Tag: lab tests

New HPV Test Enables Precision Treatment

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Researchers have made advances in improving detection of the human papillomavirus (HPV) in the bloodstream, which could further hone precision treatment of the illness.

The team sequenced circulating tumour DNA, which can lead to the detection of HPV in a person’s blood. Previous science in the field has proven that the virus, which causes cancers in the throat, mouth, and genital areas, can be found in the bloodstream but tests have had limited sensitivity. The new study enables ‘ultrasensitive’ detection, which could pave the way toward greater use of precision medicine for patients with cancers affecting these vulnerable areas of the body.

In a cohort of patients with advanced cervix cancer, the new sequencing method detected 20-fold lower levels of HPV circulating tumour DNA, making it a promising new method to monitor the disease.

The results come from the laboratory of Senior Scientist Dr Scott Bratman at Princess Margaret Cancer Center and are published in Clinical Cancer Research. “Increasingly, as clinicians we’re focused on precision medicine and making sure we’re not over-treating people while still curing them, that’s a very difficult balance to strike,” Dr Bratman said.

One way is to use liquid biopsy approaches or blood-based biomarkers, such as circulating tumour DNA, in order to monitor how the treatment is progressing, he added.

“We’re really at the cusp of a revolution from a technology, clinical implementation and standard of care standpoint, where five to 10 years from now we will not be treating everybody with the same dose of radiation and chemotherapy, and then waiting months to see if the treatment was effective,” he said. “I’m confident we will be giving much more tailored doses.”

When physicians scale back on these treatments, there is a risk of the cancer reoccurring. With more sensitive tests, reoccurrences can be detected early and patients returned to treatment.

“Patients who need more treatment will then be able to continue on, or different treatments can be added,” Dr Bratman said. “We can spare the vast majority of patients who will not need those interventions and provided them with a greater quality of life once they’re cured of the cancer.”

The work will enable further study in the field, refining the approach using larger study groups, and eventually, practice-changing clinical trials. This technique could also be applied to other cancer-causing viruses such as certain types of stomach cancer and lymphomas.

Source: Princess Margaret Cancer Center

New Test Makes Prostate Cancer Screening More Affordable

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Researchers have found that, coupled with MRI, the novel Stockholm3 blood test, could greatly cut overdiagnoses and thereby improve prostate cancer screening. The same research group previously showed that Magnetic resonance imaging (MRI) could also reduce overdiagnoses, and the Stockholm3 test can reduce the number of MRIs performed by a third while further preventing the detection of minor, low-risk tumours.

The research group published the findings of their study in The Lancet Oncology,

“Overall, our studies show that we have identified the tools needed to be able to carry out effective and safe screening for prostate cancer. After many years of debate and research, it feels fantastic to be able to present knowledge that can improve healthcare for men,” said Tobias Nordström, associate professor of urology at the Department of Clinical Sciences, Danderyd Hospital at Karolinska Institutet, who is responsible for the STHLM3MRI study.

The disease is currently screened for by using PSA (prostate-specific antigen) tests combined with traditional biopsies, result in unnecessary biopsies and overdiagnosis from detection of numerous minor, low-risk tumours. As a result of these costs outweighing benefits, no country save Lithuania has implemented nationwide screening programmes.

Results from the STHLM3MRI study published in NEJM indicated that overdiagnosis could be reduced by substituting traditional prostate biopsies with magnetic resonance imaging (MRI) and targeted biopsies. The new results, now published in y, show that the addition of the Stockholm3 test, which was developed by researchers at Karolinska Institutet, can be an important complement. It is a blood test that uses an algorithm to analyse a combination of protein markers, genetic markers and clinical data.

Fewer biopsies needed
“The availability of MRI in healthcare will be a limiting factor. We now show that a novel blood test as adjunct to MRI can reduce the number of MRIs performed by a third. Compared with traditional screening, overdiagnosis is reduced by as much as 69 percent. At the same time, the number of biopsies is halved, while we can find just as many clinically significant tumours,” said Martin Eklund, associate professor at the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet.

In the STHLM3MRI study, 12 750 male participants provided an initial blood sample for PSA analysis and analysis using the new Stockholm3 test. Men with test results showing elevated PSA levels were then randomly selected for traditional biopsies or MRI. In the MRI group, biopsies were conducted strictly on suspected tumours identified by MRI.

“Separate use of the Stockholm3 test and MRI has previously been shown to be cost-effective. We have now analysed the cost-effectiveness when these tools are combined and will shortly report exciting results from that analysis,” Tobias Nordström concluded.

Source: Karolinska Institute

‘Vast Majority’ of Urine Tests Before Planned Surgery Unnecessary

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“The vast majority” of urine tests conducted prior to scheduled surgeries to check for infections “were not plausibly indicated,” according to US researchers in a study of claims data.

Though the individual tests were inexpensive at $17 each, over the study’s 11-year duration they came to $50 million, plus another $5 million for antibiotics prescribed to patients with no clinical signs of infection.

“Patients and society bear the risk of inappropriate antibiotic use, which can result in adverse drug reactions, increased risk of infections such as Clostridioides difficile, and emergence of antibiotic resistance,” wrote authors Erica Shenoy, MD, PhD, of Massachusetts General Hospital in Boston, and two colleagues in a JAMA Internal Medicine research letter, published in the journal’s ‘Less Is More’ series which highlights overused tests and treatments.

Once, preprocedural urinalyses were routinely done to check for infections that could increase complication risk. However studies have since shown that such testing rarely improves outcomes or even changes clinical management. Organisations such as the Infectious Diseases Society of America and the US Preventive Services Task Force have recommended against testing and prescribing for asymptomatic infections except in certain narrow indications.

To see just how common the practice has been, the researchers used data on some 13 million procedures performed from 2007 to 2017 from Medicare and the IBM Watson Marketscan database of commercial insurance claims, spanning 14 specialties. The researchers did not count kidney and urological surgeries since urinalysis is recommended by guidelines for most such procedures.

Urinalysis was deemed appropriate for the others when urinary tract symptoms, fever, or altered mental state was mentioned. Without those codes, the procedures were “not plausibly indicated.”

While 75% of surgeries in the data did not involve preprocedural urinalysis, suggesting good adherence, in the 25% that did, fully 89% across all types of surgery had no apparent indication; with the lowest non-indicated testing rate being 84%.

The results show that traditional practice patterns “remain entrenched”, according to the researchers, who called on insurers to take more steps to be more aggressive in denying claims for unneeded testing.

Limitations included incomplete patient data as patients may have had legitimate indications for testing and antibiotic prescriptions that were not recorded with the relevant diagnostic codes. Also, about half of the 11-year study period preceded the movement to limit ‘low-value’ testing.

Source: MedPage Today

Protein Markers Distinguish Between Stable and Progressive Leukaemia

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Scientists have identified protein markers which are related to the most common form of leukaemia.

Chronic lymphocytic leukaemia (CLL) is the most common leukaemia in the Western world. A new study published in the Journal of Leukocyte Biology shows that certain protein markers may indicate which patients have stable forms of CLL and which have more aggressive types.

Identifying these proteins may not only help determine patients’ prognoses but also point to potential therapeutic targets for investigators who are searching for new CLL treatments.

The study examined CLL B-cells’ proteomic profile from untreated CLL patients to see which biologic processes  that are affected early on and during disease evolution as stable or progressive. Of the 11 patients included in the study, six evolved to either progressive and five to stable disease. Purified B cells from the  patients were tested at two time points by liquid chromatography–tandem mass spectrometry. 

First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed protein, samples were separated into stable and progressive clusters with the main differentiating factor being the RNA splicing pathway.

An RNA-Seq study was conducted which showed 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be six times more frequent in the progressive CLL group. 

The main aberrant biologic processes controlled by DEPs and spliced genes in the progressive group were cytoskeletal organisation, Wnt/β-catenin signaling, and mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. 

The study suggests that proteomic profiles of early stage CLL can discriminate progressive from stable disease. Furthermore, it appears RNA splicing dysregulation underlies CLL evolution, opening new avenues for biomarkers and therapy.

“The results offer a meaningful biological approach into the protein composition of CLL cells at an early stage of the disease, when the clinical characteristics of patients are similar and the course of the disease is difficult to predict. Our results showed that the protein profile can however predict how the disease will further evolve,” said lead author Cristina Bagacean, PhD, of CHU de Brest, in France. “This approach could identify putative therapeutic targets in order to prevent CLL progression.”

Source: Wiley

Journal information: Bagacean, C., et al. (2021) Identification of altered cell signaling pathways using proteomic profiling in stable and progressive chronic lymphocytic leukemia. Journal of Leukocyte Biology. doi.org/10.1002/JLB.4HI0620-392R.

Chemical Fingerprints Improve Stem Cell Production

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Researchers in Japan have developed a new, noninvasive way to monitor the tricky art of stem cell production.

The current era of ethical stem cell research was ushered in by the 2012 Nobel prize-winning discovery that ordinary cells could be coaxed to revert to their earliest pluripotent stage ushered in. Suddenly, scientists could have an ethical, near-inexhaustible supply of pluripotent stem cells — the most versatile of stem cells — that can become any type of cell much like how embryonic stem cells function.

These reprogrammed cells called induced pluripotent stem cells (or iPS cells) hold great promise for regenerative medicine, where they can be used to develop tissue or organ replacement-based treatments for life-threatening diseases.

One key challenge is that it is a lengthy and delicate process to artificially induce ordinary cells to reset back to pluripotency. Obtaining iPS cells therefore is a matter of chance. However, knowing all they can about the complex chemical changes happening inside during reprogramming can help scientists increase the chances of successfully obtaining viable iPS cells for clinical applications. Current methods that track reprogramming status, however, use destructive and costly techniques.

A study led by Dr Tomonobu Watanabe, professor at Hiroshima University’s Research Institute for Radiation Biology and Medicine, showed that Raman spectroscopy could be a low-cost, simpler, and non-intrusive technique to monitor the cell’s internal environment as it transitions.

Dr Watanabe explained: “The quality evaluation and sorting of existing cells have been carried out by investigating the presence or absence of expression of surface marker genes. However, since this method requires a fluorescent antibody, it is expensive and causes a problem of bringing the antibody into the cells.”

He added that the “solution of these problems can accelerate the spread of safe and low-cost regenerative medicine using artificial tissues. Through our method, we provide a technique for evaluating and sorting the quality of iPS cells inexpensively and safely, based on scattering spectroscopy.”

Raman spectroscopy is an alternative to invasive approaches that require dyes or labels to extract biochemical information. It instead makes use of vibration signatures produced when light beams interact with chemical bonds in the cell. Since each chemical has its own distinct vibration frequency, scientists can use it to identify the cell’s molecular makeup.

The team used this spectroscopic technique to get the “chemical fingerprints” of mouse embryonic stem cells, the neuronal cells they specialised into, and the iPS cells formed from those neuronal cells. These data were then used to train an AI model to can track the reprogramming is progressing, and verify iPS cell quality by checking for a “fingerprint” match with the embryonic stem cell.

To measure the progress, they assigned the “chemical fingerprint” of neuronal cells as the transformation starting point and the embryonic stem cell’s patterns as the desired end goal. Along the axis, they used “fingerprint” samples collected on days 5, 10, and 20 of the neuronal cells’ reprogramming as reference points on how the process is advancing.

“The Raman scattering spectrum contains comprehensive information on molecular vibrations, and the amount of information may be sufficient to define cells. If so, unlike gene profiling, it allows for a more expressive definition of cell function,” Dr Watanabe said.

“We aim to study stem cells from a different perspective than traditional life sciences.”

Source: Hiroshima University

Journal information: Germond, A., et al. (2020) Following Embryonic Stem Cells, Their Differentiated Progeny, and Cell-State Changes During iPS Reprogramming by Raman Spectroscopy. Analytical Chemistry doi.org/10.1021/acs.analchem.0c01800.

T-Cells Could Identify ‘The Bends’ in Divers

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A new study investigated genetic changes that occur in a serious condition affecting scuba divers — ‘the bends’ — and found that inflammatory genes and white blood cell activity are upregulated. The findings could lead to biomarkers that will help doctors to diagnose the condition more precisely.

The bends, more formally known as decompression sickness, is a potentially lethal condition that can affect divers. Symptoms include joint pain, a skin rash, and visual disturbances. In some patients, the condition can be severe, potentially leading to paralysis and death. The bends can also affect people working in submarines, flying in unpressurised aircraft or in spacewalks.

It has been studied for a long time: a 1908 paper correctly hypothesised that it involves bubbles of gas forming in the blood and tissue due to pressure decrease. Yet even after a century the precise mechanisms underlying the condition are not well understood. Animal studies have suggested that inflammatory processes may have a role in decompression sickness, but no-one had studied this in humans.

Nowadays, getting ‘the bends’ is rare as divers have well-established methods to mitigate risk, such as controlled ascents from the depths. Nevertheless, doctors have no means to test for the condition, if they do encounter it, and instead rely on observing symptoms and seeing whether patients respond to hyperbaric oxygen therapy.

To investigate decompression sickness, the researchers sampled the blood of divers who had been diagnosed with decompression sickness and also divers who had completed a dive without it. The blood samples were drawn at two times: within 8 hours of the divers emerging from the water, and 48 hours afterwards, when those divers with decompression sickness had undergone hyperbaric oxygen treatment. RNA sequencing analysis was done to measure gene expression changes in white blood cells.

“We showed that decompression sickness activates genes involved in white blood cell activity, inflammation and the generation of inflammatory proteins called cytokines,” explained Dr Nikolai Pace of the University of Malta, a researcher involved in the study. “Basically, decompression sickness activates some of the most primitive body defense mechanisms that are carried out by certain white blood cells.”

These genetic changes had diminished in samples from 48 hours after the dive, after the patients had been treated with hyperbaric oxygen therapy — an interesting finding. The results provide a first step towards a diagnostic test for decompression sickness, and may also reveal new treatment targets.

“We hope that our findings can aid the development of a blood-based biomarker test for human decompression sickness that can facilitate diagnosis or monitoring of treatment response,” said Prof Ingrid Eftedal of the Norwegian University of Science and Technology, who was also involved in the project. “This will require further evaluation and replication in larger groups of patients.”

Source: EurekaAlert!

Journal information: “Acute effects on the human peripheral blood transcriptome of decompression sickness secondary to scuba diving” Frontiers in Physiology, DOI: 10.3389/fphys.2021.660402

Stemming the Flow of the ‘Spice’ Drug

The ‘spice’ drug, which has dangerous side effects, is becoming more popular around the world, partly due to the difficulty in detecting its presence.

Spice is the street name for one type of synthetic cannabinoids (SC), which a heterogeneous group of compounds developed to probe the endogenous cannabinoid system or as potential therapeutics. Clandestine laboratories subsequently used published data to develop SC variations marketed as abusable ‘designer drugs’. In the early 2000’s, SC became popular as ‘legal highs’, partly due to their ability to escape detection by standard cannabinoid screening tests. While they provide a similar ‘high’ to cannabis, they are seen as safer but in fact they have serious and potentially fatal side effects.

In 2019, the team developed a prototype of their spice-detecting device and found it could detect the drug from saliva and street material in under five minutes. The current test involves lab analysis of urine, with results after three to seven days.

Dr Chris Pudney from the University’s Department of Biology & Biochemistry, and creator of the new technology, said faster testing is essential if users are to receive treatment and harm-reduction interventions.

“There is no way of knowing if spice has been taken if someone presents with psychosis or intoxication symptoms that could also be due to other reasons,” said Dr Pudney. “So we see the detection technology as a way to inform care in case of overdose.”

The test’s obvious advantages have resulted in great interest, resulting in a grant which the Bath research team will use to create a simple field-usable testing solution.

Dr Pudney said: “Spice is endemic in homeless communities and prisons. It’s highly potent, addictive and poses severe health risks to users including psychosis, stroke, epileptic seizures and can kill. We want to deliver a detection system both to raise the prospect of rapid treatment and to stem the flow of drugs in these communities.”

There are also recent reports of children ‘mistaking’ spice for cannabis, resulting in numerous hospital admissions.

“Drug testing and checking, which is increasing in many countries around the world and in the UK, has been shown to have an impact on drug-taking behaviour and to potentially reduce risk,” said Dr Jenny Scott from the University’s Department of Pharmacy & Pharmacology and who is also involved in the research.

“Spice use is a particular issue in homeless communities. In the future, we hope our technology can be used to offer drug testing to spice users and to tailor harm-reduction information to these vulnerable people. The machines could be used in drugs services, homeless hostels and further down the line, in pharmacies.”

The new spice-testing technology will be based on a cloud-hosted data analytics platform.

“We hope to combine this technology with a deeper understanding of the communities that use spice so that we can deploy the spice-detecting technology in the most effective way possible to benefit the most vulnerable in society,” said Dr Pudney. “Our ultimate aim is to save both money and lives.”

By the end of the grant period, the group aims to start a not-for-profit social enterprise to bring their technology to the mainstream. The group plans to roll out the full range of activities needed to deliver the technology, including portable device design, analytical software development, chemical fingerprint libraries and the associated community pharmacy practice advice to deploy the technology effectively.

“We believe the scope and potential of our research is truly unique and presents the best chance for tackling spice use in the UK and more widely,” said Dr Chris Pudney.

Source: News-Medical.Net

New Bioluminescent System Illuminates Biological Processes

Scientists at the Federal University of São Carlos (UFSCar) have developed a new bioluminescent system that can enable greatly improved imaging of biological and pathological processes in organisms.

Luciferases are enzymes that catalyse the oxidation of luciferins present in organisms such as fireflies, which results in bioluminescence in the visible light spectrum. Images of cell cultures and live animal models are made using the luciferin-luciferase system found in fireflies. For example, this can show the structure and activity of tumours, or follow the viral process in cells, helping physicians develop treatments.

“We obtained a novel luciferin-luciferase system that produces far-red light at the wavelength of 650 nanometres and emits the brightest bioluminescence ever reported in this part of the spectrum,” said principal investigator Professor Vadim Viviani, biochemist at UFSCar. “It’s a highly promising result for bioluminescence imaging of biological and pathological processes in mammalian tissues.”

“Red bioluminescence is preferred when imaging biological or pathological processes in mammalian tissues because haemoglobin, myoglobin and melanin absorb little long-wavelength light. Detection is best of all in the far red and near-infrared bands, but bioluminescent systems that naturally emit far red light don’t exist,” Prof Viviani added.

“Some genetically modified forms of luciferase and synthetic analogs of natural luciferins are produced commercially. In conjunction, they produce light at wavelengths as long as 700 nanometers, but the light produced by these artificial systems is generally much weaker and more short-lived than light from natural bioluminescent systems.”

Prof Viviani and collaborators genetically modified luciferase from the Railroad worm Phrixothrix hirtus, the only luciferase that naturally emits red light, and combined with luciferin analogues synthesised by colleagues at the University of Electro-Communications in Tokyo. The resulting luciferin-luciferase generates a much more efficient far-red bioluminescence.

“Our best combination produces far-red at 650 nanometres, three times brighter than natural luciferin and luciferase, and roughly 1000 times brighter than the same luciferase with a commercial analog,” Viviani said.

“Besides the long-wavelength and intense brightness, our combination has better thermal stability and cell membrane penetrability. Above all, it produces more lasting continuous bioluminescence, taking at least an hour to decay and significantly facilitating the real-time imaging of biological and pathological processes.”

Source: News-Medical.Net

Journal information: Viviani, R. V, et al. (2021) A Very Bright Far-Red Bioluminescence Emitting Combination Based on Engineered Railroad Worm Luciferase and 6′-Amino-Analogs for Bioimaging Purposes. International Journal of Molecular Sciences. doi.org/10.3390/ijms22010303.

New Test Picks up Concussion Biomarkers in Saliva

A new test has been found to effectively pick up concussion biomarkers in the saliva of rugby players.

This paves the way for a non-invasive, easy-to-use pitch-side test to rapidly detect concussions for early treatment. Concussion is a serious problem in contact sports, with players such as college American Football athletes consistently underestimating its risk. Missing a concussion can have a range of consequences, from delayed recovery to more serious (albeit rare) injuries such as traumatic brain swelling.

Detecting concussions requires an assessment by a clinician of the signs and symptoms of the injury. However, recent advances in DNA sequencing technology have made it possible to use small non-coding RNAs (sncRNAs) as biomarkers in rapid tests. sncRNAs regulate the expression of different cellular proteins associated with various diseases, such as cancer and Alzheimer’s disease.

t is thought that since saliva can receive cellular signals directly from the cranial nerves in the mouth and throat, biomarkers from a brain injury would quickly show up.

A panel of 14 sncRNAs differentiated concussed players from those where traumatic brain injury had been suspected but ruled out, and from the comparison group, both straight after the game and 36–48 hours later.

Over two seasons, samples were collected before the rugby season began from 1028 players from the two elite professional tiers, and during standardised ‘gold standard’ head injury assessments at three time points—during the game, afterwards, and 36–48 hours later from 156 of these players .

The researchers also took saliva samples from a comparison group of 102 uninjured players, as well as 66 with muscle or joint injuries, and so had not had head injury assessments.

However, the researchers stressed that the observational study nature and design of this study cannot show that the biomarker test is any better than a gold standard clinical test for concussion.

“In community sport, [sncRNAs] may provide a non-invasive diagnostic test that is comparable in accuracy to the level of assessment available in a professional sport setting,” while the test could be added to current head injury evaluation protocols at the elite level,” they add.

And as the biology of concussion is still not fully understood, sncRNAs might help to shed light on the response to injury as this evolves over time, they suggest.

“The detection of signatures of concussion at early time points in saliva (a non-invasively sampled biofluid) presents both at the pitch side, and in primary care and emergency medicine departments, an opportunity to develop a new and objective diagnostic tool for this common clinical presentation,” they conclude.

As an addendum to their findings, they added: “A patented salivary concussion test is in the process of being commercialized as an over-the-counter test for elite male athletes.

“Meanwhile our research team aims to collect further samples from players in two elite men’s rugby competitions to provide additional data to expand the test and develop its use. This will guide the prognosis and safe return to play after concussion and further establish how the test will work alongside the head injury assessment process.”

The researchers plan to add more participants to the SCRUM study, such as female athletes and community players.
Source: Medical Xpress

Journal information: Valentina Di Pietro et al. Unique diagnostic signatures of concussion in the saliva of male athletes: the Study of Concussion in Rugby Union through MicroRNAs (SCRUM), British Journal of Sports Medicine (2021). DOI: 10.1136/bjsports-2020-103274

New French COVID Variant Invisible to PCR Tests

French authorities have announced the detection of a variant of SARS-CoV-2 in the northwestern region of Brittany that has escaped detection by standard polymerase chain reaction (PCR) tests.

Real-time PCR tests are considered to be the current gold standard for detection of SARS-CoV-2, and currently take 4-6h to yield a result. PCR tests make millions to billions of copies of a small sample of DNA to create a larger sample for analysis.

Eight carriers of the variant were identified using genomic sequencing among a cluster of 79 cases in the town of Lannion in the Côtes d’Armor on March 13th.

In a statement on Monday, the French health ministry said that according to initial analyses, the new variant did not appear more transmissible or cause more severe disease. However, on Tuesday, authorities said that this variant was able to escape detection in PCR tests is raising concern.

Belgian virologist and interfederal COVID spokesperson Steven Van Gucht clarified the situation, in that about eight individuals presented with standard coronavirus symptoms, “but the tests remained negative.”

The World Health Organization has labelled this new French COVID variant a ‘variant under investigation’ (VUI), of which there are many thousands currently being monitored, as opposed to more serious variants like the South African B.1.351 variant which is more transmissible and is a ‘variant of concern’ (VOC).

However, just because this variant escaped the PCR tests being used in that area does not mean that it necessarily can escape all of them, as laboratories vary in the tests that they perform.

According to Gucht, tests differ in the different parts of the virus they look for, and also test for at least two to three. “Usually, a good test does not depend on detecting one specific part. So, if there is a mutation in one part of the virus, that signal may be lost, but there is usually a second or third signal that will be found,” explained Gucht.

French authorities are setting up systems to monitor the spread of this variant, and are also putting measures in place to contain it.

Source: News-Medical.Net