The molecular diagnostic tests that can be done with smartphone attachments—such as those developed by Ozcan and Nilsson—represent another way of using a smartphone in the healthcare arena, The Pathologist points out. Their invention combines the smartphone’s native camera, an app, optomechanical lasers, and an algorithm contained within the attachment to carry out fluorescence microscopy in the field.
Future of Mobile-Testing
An article appearing in the Financial Times describes some of the ways mobile technology is changing healthcare, including diagnostics that have traditionally been performed in the medical pathology laboratories.
“Doctors scan your body to look for irregularities, but they rely on pathologists in the lab to accurately diagnose any infection,” the article notes. “There, body fluids such as blood, urine, or spit are tested for lurking microbes or unexpected metabolites or chemicals wreaking havoc in your body. Now companies are miniaturizing these tests to create mobile pathology labs.”
Apple introduced the first iPhone in 2007. It’s doubtful anyone imagined the innovations in diagnostics and pathology that would soon follow. Thus, trying to predict what may be coming in coming decades—or even next year—would be futile. However, scientists and researchers themselves are indicating the direction development is headed.
Should Essenlix and other mobile-lab-test developers succeed in their efforts, it would represent yet another tectonic shift for medical pathology laboratories. Clinical laboratory managers and stakeholders should be ready, for the words of the ancient Greek philosopher Heraclitus have never been truer: “Change is the only constant in life.”
If validated in clinical trials, this novel technology has the potential to shift some glucose testing from the clinical laboratory by offering diabetics a convenient, painless blood sugar test
Glucose testing is both a headache and an opportunity for clinical laboratories here in the United States and across the globe. It is a headache because many point-of-care and patient self-test glucose devices in wide use today lack the reliability of glucose testing performed in medical laboratories that use sophisticated diagnostic instruments.
It is an opportunity because, here in the United States and across the globe, there are tens of millions of type 2 diabetics and hundreds of millions of pre-diabetics. Health systems have an unmet demand for glucose testing that is non-invasive, accurate, can be done in patient care settings, and is cheap.
Recently, researchers at Princeton University announced development of noninvasive, in vivo glucose sensor technology that uses a broad-spectrum band of infrared (IR) light to accurately measure blood sugar.
The clinical market for such a device is huge. Just in the United States, there are more than 30 million diagnosed with type 2 diabetes, and more than 70 million pre-diabetics. Researchers have been working for some time to develop a patient-friendly glucose-monitoring technology that does not require a needle stick or venipuncture. (more…)
If successful, the knowledge gained from this research may provide new tools and medical laboratory tests that pathologists can use in the management of geriatric patients
Google’s founders believe that analysis of the genomes of people who live to be 100 years old and are relatively healthy will allow them to solve the puzzle of human aging. They have funded a new company specifically to pursue this goal.
In the near future, it is unlikely that any of the science developed by this venture will lead to a diagnostic profile or clinical laboratory tests that pathologists can use to help clinicians who deal with the diseases associated with aging. But should the research team at Calico develop a better understanding of the dynamics of human aging, it would certainly be expected that this knowledge would be used to develop appropriate medical laboratory tests. (more…)
