Tag Archives: #virus

Gene Sequencing Tools Pinpoint Origins of Bundibugyo Virus Disease Outbreak (Biology)

New research sheds light on the origins of a 2012 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo, according to a report published online this week in the journal Cell Reports Medicine. The work also demonstrates the importance of using high throughput sequencing to understand virus “spillover” events in order to more effectively manage disease outbreaks.

In the study, an international team led by the U.S. Army Medical Research Institute of Infectious Diseases demonstrates how high throughput sequencing—one of USAMRIID’s core competencies—can be used retrospectively to pinpoint the origins of a disease outbreak and provide key information about emerging pathogens of military and public health importance.

Bundibugyo virus is one of four ebolaviruses known to cause human disease, and multiple outbreaks have occurred on the African continent. It is characterized by flu-like symptoms that are sometimes followed by diarrhea, vomiting, chest pain, and hemorrhage. Survivors may suffer from joint pain, blurred vision and hearing loss.

As is the case with other ebolaviruses, the “reservoir” of Bundibugyo—meaning the primary host that harbors the virus—remains unknown, according to the authors. Thus, the ecology of the virus and its transmission mechanism into the human population are poorly understood.

The 2012 outbreak resulted in 38 laboratory-confirmed cases of human infection, 13 of whom died. However, only 4 patient specimens from that outbreak had been sequenced until now, according to MAJ Jeffrey R. Kugelman, Ph.D., one of the study’s lead authors.

USAMRIID’s analysis of sequences from 7 additional patients shows that multiple virus “spillover” events contributed to the outbreak—not a single event, as previously described—and that one of the spillover events likely occurred weeks earlier than previously thought.

 “Analysis of the molecular epidemiology and evolutionary dynamics of the 2012 outbreak with these additional isolates challenges the current hypothesis that the outbreak was the result of a single spillover event,” said MAJ Christine Hulseberg, Ph.D., the paper’s first author.  “In addition, phylogenetic analysis suggests that the initial emergence of the virus occurred 50 days earlier than previously accepted.”

In addition to playing a key role in identifying chains of transmission as an outbreak unfolds, viral genome sequencing helps scientists to better understand general patterns of spread, and informs public health efforts to control future outbreaks. It also allows for examination of genetic mutations that may affect the ability of the virus to survive and cause disease.

This study was conducted at USAMRIID as part of an ongoing Ebola virus response and surveillance effort under the project, “Assessment of Human Clinical Samples from Viral Hemorrhagic Fevers of Known and Unknown Etiology.” It is also among the first of several planned collaborations with the Icahn School of Medicine at Mount Sinai, New York, laying a foundation for future joint research initiatives to protect national and global public health. USAMRIID’s partnership with ISMMS is designed to maximize the impact of DoD’s research, development, and testing and evaluation investment by ensuring integration and cooperation with biomedical infectious disease research centers with similar goals.

Featured image: A researcher prepares a sample for genomic analysis at the U.S. Army Medical Research Institute of Infectious Diseases, where scientists are using next-generation sequencing to improve disease surveillance. Credit: John W. Braun, Jr., USAMRIID Visual Information Office


Reference: Christine E. Hulseberg et al, Molecular analysis of the 2012 Bundibugyo virus disease outbreak, Cell Reports Medicine (2021). DOI: 10.1016/j.xcrm.2021.100351


Provided by US Army Medical Research Institute of Infectious Diseases

AI Reveals How Glucose Helps The SARS-CoV-2 Virus (Biology)

Why do some people get sick and die from COVID-19 while others seem to be completely unaffected? EPFL’s Blue Brain Project deployed its powerful brain simulation technology and expertise in cellular and molecular biology to try and answer this question.

A group in the Blue Brain assembled an AI tool that could read hundreds of thousands of scientific papers, extract the knowledge and assemble the answer – A machine-generated view of the role of blood glucose levels in the severity of COVID-19 was published today by Frontiers in Public Health, Clinical Diabetes.

In response to the COVID-19 pandemic, the COVID-19 Open Research Dataset (CORD-19) of over 400,000 scholarly articles was made open access, including over 150,000 with full text papers related to COVID-19, SARS-CoV-2, and other coronaviruses. The CORD-19 dataset is the most extensive coronavirus literature collection available for data mining to date and the coalition behind it has challenged AI experts to apply their skills in natural language processing and other machine learning techniques in order to generate new insights that may help in the ongoing fight against COVID-19.

“Since early 2020, Blue Brain has been proactively contributing to the fight against COVID-19,” explains Prof. Henry Markram, Founder and Director of the Blue Brain Project. “With this call to action, we realized we could use our Machine Learning technologies and Data and Knowledge Engineering expertise to develop text and data mining tools required to try and help the medical community. Blue Brain set out to answer one of the most puzzling aspects of this pandemic – why some people get very sick, while others are completely unaffected”.

Building and using the text and data mining tools

Accordingly, Blue Brain built and trained machine-learning models to mine these papers and extract structured information from text sources. A simple analysis by this text mining toolbox ‘Blue Brain Search’ of the CORD-19v47 dataset revealed papers that all pointed to glucose metabolism as the most frequently mentioned biological variable.

Using Blue Graph, a unifying Python framework that analyses extracted text concepts to construct knowledge graphs, the group constructed specific knowledge graphs to focus on all the findings that considered glucose in the context of respiratory diseases, coronaviruses, and COVID-19. This allowed for the exploration of the potential role of glucose across many levels, from the most superficial symptomatic associations to the deepest biochemical mechanisms implicated in the disease.

From the facts and findings of thousands of papers mined, multiple lines of evidence emerged that elevated blood glucose levels were either caused by abnormal glucose metabolism, or induced during hospitalization, drug treatments or by IV administration. This approach correlated extremely well with COVID-19 severity across the population and revealed how elevated glucose helps virtually every step of the viral infection, from its onset in the lungs, through to severe complications such as Acute Respiratory Distress Syndrome, multi-organ failure and thrombotic events.

“Subsequently, in the paper, we discuss the potential consequences of this hypothesis and propose areas for further investigation into diagnostics, treatments and interventions that may help to reduce the severity of COVID-19 and help manage the public health impact of the pandemic,” discloses Blue Brain’s Molecular Biologist Dr. Emmanuelle Logette.

The potential of open access scientific papers

“Scientists immediately went to work when the pandemic started and within a year published over a hundred thousand papers. But, can anyone read so many papers? Can anyone see and understand all the patterns across all this research?” asks Prof. Henry Markram. “Fortunately, the coalition behind the CORD-19 dataset convinced all subscription publishers to bring these papers over the subscription paywall and make them openly accessible so that they can be mined with modern machine learning and knowledge engineering technologies”.

“With access to the CORD-19 dataset, Blue Brain quickly assembled an AI tool and targeted it to try and find out why some get sick and others not. Is it enough to just say that older people are more vulnerable? We must find out why. Why do some apparently healthy people die from COVID-19? Why do so many people die in the ICU? To answer these questions, we directed our AI to trace every step of the viral infection from the moment the virus enters the lungs until the time when the virus breaks out of the cells in the lungs and spreads throughout the body to infect the organs,” explains Prof. Markram. “We also built the virus at an atomistic level and developed a computational model of the infection so we could try to test what was coming out of the literature. I think we did find the most likely reason why some people get sicker than others,” he concludes.

An example of this is the team using Blue Brain BioExplorer to visually show the main impacts of high glucose in airway surface liquid on the primary step of infections in the lung and explaining the increased susceptibility to respiratory viruses in at-risk patients.

Blue Brain BioExplorer was built to reconstruct, visualize, explore and describe in detail the structure and function of the coronavirus for this study, and is open source for others to use to answer key scientific questions.

“Pioneering Simulation Neuroscience to better understand the brain has numerous collateral benefits,” states Prof. Markram. “This study shows how Blue Brain’s computing technologies and unique team of multi-disciplinary experts can quickly be redirected to help in a global health crisis.”

A major step forward for science and understanding the brain

“The COVID-19 study also shows why we believe that computational tools are so important to help us understand the brain,” explains Prof. Markram. “The problem is even bigger. There are several million scientific papers that one would need to read and understand to work out what we know about the brain. Does anyone know what we know? But, machines can read so many papers. This is the reason that the Blue Brain has developed some of the most advanced knowledge engineering, mathematical and machine learning accelerator technologies. Actually, this solves only a part of the challenge. With an AI tool that can read all these papers, we would still only know only a small fraction of what the brain contains and how it works. But building model brains using design principles, helps us to try and complete the picture.” he concludes.

Is it right to only open science during a pandemic?

Prof. Markram also expressed his frustration with the all too common practice of locking up of scientific knowledge by subscription publishers. “When the CORD-19 literature dataset was made available to us, we at Blue Brain were able to point our technology at COVID-19 and propose an answer to an important question in the battle against this deadly virus. Therefore, is it right to only make science papers (that are publicly funded) open to the public during a pandemic when the same kind of techniques can be used to help address so many other diseases, accelerate science, and help save the planet from climate change?”

About EPFL’s Blue Brain Project

The aim of the EPFL Blue Brain Project, a Swiss brain research initiative founded and directed by Professor Henry Markram, is to establish simulation neuroscience as a complementary approach alongside experimental, theoretical and clinical neuroscience to understanding the brain, by building the world’s first biologically detailed digital reconstructions and simulations of the mouse brain. 

https://www.epfl.ch/research/domains/bluebrain/

Funding

This study was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government ETH Board of the Swiss Federal Institutes of Technology.

References

Emmanuelle Logette, Charlotte Lorin, Cyrille Favreau, Eugenia Oshurko, Jay S. Coggan, Francesco Casalegno, Mohameth François Sy, Caitlin Monney, Marine Bertschy, Emilie Delattre, Pierre-Alexandre Fonta, Jan Krepl, Stanislav Schmidt, Daniel Keller, Samuel Kerrien, Enrico Scantamburlo, Anna-Kristin Kaufmann, Henry Markram. A machine-generated view of the role of Blood Glucose Levels in the severity of COVID-19. Frontiers in Public Health, 28 July 2021. doi.org/10.3389/fpubh.2021.695139

Featured image: Digital reconstruction of SARS-CoV-2 virus in the lung environment. Credit: Blue Brain Project


Provided by Ecole Polytechnique Federale de Lausanne

Virus That Causes COVID-19 Can Find Alternate Route To Infect Cells (Medicine)

COVID-19 drugs, vaccines still effective against mutating virus

Early in the COVID-19 pandemic, scientists identified how SARS-CoV-2, the virus that causes COVID-19, gets inside cells to cause infection. All current COVID-19 vaccines and antibody-based therapeutics were designed to disrupt this route into cells, which requires a receptor called ACE2.

Now, researchers at Washington University School of Medicine in St. Louis have found that a single mutation gives SARS-CoV-2 the ability to enter cells through another route – one that does not require ACE2. The ability to use an alternative entry pathway opens up the possibility of evading COVID-19 antibodies or vaccines, but the researchers did not find evidence of such evasion. However, the discovery does show that the virus can change in unexpected ways and find new ways to cause infection. The study is published June 23 in Cell Reports.

“This mutation occurred at one of the spots that changes a lot as the virus circulates in the human population,” said co-senior author Sebla Kutluay, PhD, an assistant professor of molecular microbiology. “Most of the time, alternative receptors and attachment factors simply enhance ACE2-dependent entry. But in this case, we have discovered an alternative way to infect a key cell type — a human lung cell — and that the virus acquired this ability via a mutation that we know arises in the population. This is something we definitely need to know more about.”

The finding was serendipitous. Last year, Kutluay and co-senior author M. Ben Major, PhD,  the Alan A. and Edith L. Wolff Distinguished Professor of Cell Biology & Physiology, planned to study the molecular changes that occur inside cells infected with SARS-CoV-2. Most researchers study SARS-CoV-2 in primate kidney cells because the virus grows well in them, but Kutluay and Major felt it was important to do the study in lung or other cells similar to the ones that are naturally infected. To find more relevant cells capable of growing SARS-CoV-2, Kutluay and Major screened a panel of 10 lung and head-and-neck cell lines.

“The only one that was able to be infected was the one I had included as a negative control,” Major said. “It was a human lung cancer cell line with no detectable ACE2. So that was a crazy surprise.”

Kutluay, Major and colleagues — including co-first authors and postdoctoral researchers Maritza Puray-Chavez, PhD, and Kyle LaPak, PhD, as well as co-authors Dennis Goldfarb, PhD, an assistant professor of cell biology & physiology and of medicine, and Steven L. Brody, MD, the Dorothy R. and Hubert C. Moog Professor of Pulmonary Diseases in Medicine, and a professor of radiology — discovered that the virus they were using for experiments had picked up a mutation. The virus had originally been obtained from a person in Washington state with COVID-19, but as it was grown over time in the laboratory, it had acquired a mutation that led to a change of a single amino acid at position 484 in the virus’s spike protein. SARS-CoV-2 uses spike to attach to ACE2, and position 484 is a hot spot for mutations. A variety of mutations at the same position have been found in viral variants from people and mice, and in virus grown in the lab. Some of the mutations found in virus samples taken from people are identical to the one Kutluay and Major found in their variant. The Alpha and Beta variants of concern have mutations at position 484, although those mutations are different.

“This position is evolving over time within the human population and in the lab,” Major said. “Given our data and those of others, it is possible that the virus is under selective pressure to get into cells without using ACE2. In so many ways, it is scary to think of the world’s population fighting a virus that is diversifying the mechanisms by which it can infect cells.”

To determine whether the ability to use an alternative entry pathway allowed the virus to escape COVID-19 antibodies or vaccines, the researchers screened panels of antibodies and blood serum with antibodies from people who have been vaccinated for COVID-19 or recovered from COVID-19 infection. There was some variation, but in general, the antibodies and blood sera were effective against the virus with the mutation.

It is not yet clear whether the alternative pathway comes into play under real-world conditions when people are infected with SARS-CoV-2. Before the researchers can begin to address that question, they must find the alternative receptor that the virus is using to get into cells.

“It is possible that the virus uses ACE2 until it runs out of cells with ACE2, and then it switches over to using this alternative pathway,” Kutluay said. “This might have relevance in the body, but without knowing the receptor, we cannot say what the relevance is going to be.”

Major added, “That’s where we’re going right now. What is the receptor? If it’s not ACE2, what is it?”

This work was supported in part by Washington University School of Medicine; V Foundation, grant number T2014-009; the National Institutes of Health (NIH), grant numbers T32CA009547-34, 5T32HL007106-39, K08HL150223, AI059371, AI157155, and 75N93019C00074; and the Defense Advanced Research Projects Agency, grant number HR001117S0019. This study utilized samples obtained from the Washington University School of Medicine’s COVID-19 biorepository supported by the NIH/National Center for Advancing Translational Sciences, grant number UL1 TR002345.

Featured image: The virus that causes COVID-19 normally gets inside cells by attaching to a protein called ACE2. Researchers at Washington University School of Medicine in St. Louis have found that a single mutation confers the ability to enter cells through another route, which may threaten the effectiveness of COVID-19 vaccines and therapeutics designed to block the standard route of entry. © Getty images


Reference: Puray-Chavez M, LaPak KM, Schrank TP, Elliott JL, Bhatt DP, Agajanian MJ, Jasuja R, Lawson DQ, Davis K, Rothlauf PW, Liu Z, Jo H, Lee N, Tenneti K, Eschbach JE, Mugisha CS, Cousins EM, Cloer EW, Vuong HR, VanBlargan LA, Bailey AL, Gilchuk P, Crowe JE, Diamond MS, Hayes DN, Whelan SPJ, Horani A, Brody SL, Goldfarb D, Major MB, Kutluay SB. Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Cell Reports. June 23, 2021. DOI: 10.1016/j.celrep.2021.109364


Provided by WUSTL

SARS-CoV-2 Infections May Trigger Antibody Responses Against Multiple Virus Proteins (Biology)

Study suggests vaccines, therapeutics, and diagnostics should not be limited to spike protein

All coronaviruses produce four primary structural proteins and multiple nonstructural proteins. However, the majority of antibody-based SARS-CoV-2 research has focused on the spike and nucleocapsid proteins. A study published in PLOS Biology by Anna Heffron, Irene Ong and colleagues at the University of Wisconsin-Madison, USA, suggests that immune responses may develop against other proteins produced by the SARS-CoV-2 virus.

The efficacy of spike protein-based vaccines is variable and not everyone infected with SARS-CoV-2 produces detectable antibodies against the spike or nucleocapsid proteins. Therefore, expanded antibody-based options have the potential to play an important role in improving vaccines, diagnostics, and therapeutics, particularly given the emergence of new variants. To investigate whether SARS-CoV-2 infection induces robust antibody responses against all SARS-CoV-2 proteins, researchers mapped 79 “epitopes” – specific regions of the viral proteome that antibodies recognize and bind to. They also tested whether antibodies that develop in response to SARS-CoV-2 or existing antibodies from previous exposures to coronaviruses might bind to any of the proteins in the six other known human coronaviruses to identify potential cross-reactive epitopes.

In addition to spike and nucleocapsid proteins, the authors located previously unknown, highly reactive B cell epitopes throughout the full array of proteins in SARS-CoV-2 and other coronaviruses, expanding the potential for future vaccine and therapeutic development. Future research is needed, however, to determine how long these antibodies remain and whether responses of vaccinated individuals differ from those who contracted COVID-19 prior to vaccination. Dr. Ong and colleagues will continue to investigate these aspects in adults and children.

Although the authors did not directly profile variants of concern that have emerged since the beginning of the COVID-19 pandemic, a comparison of the original SARS-CoV-2 genome with a few of the variants of concern identified numerous variations in regions that are at or within 3 amino acids of identified antibody binding epitopes.

According to the authors, “Our extensive profiling of epitope-level resolution antibody reactivity in COVID-19 convalescent subjects, confirmed by independent assays, provides new epitopes that could serve as important targets in the development of improved diagnostics, vaccines, and therapeutics against SARS-CoV-2, variants of concern, and dangerous human coronaviruses that may emerge in the future”.

###

Research Article

Peer reviewed; Experimental study; Cells

In your coverage please use these URLs to provide access to the freely available articles in PLOS Biologyhttp://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001265

Funding: I.M.O. acknowledges support by the Clinical and Translational Science Award (CTSA) program (ncats.nih.gov/ctsa), through the National Institutes of Health National Center for Advancing Translational Sciences (NCATS), grants UL1TR002373 and KL2TR002374. This research was also supported by 2U19AI104317-06 (to I.M.O via James Gern) and R24OD017850 (to D.H.O.) from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (http://www.niaid.nih.gov). A.S.H. has been supported by the National Institutes of Health National Research Service Award T32 AI007414 and M.F.A. by T32 AG000213 (http://www.nlm.nih.gov/ep/NRSAFellowshipGrants.html). S.J.M. acknowledges support by the National Cancer Institute, National Institutes of Health and University of Wisconsin Carbone Comprehensive Cancer Center’s Cancer Informatics Shared Resource (grant P30-CA-14520; cancer.wisc.edu/research/) and by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health 2U19AI104317-06. This project was also funded through a COVID-19 Response Grant from the Wisconsin Partnership Program and the University of Wisconsin School of Medicine and Public Health (to M.A.S.; http://www.med.wisc.edu/wisconsin-partnership-program/), startup funds through the University of Wisconsin Department of Obstetrics and Gynecology (I.M.O.; http://www.obgyn.wisc.edu/), and the Data Science Initiative (research.wisc.edu/funding/data-science-initiative/) grant from the University of Wisconsin-Madison Office of the Chancellor and the Vice Chancellor for Research and Graduate Education (with funding from the Wisconsin Alumni Research Foundation) (I.M.O.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: The authors declare the following competing interests: A.S.H., S.J.M., D.A.B., M.F.A., S.K., M.A.S., D.H.O., and I.M.O are listed as the inventors on a patent filed that is related to findings in this study. Application: 63/080568, 63/083671. Title: IDENTIFICATION OF SARS-COV-2 EPITOPES DISCRIMINATING COVID-19 INFECTION FROM CONTROL AND METHODS OF USE. Application type: Provisional. Status: Filed. Country: United States. Filing date: September 18, 2020, September 25, 2020.


Reference: Heffron AS, McIlwain SJ, Amjadi MF, Baker DA, Khullar S, Armbrust T, et al. (2021) The landscape of antibody binding in SARS-CoV-2 infection. PLoS Biol 19(6): e3001265. https://doi.org/10.1371/journal.pbio.3001265


Provided by PLOS

Scientists Develop Novel Therapy for Crimean-congo Hemorrhagic Fever Virus (Medicine)

Army scientists working as part of an international consortium have developed and tested an antibody-based therapy to treat Crimean-Congo hemorrhagic fever virus (CCHFV), which is carried by ticks and kills up to 60 percent of those infected. Their results are published online today in the journal Cell.

Using blood samples donated by disease survivors, the study’s authors characterized the human immune response to natural CCHFV infection. They were able to identify several potent neutralizing antibodies that target the viral glycoprotein–a component of the virus that plays a key role in disease development. Several of these antibodies, administered individually or in combination, protected mice from CCHFV when given prior to virus exposure.

To treat mice that had already been infected, the team created “bispecific” antibodies that combined potency with the ability to bind to two separate sites on the CCHFV glycoprotein. One of these bispecific antibodies, called DVD-121-801, overcame CCHFV infection in mice with just a single dose administered 24 hours after challenge with live virus.

Efforts are underway to develop DVD-121-801 as a potential therapeutic for human patients, according to co-first author Andrew H. Herbert, Ph.D., of the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID).

CCHFV is the most prevalent tick-borne virus that causes human disease, and is endemic in countries across Europe, Asia, and Africa. Despite its high lethality and widespread distribution, no vaccines or specific treatments are available. It has been designated a priority pathogen by the World Health Organization.

“Rodent models of CCHFV infection are useful in testing and down-selecting neutralizing antibodies,” commented Herbert. “However, to advance a lead candidate for therapeutic use, it will be necessary to conduct studies in larger animal models that more faithfully recapitulate human disease.”

In addition to USAMRIID, other institutions participating in the study were Adimab, LLC; Albert Einstein College of Medicine, Bronx, New York; Mapp Biopharmaceutical, Inc.; the University of Texas Medical Branch at Galveston; the University of Texas at Austin; Institut Pasteur in Paris, France; Ben-Gurion University of the Negev in Beer-Sheva, Israel; and Uganda Virus Research Institute in Entebbe, Uganda.

Funding: This work was supported in part by a National Institutes of Health grant to the Prometheus Center for Excellence in Translational Research, a consortium of academic, industry, and government partners working to develop antibody-based therapies against CCHFV and other highly lethal viruses. A complete list of funding organizations appears in the publication.


Reference: Fels, J.M.; Maurer, D.; Kuehne, A.I.; Abelson, D.M.; Pauli, N.T.; Herbert, A.S.; Dye, J.M.; Cross, R.W.; Geisbert, T.W.; Lobel, L.; Bornholdt, Z.A.; Walker, L.M.; Chandran, K. Neutralizing Antibodies against Crimean–Congo Hemorrhagic Fever Virus Derived from a Human Survivor. 2021. DOI: https://doi.org/10.1016/j.cell.2021.05.001


Provided by US Army

Why B.1.617 Variant Of SARS-CoV-2 Is Highly Transmissible Than Others? (Biology)

There are many variants of SARS-CoV-2, the virus which causes COVID-19, but why is B.1.617 variant of SARS-CoV-2 virus is highly transmissible among all others? Recent study done by Wendy Barclay and colleagues now answered this question. They provided experimental evidence that virus of the B.1.617 variant has enhanced spike (S) cleavage and this cleavage is enhanced by P681R monobasic mutant or by an enzyme furin. Their study recently appeared in bioRxiv.

Unlike SARS-CoV, the SARS-CoV-2 spike (S) protein contains a furin cleavage site at S1/S2 junction (as shown in figure above) that enhances SARS-CoV-2 replication in airway cells and contributes to virus pathogenicity and transmissibility. The Lineage B.1.617, also known as G/452R.V3, is one of the known variants of SARS-CoV-2, the virus that causes COVID-19. It was first identified in Maharashtra, India on 5 October 2020. As of May 2021, three sublineages/subvariants have been found. Despite its name, B.1.617.3 was the first sublineage of this variant to be detected, in October 2020 in India. This sublineage has remained relatively uncommon compared to the two other sublineages, B.1.617.1 and B.1.617.2, both of which were first detected in December 2020.

Now, Barclay and colleagues investigated whether the spike (S) protein of B.1.617 undergoes a higher degree of post translational cleavage at S1/S2 than previously circulating strains. In order to know, they isolated several B.1.617 lineage viruses (1 x B.1.617.1 and 2 x B.1.617.2) and compared their S1/S2 cleavage to that of a previously circulating strain of lineage B.1.238, which contains only D614G. They found that, B.1.617 lineage S proteins were all more highly cleaved (≥50% cleaved), with a higher proportion of cleaved S2 and a lower proportion of full-length S detectable than the control virus (~33% cleaved) (Figure 1 below).

Figure 1 – P681R results in enhanced furin cleavage of the SARS-CoV-2 B.1.617 spike protein: (left panel) Western blot analysis of spike cleavage of concentrated B.1.238 (D614G) and B.1.617 (P681R containing) SARS-CoV-2 isolates. Levels of nucleocapsid (N) protein shown as loading control. Right panel: Densitometry analysis of the western blot from part (b). Densitometry measured using J. Points indicate two technical repeats from the same concentrated virus stocks. © Barclay et al.

They also characterised which amino change in the B.1.617 S is responsible for its enhanced cleavage and suggested that P681R alone is responsible for the enhanced S cleavage seen in the B.1.617 lineages viruses.

They then performed assays to determine whether the optimised cleavage site found in the B.1.617 S enables better cleavage directly by furin (an enzyme that in humans is encoded by the FURIN gene). They showed that, P681R significantly enhanced the ability of furin to cleave the peptide confirming that the arginine substitution is responsible for the enhanced cleavage of the B.1.617 spike protein.

“The virus of the B.1.617 lineage has enhanced S cleavage, that enhanced processing of an expressed B.1.617 spike protein in cells is due to P681R, and that this mutation enables more efficient cleavage of a peptide mimetic of the B.1.617 S1/S2 cleavage site by recombinant furin.  Together, these data demonstrate viruses in this emerging lineage have enhanced S cleavage by furin which we hypothesise could be enhancing transmissibility and pathogenicity.”

Finally, they concluded that, enhanced S1/S2 cleavage seen in B.1.617 and B. 1.1.7, may be contributing to the enhanced transmissibility of these SARS-CoV-2 variants. As well as B.1.1.7 and B.1.617, several other emerging variants contain mutations in the furin cleavage site. They advise that these lineages be kept under close monitoring for any early evidence of more rapid transmission or higher pathogenesis.


Reference: Thomas P. Peacock, Carol M. Sheppard, Jonathan C. Brown, Niluka Goonawardane, Jie Zhou, Max Whiteley, PHE Virology Consortium, Thushan I. de Silva, Wendy S. Barclay, “The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin”, bioRxiv 2021.05.28.446163; doi: https://doi.org/10.1101/2021.05.28.446163


Note for editors of other websites: To reuse this article fully or partially kindly give credit either to our author/editor S. Aman or provide a link of our article

Adding Antibodies to Enhance Photodynamic Therapy For Viral and Bacterial Disease (Medicine)

Advancing PDT as a rapid response to pandemics

The COVID-19 pandemic has reinforced the pressing need to mitigate a fast-developing virus as well as antibiotic-resistant bacteria that are growing at alarming rates worldwide.

Photodynamic therapy (PDT), or using light to inactivate viruses, bacteria, and other microbes, has garnered promising results in recent decades for treating respiratory tract infections, such as pneumonia, and some types of cancer.

In Applied Physics Reviews, by AIP Publishing, researchers at Texas A&M University and the University of São Paulo in Brazil review the existing approaches and propose adding antibodies to enhance PDT efficacy. They provide a model to help expedite overall PDT development as a rapid response to emergent viral pandemic threats. The research is based on physical principles to target a wide range of diseases.

“The COVID-19 pandemic calls for extraordinary measures to address current gaps in the therapeutic treatment of infectious diseases, in general, and viral agents, in particular,” author Vladislav Yakovlev said. “We show how photodynamic therapy can be capable of providing an inexpensive alternative strategy in the fight against viral and bacterial infections.”

In PDT, photosensitizers (dyes and other light-reacting compounds) are typically administered intravenously or applied on the skin where treatment is needed. Microbes or cancer cells absorb the photosensitizers. The compounds react to light from a laser to form reactive oxygen species, toxic oxygen molecules that kill the cancer cells or pathogen.

One of the most promising PDT methods highlighted by the researchers is antibody PDT, or aPDT. The method involves attaching photosensitizers to viral antibodies to increase the immune response. The antibody is modified by attaching a small light-absorbing molecule, which upon illumination, can transfer the photon energy to the targeted virus particles, resulting in their destruction while reducing harm to host cells and healthy tissue.

“The aPDT process is characterized by high selectivity, rapid microbial killing, minimal invasiveness, and low occurrence of side effects,” Yakovlev said. “It also ideal for repetitive application without the concern of bacterial resistance.”

The researchers developed a mathematical model to compare PDT to other antiviral treatment by focusing on three parameters critical in modifying the treatment response to determine efficacy: photosensitizer, light, and oxygen.

Molecular oxygen is considered intrinsic to the biological system since it is present at the site of infection. On the other hand, the light dose and the photosensitizer concentration are flexible parameters to achieve efficient results in treatment.

Research protocols, therefore, should consider not only the photosensitizing molecule appropriate to the biological target and adequate wavelength but also the photosensitizer concentration, incubation time, and light dose.

The article “Photodynamic viral inactivation: Recent advances and potential applications” is authored by Jace A. Willis, Vsevolod Cheburkanov, Giulia Kassab, Jennifer M. Soares, Kate C. Blanco, Vanderlei X. Bagnato, and Vladislav V. Yakovlev. The article will appear in Applied Physics Reviews on May 18, 2021 (DOI: 10.1063/5.0044713). After that date, it can be accessed at https://aip.scitation.org/doi/10.1063/5.0044713.

Featured image: Schematic illustration of photodynamic inactivation of various viruses. © Vladislav Yakovlev/Texas A&M University


Provided by American Institute of Physics

Box Fan Air Cleaner Greatly Reduces Virus Transmission (Engineering)

Decades-old public classrooms with inadequate ventilation can be made safer with the use of a cardboard frame, air filter, and a low-cost box fan

Improved ventilation can lower the risk of transmission of the COVID-19 virus, but large numbers of decades-old public school classrooms lack adequate ventilation systems. A systematic modeling study of simple air cleaners using a box fan reported in Physics of Fluids, by AIP Publishing, shows these inexpensive units can greatly decrease the amount of airborne virus in these spaces, if used appropriately.

A low-cost air cleaner can be easily constructed from a cardboard frame topped by an air filter and a box fan. The air filter is placed between the fan and the cardboard base. The fan is oriented so that air is drawn in from the top and forced through the filter, discharging cleaned air downward.

The investigators measured the clean air delivery rate of the air cleaning system in experiments conducted at two independent laboratories. Tobacco smoke was used to simulate the airborne virus, since the virus is known to travel through the air after exhalation in droplets about the same size as smoke particulates.

The experimental measurements were incorporated into a detailed computational model of a classroom. In addition to the box fan air cleaner, a ventilation unit known as an HUV, or a horizontal unit ventilator, was included in the simulation. This type of ventilation system is very common in public schools and is usually placed along an outside wall, drawing in air near the floor and exhausting it at the top to circulate fresh air around a classroom.

A cloud of virus particles was assumed to enter the simulation from an infected individual. The investigators assumed this individual was the instructor and experimented with different placements of the box fan air cleaner.

“Placing the air cleaner near the potential infector is the most effective way to reduce the aerosol spread,” said author Jiarong Hong.

The simulations showed the best results were obtained by shifting both the box fan air cleaner and the infected instructor to a location near the HUV.

“At this location, owing to its proximity to both the infector and the HUV, the air cleaner extracts the majority of aerosols, leaving only a small percentage suspended in the air,” Hong said.

Although placing the air cleaner near an infected individual is best, it is not always possible to know who is infected. In this situation, the investigators recommend placing the air cleaner near the HUV, with the air cleaner outflow pointing toward the inlet of the HUV.

“In addition, we find that in large classrooms, distributing multiple air cleaners in the space is more effective in controlling aerosol spread than simply enhancing the flow rate of the HUV or air cleaners alone,” Hong said.

The article “Airborne transmission of COVID-19 and mitigation using box fan air cleaners in a poorly ventilated classroom” is authored by Ruichen He, Wanjiao Liu, John Elson, Rainer Vogt, Clay Maranville, and Jiarong Hong. The article will appear in Physics of Fluids on May 11, 2021 (DOI: 10.1063/5.0050058). After that date, it can be accessed at https://aip.scitation.org/doi/10.1063/5.0050058.

Featured image: Low-cost portable air cleaner for reducing virus spread in public school classrooms. © Ruichen He, Jiarong Hong


Provided by American Institute of Physics

Researchers Have Identified A Novel Autoantigen in Narcolepsy, A Mimic of a Protein From Swine Flu Virus (Medicine)

Researchers at the University of Helsinki have identified influenza virus peptides that resemble human protein fragments and can cause an immune response against the body’s own cells due to cross-reactivity. The recently completed study confirms the notion that influenza A (H1N1) virus peptides can trigger an autoimmune reaction in genetically predisposed individuals, that results in the onset of narcolepsy with cataplexy.

Narcolepsy with cataplexy, or narcolepsy type 1 (NT1), is a rare and chronic neurological disease whose prevalence increased in children and adolescents after the administration of Pandemrix swine flu vaccine in 2009–2010. It is an autoimmune disease to which a specific inherited tissue type (HLA-DQB1*0602) predisposes people.

The disease mechanism of NT1 was investigated in a collaborative study carried out by PhD student Arja Vuorela and university researcher Dr. Tobias Freitag, working in the research groups of Prof. Outi Vaarala and Prof. Seppo Meri. The study analyzed the cell-mediated immune response targeting three different proteins of influenza A (H1N1) virus included in the Pandemrix vaccine, in Finnish children and adolescents who developed narcolepsy after Pandemrix vaccination.

The study was published in the journal Nature Communications.

Im­mune cells are ac­tiv­ated by the body’s own pro­teins in nar­co­lepsy pa­tients

The researchers found that immune cells in the blood of narcolepsy patients mounted stronger responses against two peptides originating from swine flu virus neuraminidase or nucleoprotein, compared to the cells of vaccinated control subjects.

By investigating similarities between the two identified viral peptides and human proteins, the researchers identified similar sequences in two self proteins present in the human brain. This led them to study immune responses in narcolepsy patients also to these self proteins.

What they found demonstrated that patient lymphocytes recognised a fragment derived from the human protein-O-mannosyl-transferase 1 enzyme (POMT1). This POMT1 peptide mimics the peptide from influenza A (H1N1) neuraminidase, that is a target of the immune response generated by Pandemrix vaccine.

“Interestingly, immune cells in patient blood produced the same mediators of inflammation as a response to the peptides of both viral neuraminidase or human POMT1 enzymes. Both peptides also brought about the development and selection of identical or similar T lymphocyte clones,” says University Researcher Tobias Freitag.

On­set of autoim­mune dis­eases likely ex­plained by cross-re­act­iv­ity

Prior research has uncovered that “molecular mimicry”, the similarity between proteins produced by pathogens or expressed in human tissues, may trigger the development of autoimmune diseases in people genetically at risk.

According to the latest study, lymphocytes which recognise the virus cross-react with human brain tissue and, consequently, contribute to the development of NT1. Autoantibodies recognizing the human POMT1 enzyme were also found at higher levels in individuals vaccinated with Pandemrix.

“The results indicate that the Pandemrix vaccine triggered an autoimmune response in genetically predisposed people. All of the individuals who developed narcolepsy had the same HLA-DQB1*0602 tissue type, which predisposes people to the disease. Most likely, the effective adjuvant included in the vaccine also contributed to the autoimmune response,” says Professor of Immunology Seppo Meri from the University of Helsinki. NT1 is a multifactorial disease.

The findings can boost further research aimed at the improvement of diagnostics and treatments for NT1, including therapeutic strategies modifying or redirecting the immune system.

“The findings of this study serve as a reminder that no medical procedure, including vaccination, is entirely without risk. As with all clinical decision making, vaccination recommendations need to consider both benefits and possible adverse effects. When new vaccines are introduced, especially those based on novel adjuvants or vaccine technologies, recommendations need to be tailored to different age and risk groups” Freitag points out.

The study was carried out by the NARPANord research consortium headed by Professor Markku Partinen from the University of Helsinki and funded by the Academy of Finland, the Ministry of Social Affairs and Health, and the Sigrid Jusélius Foundation.

Featured image credit: mostphotos


Original article: A. Vuorela, T.L. Freitag, K. Leskinen, H. Pessa, T. Härkönen, I. Stracenski, T. Kirjavainen, P. Olsen, O. Saarenpää-Heikkilä, J. Ilonen, M. Knip, A. Vaheri, M. Partinen, P. Saavalainen, S. Meri, O. Vaarala: Lymphocytes specific for influenza A (H1N1) neuraminidase may cross-react with human brain protein-O-mannosyl transferase 1, to cause the immune-mediated disorder narcolepsy type 1. Nature Communications. DOI: 10.1038/s41467-021-22637-8


Provided by University of Helsinki