Tag Archives: #coronavirus

New Study Details Enzyme That Allows Coronavirus To Resist Antiviral Medications (Biology)

A new study details the structure of a critical enzyme present in SARS-CoV-2, the coronavirus that causes COVID-19. This enzyme removes nucleoside antiviral medications from the virus’s RNA, rendering many treatments ineffective. Scientists could use data uncovered in the new study to find ways to inhibit the enzyme, possibly leading to more effective treatments.

The coronavirus that causes COVID-19 has demonstrated a stubborn ability to resist most nucleoside antiviral treatments, but a new study led by an Iowa State University scientist could help to overcome the virus’s defenses.

The study, published recently in the peer-reviewed journal Science, details the structure of a critical enzyme present in SARS-CoV-2, the coronavirus that causes COVID-19. This enzyme, known as the proofreading exoribonuclease (or ExoN), removes nucleoside antiviral medications from the virus’s RNA, rendering most nucleoside analogs-based antiviral treatments ineffective. The new study presents the atomic structures of the ExoN enzyme, which could lead to the development of new methods for deactivating the enzyme and opening the door to better treatments for patients suffering from COVID-19.

“If we could find a way to inhibit this enzyme, maybe we can achieve better results to kill the virus with existing nucleoside antiviral treatments. Understanding this structure and the molecular details of how ExoN works can help guide further development of antivirals,” said Yang Yang, lead author of the study and assistant professor in the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology at Iowa State University.

SARS-CoV-2 is an RNA virus, which means its genetic material is composed of ribonucleic acid. When the virus replicates, it must synthesize RNA. But the virus’s genome is unusually large when compared to other RNA viruses, which creates a relatively high likelihood that errors arise during RNA synthesis. These errors take the form of mismatched nucleotides, and too many errors can prevent the virus from propagating.

But the ExoN enzyme acts as a proofreader, recognizing mismatches in the virus RNA and correcting errors that occur during RNA synthesis, Yang said. The enzyme is present only in coronaviruses and a few other closely related virus families, he said.

The same process that eliminates replication errors also eliminates antiviral agents delivered by the treatments commonly used to fight other RNA viruses, such as HIV, HCV and Ebola virus, which partially explains why SARS-CoV-2 has proven so difficult to treat, Yang said.

But Yang and his colleagues utilized cryogenic electron microscopy, a technique in which samples are flash cooled to cryogenic temperatures in vitreous ice to preserve their native structures, to detail the structure of the enzyme. Understanding that structure could allow for the development of molecules that bind to the enzyme and disable it. Yang said that’s the next step for his laboratory and his colleagues. Finding such a molecule could make the virus more susceptible to newly developed antivirals, Yang said. Or, it could allow for the optimization of current antivirals, such as Remdesivir.

Scott Becker, an ISU graduate student in the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, also contributed to the study. The study also included scientists from Yale University and the Hormel Institute at the University of Minnesota.

Journal Reference: Chang Liu, Wei Shi, Scott T. Becker, David G. Schatz, Bin Liu, Yang Yang. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science, 2021; eabi9310 DOI: 10.1126/science.abi9310

Provided by Iowa State University

New Studies Elucidate The Effects Of Coronavirus On The Brain (Medicine)

Days after the World Health Organization (WHO) declared COVID-19 to be a pandemic, in March 2020, a study of patients in Italy reported loss of smell and taste as a symptom. The first study to analyze the neurological impact of the disease in hundreds of people was published in April. Since then, research into the consequences of COVID-19 for the brain has discussed the effects observed in the acute stage, and neurological complications reported by some 30% of patients who recover.

“COVID-19 was initially described as a viral infection of the respiratory tract, but we soon learned that the brain is one of several affected organs. Some aspects of the disease remain obscure. The impact on the brain isn’t fully understood. It’s very important to stimulate the sharing of knowledge and experience among researchers around the world,” said Luiz Eugênio Mello, Scientific Director of FAPESP, in his welcoming remarks to the online seminar What does COVID-19 have to do with the brain?, held on July 7. The webinar featured speakers from Brazil and Germany and was the latest in the series FAPESP COVID-19 Research Webinars, organized with the support of the Global Research Council (GRC).

Viral entry route 

One of the studies presented to the webinar was conducted at Charité University of Medicine Berlin (Germany) and showed that the novel coronavirus uses the olfactory mucosa as the main route to enter the brain. “This is due to the anatomical proximity between the cells of the mucosa and the blood vessels and nerve cells in the area. Once the virus has entered the olfactory mucosa, it appears to use neuroanatomical connections like the olfactory nerve to reach the brain,” said Helena Radbruch, a researcher in the Department of Neuropathology who analyzed samples from olfactory mucosa and four brain regions of 33 patients who died from severe COVID-19.

Radbruch and her team tracked 180 other patients from the acute stage of the disease until months after they recovered. “The good news, especially for those who have had COVID-19, is that the virus doesn’t stay in the brain. We found it there only in some cases, and it was no longer there a month or two after the acute stage,” she said.

They also found clear evidence of activated immune cells in the brain, medulla, and other parts of the central nervous system. In some cases, there was tissue and neuron damage due to hypercoagulation and acute infarction. 

“The entry of the virus into the central nervous system via the neurons of the olfactory mucosa and other cranial nerves appears to explain neurological symptoms such as loss of smell and taste, which isn’t at all rare among COVID-19 patients,” she said.

In Brazil, researchers at D’Or Institute (IDOR) and the Federal University of Rio de Janeiro (UFRJ) conducted a series of experiments and concluded that the virus enters the brain by other routes besides the olfactory mucosa, including systemic inflammation as the disease progresses and affects different organs.

“Unfortunately, in one autopsy we found severe viral infection of the choroid plexus, a central nervous system structure protected by the blood-brain barrier. This brain region has a large amount of ACE2, the protein to which the virus binds to invade the organism. ACE2 is also abundant in the lungs,” said Marilia Zaluar Guimarães, a researcher at UFRJ and IDOR.

The study arose from the rare case of a one-year-old infant who already suffered from encephalopathy and did not survive COVID-19. The autopsy revealed the presence of viral particles in the lungs, heart, cortex and choroid plexus. “Infection by SARS-CoV-2 caused pneumonia, meningitis and damage to multiple organs owing to thrombosis, including the kidneys, lungs, brain, heart and pancreas,” she explained.

Having confirmed that the virus can breach the blood-brain barrier and infect the brain, the researchers decided to conduct studies with brain organoids, highly simplified genetically engineered models of the brain, and laboratory-cultured neural precursor cells called neurospheres. These were originally developed during the zika epidemic using induced human pluripotent stem cells (hIPSCs), skin or blood cells reprogrammed to return to a stage similar to stem cells. The hIPSCs are stimulated to differentiate into nerve cells such as neuroprogenitors, astrocytes and neurons. 

“The organoids are a very simplified model of the brain, but they contain several cell types that let us study the progression of viral infection. In this manner, we proved that SARS-CoV-2 causes brain damage but isn’t able to replicate in the brain since three days after infection there was no viral presence in the neurospheres, which was puzzling,” Zaluar said. The researchers also found that infection reduced the number of neuroprogenitors but did not prevent these cells from proliferating.

Similar studies conducted previously had detected viral replication in brain organoids and neurospheres, but used much larger quantities of the virus and exposed the cell cultures for 24 hours (versus one hour in her study), she noted, concluding that systemic events could explain most of the neurological damage seen in severe COVID-19 patients, although the virus also causes direct brain damage and neuroinflammation.

The research presented by both Zaluar and Radbruch showed that although the virus is cleared from the brain a short time after infection, the elevated levels of pro-inflammatory cytokines persist well after the acute stage, which probably explains the neurological problems typical of long COVID. 

Glial cells

Scientists affiliated with the University of Campinas (UNICAMP) and the University of São Paulo (USP) conducted a study, with support from FAPESP, in which they analyzed data for 81 subjects who tested positive for COVID-19 but had mild symptoms or none and did not require hospitalization. More than 50 days after they were diagnosed, they were found to have alterations in the structure of the cerebral cortex associated with the olfactory tract. In addition, 28% suffered to some degree from anxiety, 20% from depression, 28% from memory loss, and 34% from cognitive impairment.

The researchers also analyzed brain tissue samples from 26 patients who died after contracting COVID-19. The presence of the virus was confirmed in all samples, and alterations that suggested damage to the central nervous system were detected in five samples. 

“We already knew of such neurological symptoms as loss of smell and taste, but our studies showed for the first time that the virus infects and replicates in astrocytes, which are the most abundant cells in the central nervous system and essential to the maintenance of neurons,” said Marcelo Mori, a professor at UNICAMP’s Institute of Biology (more at: agencia.fapesp.br/34404). 

Researchers who collaborate via the Instituto Pasteur-USP scientific platform highlighted another interesting aspect of the effects of COVID-19 on the brain. Metabolic alterations in infected glial cells (astrocytes and other cell types that support and nourish neurons) may be related not only to the effects of the disease on the brain in the acute stage of the disease but also to long-term neurological complications reported by some patients.

“Animal model studies show that the virus can infect glial cells, where it can replicate, produce new viral copies and cause structural changes that affect cell metabolism,” said Jean Pierre Peron, a researcher at USP’s Biomedical Sciences Institute (ICB) and principal investigator for a project on the topic supported by FAPESP.

The scientists conducted analyses to verify alterations in protein expression by infected cells (proteomics) and in the metabolism (metabolomics). “We found many alterations in protein expression, especially those involved in carbon and glucose metabolism,” Peron said. “Not by chance, these signaling pathways are associated with brain disorders such as Huntington’s, amyotrophic lateral sclerosis and long-term depression.”

The metabolomic analysis showed hyperactivation of glycolytic pathways and mitochondria in infected glial cells. “Overall, we found that during infection by the virus there were changes in protein expression that correlated with the carbon metabolism of these glial cells,” Peron said, noting that the alterations in the expression of the enzyme glutaminase are probably associated with viral replication. “The enzyme is extremely important to glial cells, as 90% of the synapses in the brain are glutamatergic [mediated by the neurotransmitter glutamate]. We believe the virus needs glutamine to replicate in the brain and release fully mature particles. When glutaminase is blocked, the release of pro-inflammatory cytokines is reduced,” he explained. Glutaminase is a mitochondrial enzyme that catalyzes the breakdown of glutamine to form glutamate as a part of the glutaminolysis pathway. The glutamate system is important for information processing in neuronal networks.

A recording of the complete webinar can be watched at: covid19.fapesp.br/o-que-covid-19-tem-a-ver-com-o-cerebro/550.

Featured image: A webinar held by FAPESP featured researchers from Brazil and Germany whose findings offer clues as to how SARS-CoV-2 invades the central nervous system and which cells are most affected (experiments with nerve cells conducted by researchers at D’Or Institute and UFRJ; reproduction)

Provided by FAPESP

Bioluminescent Enzyme Produced by Firefly Can Be Used To Detect Novel Coronavirus (Biology)

By combining an enzyme found in fireflies with a protein that binds to the novel coronavirus, the pathogen that causes COVID-19, researchers at the Federal University of São Carlos (UFSCar) in Brazil have developed an innovative strategy to detect antibodies against virus in biological samples.

The enzyme used in the research belongs to the class of luciferases, which catalyze reactions that convert chemical energy into light energy, a phenomenon commonly referred to as bioluminescence. The firefly Amydetes vivianii produces one of the known luciferases with the brightest and most stable bioluminescence.

The insect is found on UFSCar’s Sorocaba campus and is named for Professor Vadim Viviani, who discovered the species and cloned in bacteria the DNA that encodes its luciferase. He also investigated the enzyme’s molecular structure and functions.

“We took our brightest luciferase and used genetic engineering to couple it with a protein that binds to antibodies. If antibodies against SARS-CoV-2 are present in a sample, the reaction will take place and can be detected via the emission of light,” Viviani told Agência FAPESP.

The same technology can detect proteins specific to SARS-CoV-2, evidencing infection, in the presence of specific antibodies.

Immunoassay showing bioluminescence produced for different quantities of SARS-CoV-2 (photo: Vadim Viviani/UFSCar)

The study was completed in less than a year, in step with the speed that has characterized research focusing on the pandemic. It was supported by funding awarded by FAPESP to the Thematic Project Arthropod bioluminescence: biological diversity in Brazilian biomes, biochemical origin, structural/functional evolution of luciferases, molecular differentiation of lanterns, biotechnological, environmental and educational applications.

Patent application filed

Viviani has filed an application for a patent on the novel bioluminescent system with INPI, the Brazilian patent office. The study is so recent that he and his group are still writing it up for publication in a scientific journal. “We’ve successfully tested the method for various antibodies, which can be detected using techniques such as western blotting or immunoblotting,” he said. 

“In immunoblotting, antigen samples are immobilized on a surface and treated with materials such as blood serum from a patient. If the material contains the antibody, it binds to the antigen, forming an antigen-antibody complex that’s revealed by a secondary antibody, usually marked with a protein that generates a fluorescent or chemiluminescent signal. In our study, the marked secondary antibody is a protein with a strong affinity for antibodies, coupled with the luciferase, which generates bioluminescence.”

Immunoblotting or western blotting is a laboratory method used to detect specific protein molecules from among a mixture of proteins in a sample of biological tissues or extracts. The method separates proteins by electrophoresis, a technique that promotes ion migration in an electric field so that they can be separated according to size and charge. 

The study was conducted at UFSCar’s Biochemistry and Bioluminescent Technology Laboratory, with Paulo Lee Ho, a researcher at Butantan Institute, collaborating.

The next step is to find out whether the amount of antibodies present in saliva or nasal swab samples is sufficient to trigger bioluminescence, enabling the biosensor to be used in a rapid non-invasive COVID-19 diagnostic test.

“To move on with this second stage of the research, we’re working with Heidge Fukumasu, a researcher at the University of São Paulo [USP]. Another avenue will involve the use of nanotechnology to develop immunoassays in collaboration with Professor Iseli Nantes and her group at the Federal University of the ABC [UFABC],” Viviani said.

“This study is an example of the many benefits a small firefly species can offer society. An example of how the biodiversity of our forests and science, both so severely endangered, can join forces to produce innovative solutions and add economic and social value to a developing country like Brazil.”

Featured image: Brazilian researchers coupled the molecule with a protein that binds to SARS-CoV-2. The presence of antibodies against the virus in the sample is confirmed by light emission (firefly of the species Amydetes vivianii; photo: Vadim Viviani/UFSCar)

Provided by FAPESP

Novel Coronavirus Discovered In British Bats (Biology)

A coronavirus related to the virus that causes Covid-19 in humans has been found in UK horseshoe bats – according to new collaborative research from the University of East Anglia, ZSL (Zoological Society of London), and Public Health England (PHE).

However, there is no evidence that this novel virus has been transmitted to humans, or that it could in future, unless it mutates. 

UEA researchers collected faecal samples from more than 50 lesser horseshoe bats in Somerset, Gloucestershire and Wales and sent them for viral analysis at Public Health England.

Genome sequencing found a novel coronavirus in one of the bat samples, which the team have named ‘RhGB01’. 

It is the first time that a sarbecovirus (SARS-related coronavirus) has been found in a lesser horseshoe bat and the first to be discovered in the UK. 

The research team say that these bats will almost certainly have harboured the virus for a very long time. And it has been found now, because this is the first time that they have been tested. 

Importantly, this novel virus is unlikely to pose a direct risk to humans, unless it mutates.

A mutation could happen if a human infected with Covid-19 passes it to an infected bat, so 
anyone coming into contact with bats or their droppings, for example those engaged in caving or bat protection, should wear appropriate PPE.

Prof Diana Bell, an expert in emerging zoonotic diseases from UEA’s School of Biological Sciences, said: “Horseshoe bats are found across Europe, Africa, Asia and Australia and the bats we tested lie at the western extreme of their range.

“Similar viruses have been found in other horseshoe bat species in China, South East Asia and Eastern Europe.

“Our research extends both the geographic and species ranges of these types of viruses and suggests their more widespread presence across more than 90 species of horseshoe bats. 

“These bats will almost certainly have harboured this virus for a very long time – probably many thousands of years. We didn’t know about it before because this is the first time that such tests have been carried out in UK bats. 

“We already know that there are different coronaviruses in many other mammal species too,” she said. “This is a case of ‘seek and you will find’.

“Research into the origins of SARS-CoV-2, the virus that causes Covid-19 in humans, has focussed on horseshoe bats – but there are some 1,400 other bat species and they comprise 20 per cent of known mammals. 

“Our findings highlight the need for robust genotype testing for these types of viruses in bat populations around the world. And it raises an important question about what other animals carry these types of viruses.”

Prof Andrew Cunningham, from the Zoological Society of London, said: “Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection have been underestimated. 

“This UK virus is not a threat to humans because the receptor binding domain (RBD) – the part of the virus that attaches to host cells to infect them – is not compatible with being able to infect human cells. 

“But the problem is that any bat harbouring a SARS-like coronavirus can act as a melting pot for virus mutation. So if a bat with the RhGB01 infection we found were to become infected with SARS-CoV-2, there is a risk that these viruses would hybridise and a new virus emerge with the RBD of SARS-CoV-2, and so be able to infect people.

“Preventing transmission of SARS-CoV-2 from humans to bats, and hence reducing opportunities for virus mutation, is critical with the current global mass vaccination campaign against this virus.”

Prof Bell added: “The main risks would be for example a bat rehabilitator looking after a rescued animal and infecting it with SARS-CoV2 – which would provide an opportunity for genetic recombination if it is already carrying another sarbecovirus. 

“Anyone coming into contact with bats or their droppings, such as bat rescuers or cavers, should wear appropriate PPE – in order to reduce the risk of a mutation occurring.

“We need to apply stringent regulations globally for anyone handling bats and other wild animals,” she added. 

The new virus falls within the subgroup of coronaviruses called sarbecoviruses which contains both SARS-CoV-2 (responsible for the current pandemic) and SARS-CoV (responsible for the initial 2003 SARS outbreak in humans).

Further analysis compared the virus with those found in other horseshoe bat species in China, South East Asia and Europe and showed that its closest relative was discovered in a Blasius’s bat from Bulgaria in 2008.

The UK discovery was made by undergraduate ecology student Ivana Murphy, from UEA’s School of Biological Sciences, who collected bat droppings as part of her final year research dissertation. Jack Crook conducted the genetic analyses in partnership with other researchers at PHE.  

A total of 53 bats were captured, and their faeces collected in sterile bags. The research was conducted under strict Health and Safety protocols. Full PPE was worn and Ivana was regularly tested for Covid-19 to avoid any chance of cross contamination. The bats were released immediately after their droppings had been collected.

Ivana said: “More than anything, I’m worried that people may suddenly start fearing and persecuting bats, which is the last thing I would want and would be unnecessary. As like all wildlife, if left alone they do not pose any threat.” 

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe’ is published in the journal Scientific Reports on July 19, 2021. 

Provided by University of East Anglia

Novel Coronavirus Infects And Replicates in Salivary Gland Cells (Medicine)

In Brazil, researchers at the University of São Paulo’s Medical School (FM-USP) have discovered that SARS-CoV-2 infects and replicates in the salivary glands. 

Analysis of samples from three types of salivary gland obtained during a minimally invasive autopsy procedure performed on patients who died from complications of COVID-19 at Hospital das Clínicas, FM-USP’s hospital complex, showed that tissues specializing in producing and secreting saliva serve as reservoirs for the novel coronavirus. 

The study was supported by FAPESP and reported in an article published in the Journal of Pathology.

The researchers said the discovery helps explain why the virus is so abundant in saliva and has enabled scientists to develop saliva-based diagnostic tests for COVID-19. 

“This is the first report of a respiratory virus’s capacity to infect and replicate in salivary glands. Until now it was thought that only viruses that cause highly prevalent diseases such as herpes used salivary glands as reservoirs. The discovery may help explain why SARS-CoV-2 is so infectious,” Bruno Fernandes Matuck, a PhD candidate at USP’s Dental School and first author of the article, told Agência FAPESP.

A previous study by the same group had already demonstrated the presence of RNA from SARS-CoV-2 in the periodontal tissue of patients who died from COVID-19 (more at: agencia.fapesp.br/35675/). 

Because SARS-CoV-2 is highly infectious compared with other respiratory viruses, they raised the hypothesis that it may replicate in cells of the salivary glands and hence be present in saliva without coming into contact with nasal and lung secretions. Prior research detected ACE2 receptors in salivary gland ducts. The spike protein in SARS-CoV-2 binds to ACE2 in order to invade and infect cells. More recently, other research groups have conducted studies in animals showing that other receptors besides ACE2, such as transmembrane serine protease 2 (TMPRSS2) and furin, both of which are present in salivary glands, are targets of SARS-CoV-2.

To test this hypothesis in humans, ultrasound-guided autopsies were performed on 24 patients who died from COVID-19, with a mean age of 53, to extract tissue samples from the parotid, submandibular and minor salivary glands. 

The tissue samples were submitted to molecular analysis (RT-PCR), which detected the presence of the virus in more than two-thirds. Immunohistochemistry – a form of immunostaining in which antibodies bind to the antigen in the tissue sample, a dye is activated, and the antigen can then be seen under a microscope – also demonstrated the presence of the virus in the tissue. Finally, examination under an electron microscope detected not just the presence of the virus but also its replication in cells and the type of organelle it uses to replicate. 

“We observed several viruses clustering in salivary gland cells, which showed that they were replicating there. They weren’t in these cells passively,” Matuck said.

The mouth as direct point of entry

The researchers now plan to see whether the mouth can be a direct point of entry for SARS-CoV-2, given that ACE2 and TMPRSS2 are found in various parts of the cavity, as well as in gum tissue and oral mucosa. In addition, the mouth has a larger contact area than the nasal cavity, which is widely considered the main way in for the virus.

“We’re going to partner with researchers at the University of North Carolina in the United States to map the distribution of these receptors in the mouth and quantify viral replication in oral tissues,” said Luiz Fernando Ferraz da Silva, a professor at FM-USP and principal investigator for the project.

“The mouth could be a viable medium for the virus to enter the body directly,” Matuck said.

Another idea is to find out whether older people have more ACE2 receptors in their mouths than younger people, given the decrease in salivary secretion with age. Nevertheless, the researchers found a high viral load even in older patients, who have less salivary tissue.

“These patients had almost no salivary tissue, almost only fatty tissue. Even so, viral load was relatively high,” Matuck said.

The article “Salivary glands are a target for SARS-CoV-2: a source for saliva contamination” (doi: 10.1002/path.5679)  by Bruno Fernandes Matuck, Marisa Dolhnikoff, Amaro Nunes Duarte-Neto, Gilvan Maia, Sara Costa Gomes, Daniel Isaac Sendyk, Amanda Zarpellon, Nathalia Paiva de Andrade, Renata Aparecida Monteiro, João Renato Rebello Pinho, Michele Soares Gomes-Gouvêa, Suzana C.O.M. Souza, Cristina Kanamura, Thais Mauad, Paulo Hilário Nascimento Saldiva, Paulo H. Braz-Silva, Elia Garcia Caldini and Luiz Fernando Ferraz da Silva is at: onlinelibrary.wiley.com/doi/10.1002/path.5679.

Featured image: A study conducted at the University of São Paulo suggests that tissues specializing in saliva production and secretion serve as reservoirs for SARS-CoV-2, magnifying its infectious potential (electron microscope image showing novel coronavirus inside salivary glands; credit: Bruno Matuck/USP)

Provided by FAPESP

New Technology Detects Greater Variety of T cells That Respond To Coronaviruses (Medicine)

Scientists have developed a new technology to detect a wider variety of T cells that recognize coronaviruses, including SARS-CoV-2. The technology revealed that killer T cells capable of recognizing epitopes conserved across all coronaviruses are much more abundant in COVID-19 patients with mild disease versus those with more severe illness, suggesting a protective role for these broad-affinity T cells.

The ability to distinguish T cells based on their affinities to SARS-CoV-2 could help scientists elucidate the disparity in COVID-19 outcomes and determine which COVID-19 patients will or will not exhibit a successful immune response against the virus, the authors say.

Their work improves upon the primary tool used to identify T cells – antigen tetramers bound to MHC – by instead attracting the cells to multimerized complexes of antigens bound to MHC called “spheromers.” Because tetramers can harbor a maximum of four MHC-antigen complexes, they tend to miss T cells with a low affinity for certain antigens.

Vamsee Mallajosyula and colleagues tackled these limitations with their spheromers, each of which simultaneously displays 12 copies of an individual peptide-MHC complex. The spheromer is easy to produce and compatible with currently available MHC molecules and tetramer components, allowing for easy adoption of their new protocol, the authors say.

When applied to blood samples from COVID-19 patients and individuals not yet exposed to SARS-CoV-2, the spheromers stained specific T cells more efficiently and captured a more diverse repertoire of TCRs compared with the tetramer.

Using the technology, the authors found that T cells capable of recognizing peptides conserved across all coronaviruses were more abundant and exhibited a “memory” phenotype – a desirable feature among T cells targeted by vaccines – compared with T cells that only recognize SARS-CoV-2.

Indeed, COVID-19 patients with mild disease harbored a greater number of killer T cells with these conserved specificities than those with more severe illness, suggesting the broad-affinity T cells are protective, the authors say. Next steps will require enhancing the spheromer technology to include more MHC proteins, they add.

Reference: Vamsee Mallajosyula, Conner Ganjavi, Saborni Chakraborty, Alana M. McSween, Ana Jimena Pavlovitch-Bedzyk, Julie Wilhelmy, Allison Nau, Monali Manohar, Kari C. Nadeau, Mark M. Davis, “CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients”, Science Immunology  01 Jul 2021: Vol. 6, Issue 61, eabg5669 DOI: https://doi.org/10.1126/sciimmunol.abg5669

Provided by AAAS

Test Distinguishes SARS-CoV-2 From Other Coronaviruses with 100% Accuracy (Medicine)

Platform could also predict COVID-19 case severity and immunity against variants

Biomedical engineers at Duke University have demonstrated a tablet-sized device that can reliably detect multiple COVID-19 antibodies and biomarkers simultaneously.

Initial results show the test can distinguish between antibodies produced in response to SARS-CoV-2 and four other coronaviruses with 100% accuracy.

The researchers are now working to see if the easy-to-use, energy-independent, point-of-care device can be used to predict the severity of a COVID-19 infection or a person’s immunity against variants of the virus.

Having also recently shown the same “D4 assay” platform can detect Ebola infections a day earlier than the gold standard polymerase chain reaction (PCR) test, the researchers say the results show how flexible the technology can be to adapt to other current or future diseases.

The results appear online on June 25 in Science Advances.

“The D4 assay took six years to develop, but when the WHO declared the outbreak a pandemic, we began working to compress all of that work into a few months so we could explore how the test could be used as a public health tool,” said Ashutosh Chilkoti, the Alan L. Kaganov Distinguished Professor and Chair of Biomedical Engineering at Duke. “Our test is designed to be both adaptable and truly point-of-care, and this is clearly a scenario when a portable, fast and cost-effective diagnostic would be most useful.”

This point-of-care device uses the physics of fluids to draw a few drops of blood and biomedical lubricant through its components to test for COVID-19 antibodies and biomarkers without the need of any electricity. © Jake Heggestad

The technology hinges on a polymer brush coating that acts as a sort of non-stick coating to stop anything but the desired biomarkers from attaching to the test slide when wet. The high effectiveness of this non-stick shield makes the D4 assay incredibly sensitive to even low levels of its targets. The approach allows researchers to print different molecular traps on different areas of the slide to catch multiple biomarkers at once.

The current iteration of the platform also features tiny patterned tunnels that use the physics of liquids to draw samples through the channels without needing any electricity. With just a drop of blood and a drop of biomolecular lubricant, the test runs autonomously in a matter of minutes and can be read with a detector roughly the size of a very thick iPad.

“The detector is battery powered and the test doesn’t require any power at all, so you can throw the whole thing into a backpack and truly test at the point-of-care with minimal resources,” said Jason Liu, a PhD student working in the Chilkoti lab who designed and built the detector.

In the current study, the researchers tested the D4 assay’s ability to detect and quantify antibodies produced against three parts of the COVID-19 virus — a subunit of the spike protein, a binding domain within the spike protein that grabs on to cells, and the nucleocapsid protein that packages the virus’s RNA. The test was able to spot the antibodies in all of the 31 patients tested with severe cases of COVID-19 after two weeks. It also reported zero false-positives in 41 samples taken from healthy people before the pandemic started as well as 18 samples taken from individuals infected with four other widely circulating coronaviruses.

With the pandemic on the downswing in the United States and hundreds of other COVID-19 antibody tests in development, the researchers don’t believe this particular test is likely to be deployed in large numbers. But they say that the platform’s proven accuracy and flexibility make it a prime candidate for developing into other types of tests or for use in future outbreaks.

For example, the platform could potentially be able to test whether or not people have immunity to the various strains of COVID-19 that continue to emerge.

“There’s lots of questions from people about whether or not they’re protected from new variants of COVID-19, and our test could answer some of those,” said Jake Heggestad, a PhD student working in the Chilkoti lab who developed the chip for the test. “We believe that our platform should be able to distinguish between whether people have antibodies that can neutralize emerging variants of concern or if those antibodies aren’t going to be protective against new variants.”

The researchers are also working to develop the platform into a test for multiple prognostic markers of COVID-19 that together could indicate whether or not a patient is likely to have a severe case of the disease.

“We’re platform builders, so we’re working to show ways this technology can be easily modified to do different things,” said David Kinnamon, a graduate student who developed the liquid handling system for the test. “We’re showing this single platform can work as a diagnostic, assess immune response after infection and predict disease outcome, potentially all at the same time. I don’t know of many tests that can do that.”

“And it can do all of this on a platform that is super user-friendly and transportable,” said Heggestad. “It’s one thing to do all of this in a centralized facility like Duke, but it’s another to be able to do large-scale testing and get good, sensitive results in remote locations around the world.”


This research was supported by the National Science Foundation (CBET2029361), the National Cancer Institute (P30-CA014236, R01-CA248491, UH3-CA211232), the Department of Defense (W81XWH-16-C-0219), Defense Academy of the United Kingdom (ACC6010469), and the Combat Casualty Care Research Program (W81XWH-17-2-0045).

Featured image: The D4 assay is read by this battery-powered, tablet-sized scope, allowing the whole thing to be thrown into a backpack and be used at the point-of-care with minimal resources. © Jake Heggestad

Reference: “Multiplexed, Quantitative Serological Profiling of COVID-19 from Blood by a Point-Of-Care Test,” Jacob T. Heggestad, David S. Kinnamon, Lyra B. Olson, Jason Liu, Garrett Kelly, Simone A. Wall, Solomon Oshabaheebwa, Zachary Quinn, Cassio M. Fontes, Daniel Y. Joh, Angus M. Hucknall, Carl Pieper, Jack G. Anderson, Ibtehaj A. Naqvi, Lingye Chen, Loretta G. Que, Thomas Oguin III, Smita K. Nair, Bruce A. Sullenger, Christopher W. Woods, Thomas W. Burke, Gregory D. Sempowski, Bryan D. Kraft, Ashutosh Chilkoti. Science Advances, June 25, 2021. DOI: sciadv.abg4901

Provided by Duke University

Coronaviruses May Achieve Their Pathogenic Edge By Triggering Programmed Cell Death (Medicine)

Targeting highly pathogenic coronavirus-induced apoptosis reduces viral pathogenesis and disease severity

A new study using cells, transgenic mouse models, and cultured human lung tissue provides evidence that the ability to trigger programmed cell death (apoptosis) may enable highly pathogenic coronaviruses to spread within their hosts so successfully.

Targeting this process may reduce the severity of coronavirus diseases, the study goes on to show. While scientists have been aware that highly pathogenic coronaviruses leave substantial cell death in their wake as they infiltrate the body, the importance of apoptosis to the internal spread of coronavirus infections – and the underlying mechanisms that account for the virus’ high pathogenicity – have not been clear.

To fill this research gap, Hin Chu and colleagues first observed MERS-CoV in cultured human lung tissue and in the lungs of infected transgenic mice, finding that the virus induced substantial apoptosis. To explore how the virus triggered programmed cell death in its host organ’s cells, the researchers analyzed the mRNA transcripts of human bronchial epithelial cells at 12 and 24 hours after infection with MERS-CoV, finding that genes regulated by the protein kinase R-like endoplasmic reticulum kinase (PERK), which are associated with cell death, were highly expressed.

When Chu et al. inhibited PERK signaling in the infected human lung tissues, they saw substantial reductions in both the cell-to-cell spread of MERS-CoV and in cell death induced by the virus. The researchers also performed tests in which they inhibited PERK signaling in transgenic mice infected with the virus. This treatment down-regulated genes involved in apoptosis and reduced lung damage.

While the authors found that PERK inhibitors did not suppress apoptosis triggered by SARS-CoV or SARS-CoV-2, they did observe that an intrinsic apoptosis inhibitor effectively suppressed the process in mice infected with either SARS-CoV or SARS-CoV-2 and reduced lung damage from SARS-CoV-2.

These findings suggest that while the three highly pathogenic human coronaviruses – SARS-CoV, MERS-CoV, and SARS-CoV-2 – may trigger apoptosis through different mechanisms, inhibiting apoptosis may attenuate the pathogenesis of all three.

The study, “Targeting highly pathogenic coronavirus-induced apoptosis reduces viral pathogenesis and disease severity”, Published in Science Advances on 16 June 2021.

Provided by AAAS

How Coronavirus Aerosols Travel Through Our Lungs? (Medicine)

A new study led by Dr Saidul Islam from the UTS Faculty of Engineering models what happens when we inhale coronavirus aerosols.

When we inhale isolated coronavirus particles, more than 65% reach the deepest region of our lungs where damage to cells can lead to low blood oxygen levels, new research has discovered, and more of these aerosols reach the right lung than the left.

Lead author of the study Dr Saidul Islam, from the University of Technology Sydney, said while previous research has revealed how virus aerosols travel through the upper airways including the nose, mouth and throat – this study was the first to examine how they flow through the lower lungs.

“Our lungs resemble tree branches that divide up to 23 times into smaller and smaller branches. Due to the complexity of this geometry it is difficult to develop a computer simulation, however we were able to model what happens in the first 17 generations, or branches, of the airways,” said Dr Islam.

“Depending on our breathing rate, between 32% and 35% of viral particles are deposited in these first 17 branches. This means around 65% of virus particles escape to the deepest regions of our lungs, which includes the alveoli or air sacs,” he said.

aerosol deposition in the lungs
Computer modelling shows the pattern of aerosol deposition in the lungs. © UTS

The alveolar system is critical to our ability to absorb oxygen, so significant amounts of virus in this region, along with inflammation caused by our body’s immune response, can cause severe damage, reducing the amount of oxygen in the blood and increasing the risk of death.

The study also revealed that more virus particles are deposited in the right lung, especially the right upper lobe and the right lower lobe, than in the left lung. This is due to the highly asymmetrical anatomical structure of the lungs and the way air flows through the different lobes.

The research is backed up by a recent study of chest CT scans of COVID-19 patients showing greater infection and disease in the regions predicted by the model.

The researchers modelled three different flow rates – 7.5, 15 and 30 litres per minute. The model showed greater virus deposition at lower flow rates.

As well as improving our understanding of coronavirus transmission, the findings have implications for the development of targeted drug delivery devices that can deliver medicine to the areas of the respiratory system most affected by the virus.

“Normally when we inhale drugs from a drug delivery device most of it is deposited in the upper airways, and only a minimum amount of drugs can reach the targeted position of the lower airways. However, with diseases like COVID-19 we need to target the areas most affected,” said Dr Islam.

“We are working to develop devices that can target specific regions, and we also hope to build age and patient specific whole lung models to increase understanding of how SARS CoV-2 aerosols affect individual patients,” said co-author and group leader of UTS Computer Simulations and Modelling group, Dr Suvash Saha.

The World Health Organisation recently updated its advice about the importance of aerosol transmission, warning that because aerosols can remain suspended in the air, crowded indoor settings and areas with poor ventilation pose a significant risk for transmission of Covid-19.

“When we use an aerosol deodorant, the smallest particles of that liquid fall on us under extreme pressure in the form of gas. Similarly, when an infected person speaks, sings, sneezes or coughs, the virus is spread through the air and can infect those nearby,” said Dr Saha.

The study has further applications, with researchers using portable devices to examine air quality – including PM2.5 and PM10 concentration and gasses such as carbon dioxide, formaldehyde and sulphur dioxide – in spaces such as train carriages. The researchers can then use this data to model the impact on our lungs.

The study, SARS CoV-2 aerosol: How far it can travel to the lower airways, was recently published in the journal Physics of Fluids.

Provided by UTS