Tag Archives: Antigen

Microbiology

First-in-human nanoparticle HIV vaccine induces broad and publicly targeted helper T cell responses

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Reviewed by Lily Ramsey, LLMMay 25 2023

Researchers from Fred Hutchinson Cancer Center in Seattle, Scripps Research in La Jolla, California, IAVI and other collaborating institutions have characterized robust T-cell responses in volunteers participating in the IAVI G001 Phase 1 clinical trial to test the safety and immune response of a self-assembling nanoparticle HIV vaccine.

Their work, published in Science Translational Medicine, signals a major step toward development of a vaccine approach to end the HIV/AIDS epidemic worldwide. The antigen used in this study was jointly developed by IAVI and Scripps Research and has been shown in previous analyses to stimulate VRC01-class B cells, an immune response considered promising enough for boosting in further studies.

We were quite impressed that this vaccine candidate produced such a vigorous T-cell response in almost all trial participants who received the vaccine. These results highlight the potential of this HIV-1 nanoparticle vaccine approach to induce the critical T-cell help needed for maturing antibodies toward the pathway of broadly neutralizing against HIV.”

Julie McElrath, MD, PhD, senior vice president and director of Fred Hutch’s Vaccine and Infectious Disease Division and co-senior author of the study

However, she added, this is the first step, and heterologous booster vaccines will still be needed to eventually produce VRC01-class broadly neutralizing antibodies, which in previous studies have demonstrated the ability to neutralize approximately 90% of HIV strains.

“We showed previously that this vaccine induced the desired B-cell responses from HIV broadly neutralizing antibody precursors. Here we demonstrated strong CD4 T-cell responses, and we went beyond what is normally done by drilling down to identify the T cell epitopes and found several broadly immunogenic epitopes that might be useful for developing boosters and for other vaccines,” William Schief, PhD, executive director of vaccine design for IAVI’s Neutralizing Antibody Center at Scripps Research and professor, Department of Immunology and Microbiology, at Scripps Research, who is co-senior author of the study.

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The trial is a phase 1, randomized, double-blind and placebo-controlled study to evaluate the safety and effectiveness of a nanoparticle HIV vaccine in healthy adult volunteers without HIV. It was comprised of two groups with 18 vaccine and six placebo recipients per group, with 48 total enrollees. Participants were given two doses of the vaccine or placebo eight weeks apart.

McElrath acknowledged the groundbreaking work of her lab team, the biostatistical team and Fred Hutch’s Vaccine Trials Unit for their invaluable contributions to the study. The Vaccine Trials Unit conducts multiple vaccine trials and was one of only two sites for this study.

Findings from the study include:

  • Vaccine-specific CD4 T cells were induced in almost all vaccine recipients.
  • Lymph node GC T follicular helper cells increased after vaccination compared to placebo.
  • Lumazine synthase protein, needed for self-assembly of the particle, also induced T-cell responses that can provide additional help to ultimately enhance efficacy in a sequential vaccine strategy.
  • Vaccine-specific CD4 T cells were polyfunctional and had diverse phenotypes.
  • LumSyn-specific CD8 T cells were highly polyfunctional and had a predominantly effector memory phenotype.
  • CD4 T-cell responses were driven by immunodominant epitopes with diverse and promiscuous HLA restriction.
  • CD8 T-cell responses to LumSyn were driven by HLA-A*02-restricted immunodominant epitopes B- and T-cell responses correlated within but not between LN and peripheral blood compartments.

This study was funded by the Bill & Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery; IAVI Neutralizing Antibody Center; National Institute of Allergy and Infectious Diseases; and Ragon Institute of MGH, MIT and Harvard.

Study authors WRS and SM are inventors on a patent filed by Scripps and IAVI on the eOD-GT8 monomer and 60-mer immunogens (patent number 11248027, “Engineered outer domain (eOD) of HIV gp 120 and mutants thereof”). WRS, KWC and MJM are inventors on patents filed by Scripps, IAVI and Fred Hutch on immunodominant peptides from LumSyn (Title: Immunogenic compositions; filing no. 63127975).

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Source:

Fred Hutchinson Cancer Center

Journal reference:

Cohen, K. W., et al. (2023) A first-in-human germline-targeting HIV nanoparticle vaccine induced broad and publicly targeted helper T cell responses. Science Translational Medicine. doi.org/10.1126/scitranslmed.adf3309.

Microbiology

Mouse study offers clues to developing an effective vaccine for Klebsiella bacteria

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Reviewed by Danielle Ellis, B.Sc.May 18 2023

A mouse study at Washington University School of Medicine in St. Louis points to data that could be key to developing an effective vaccine for the bacterium Klebsiella pneumoniae. The bug is often resistant to antibiotics, making it difficult to treat in some.

In the U.S., the bacterium Klebsiella pneumoniae is a common cause of urinary tract infection, bloodstream infection and pneumonia. While infections with the bacterium can be easily treated in some, Klebsiella has a dangerous flip side: It also is frequently resistant to antibiotics, making it extraordinarily difficult to treat in others. About half of people infected with a hypervirulent, drug-resistant strain of the bacterium die.

Scientists are working on vaccines for Klebsiella, but the optimal vaccine design is still unknown. However, a new study in mice by scientists at Washington University School of Medicine in St. Louis and Omniose, a St. Louis startup company specializing in vaccine production, provides critical data that could be key to developing an effective vaccine for Klebsiella. The findings, published in PLoS Pathogens, are a step toward taming the superbug.

When you think about the bugs that can be resistant to almost all antibiotics — the scary superbugs in the news — a lot of them are strains of Klebsiella. For a long time, the bacterium wasn’t even a pressing issue. But now it is, due to an explosion in antibiotic-resistant Klebsiella. Our goal is to diminish Klebsiella’s superbug status by developing a vaccine before hypervirulent or resistant strains sicken and kill even more people.”

David A. Rosen, MD, PhD, study’s senior author, assistant professor of pediatrics and of molecular microbiology at Washington University

Hypervirulent Klebsiella strains have spread globally, often causing community-acquired infections.

In the U.S., Klebsiella infections primarily occur in health-care facilities where medically vulnerable patients are immunocompromised, require long courses of antibiotics to treat other conditions, have chronic diseases, or are elderly people or newborns. “But now we’re seeing the emergence of hypervirulent strains dangerous enough to cause serious disease or death among healthy people in the community,” Rosen said.

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Most concerning among scientists are the strains of Klebsiella impervious to carbapenems, a class of broad-spectrum antibiotics used to treat the most severe bacterial infections. For this reason, the World Health Organization and the U.S. Centers for Disease Control and Prevention have identified carbapenem-resistant Klebsiella as an urgent threat to public health.

The rod-shaped bacterium is immobile and, like chocolate-covered candies, encapsulated in sugar coatings. In the new study, researchers created two experimental vaccines based on two different sugars, or polysaccharides, on Klebsiella’s surface: the terminal sugars on lipopolysaccharide, called O-antigen, and a capsular polysaccharide, or K-antigen. Since sugars by themselves tend to produce weak immune responses, the researchers linked each of the sugars to a protein to boost the immune response, creating so-called conjugate vaccines. Sugar-protein conjugate vaccines have proven successful in combating several bacteria including Streptococcus pneumoniae, the most common cause of pneumonia. Historically, this connection between the sugar and protein carrier has been achieved using synthetic chemistry in a test tube; however, the vaccines created for this study are called bioconjugate vaccines, because the researchers connected the sugar to the protein all within an engineered bacteria system.

Once the vaccines were created, the researchers tested the experimental bioconjugate vaccines’ ability to protect mice from disease caused by Klebsiella.

“It turned out that the capsule vaccine was far superior to the O-antigen vaccine,” said the study’s first author, Paeton Wantuch, PhD, a postdoctoral associate in Rosen’s lab. “Mice that received the capsule vaccine were significantly more likely to survive Klebsiella infection in their lungs or their bloodstream than mice that received the O-antigen vaccine.”

Both vaccines elicited high levels of antibodies against their respective targets. But the antibodies against the O-antigen just weren’t as effective as the ones against the capsule. In some strains of Klebsiella, the O-antigen may be obscured by other sugars, so the antibodies that target the O-antigen cannot make contact with their target.

“Our findings suggest that we may also need to include the capsule-based antigens in vaccine formulations developed against Klebsiella,” Rosen said. “This is why it’s so important for us to continue studying antibody-antigen interactions in the different strains, with the goal of identifying the ideal vaccine composition for clinical trials soon. The need has never been more imperative, especially as Klebsiella’s drug-resistant, hypervirulent strains become stronger, bolder and more dangerous to human health.”

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Source:

Washington University School of Medicine

Journal reference:

Wantuch, P. L., et al. (2023) Area-deprivation, social care spending and the rates of children in care proceedings in local authorities in Engl Capsular polysaccharide inhibits vaccine-induced O-antigen antibody binding and function across both classical and hypervirulent K2:O1 strains of Klebsiella pneumoniae. PLOS Pathogens. doi.org/10.1371/journal.ppat.1011367.

Microbiology

Novel computational platform can expand the pool of cancer immunotherapy targets

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Reviewed by Megan Craig, M.Sc.May 17 2023

Researchers at Children’s Hospital of Philadelphia (CHOP) and the University of California, Los Angeles (UCLA) have developed a computational platform capable of discovering tumor antigens derived from alternative RNA splicing, expanding the pool of cancer immunotherapy targets. The tool, called “Isoform peptides from RNA splicing for Immunotherapy target Screening” (IRIS), was described in a paper published today in the Proceedings of the National Academy of Sciences.

Immunotherapy has revolutionized cancer treatment, but for many cancers including pediatric cancers, the repertoire of antigens is incomplete, underscoring a need to expand the inventory of actionable immunotherapy targets. We know that aberrant alternative RNA splicing is widespread in cancer and generates a range of potential immunotherapy targets. In our study, we were able to show that our computational platform was able to identify immunotherapy targets that arise from alternative splicing, introducing a broadly applicable framework for discovering novel cancer immunotherapy targets that arise from this process.”

Yi Xing, PhD, co-senior author, director of the Center for Computational and Genomic Medicine at CHOP

Cancer immunotherapy has ushered in a sea change in the treatment of many hematologic cancers, harnessing the power of a patient’s own immune system to fight the disease. Chimeric antigen receptor T-cell (CAR-T) and T cell receptor-engineered T cell (TCR-T) therapies modify a patient’s own T cells to attack known antigens on the surface of cancer cells and have often led to durable responses for cancers that were once considered incurable. However, the field has encountered challenges in the solid tumor space, in large part due to a lack of known and suitable targets for these cancers, highlighting the need for novel approaches to expand the pool of immunotherapy targets.

Alternative splicing is an essential process that allows for one gene to code for many gene products, based on where the RNA is cut and joined, or spliced, before being translated into proteins. However, the splicing process is dysregulated in cancer cells, which often take advantage of this process to produce proteins that promote growth and survival, allowing them to replicate uncontrollably and metastasize. This happens in many adult and pediatric cancers. Scientists have suggested splicing dysregulation could be a source of novel tumor antigens for immunotherapy, but identifying such antigens has been a challenge.

To address this difficulty, the researchers created IRIS to leverage large-scale tumor and normal RNA sequencing data and incorporate multiple screening approaches to discover tumor antigens that arise due to alternative splicing. Integrating RNA sequencing-based transcriptomics data and mass spectrometry-based proteomics data, the researchers showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules, the part of the human immune system that presents antigens to T cells.

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The researchers then applied IRIS to RNA sequencing data from neuroendocrine prostate cancer (NEPC), a metastatic and highly lethal disease known to involve shifts in RNA splicing, as discovered in a prior study by CHOP and UCLA researchers. From 2,939 alternative splicing events enriched in NEPC, IRIS predicted 1,651 peptides as potential TCR targets. The researchers then applied a more stringent screening test, which prioritized 48 potential targets. Interestingly, the researchers found that these targets were highly enriched for peptides encoded by short sequences of less than 30 nucleotides in length – also known as “microexons” – which may arise from a unique program of splicing dysregulation in this type of cancer.

To validate the immunogenicity of these targets, the researchers isolated T cells reactive to IRIS-predicted targets, and then used single-cell sequencing to identify the TCR sequences. The researchers modified human peripheral blood mononuclear cells with seven TCRs and found they were highly reactive against targets predicted by IRIS to be good immunotherapy candidates. One TCR was particularly efficient at killing tumor cells expressing the target peptide of interest.

“Immunotherapy is a powerful tool that has had a significant impact on the treatment of some cancers, but the benefits have not been fully realized in many lethal cancers that could benefit from this approach,” said Owen N. Witte, MD, University Professor of Microbiology, Immunology, and Molecular Genetics and member of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA. “The discovery of new antigenic targets that may be shared among different patients – and even different tumor types – could be instrumental in expanding the value of cell-based therapies. Analyzing massive amounts of data on tumor and normal tissues, which requires sophisticated computational tools like those developed by the Xing Lab, provides actionable insights on targets that one day could be tested in the clinic.”

“This proof-of-concept study demonstrates that alternatively spliced RNA transcripts are viable targets for cancer immunotherapy and provides a big data and multiomics-powered computational platform for finding these targets,” Dr. Xing added. “We are applying IRIS for target discovery across a wide range of pediatric and adult cancers. We are also developing a next-generation IRIS platform that harnesses newer transcriptomics technologies, such as long read and single cell analysis.”

This research was supported in part by the Immuno-Oncology Translational Network (IOTN) of the National Cancer Institute’s Cancer Moonshot Initiative, other National Institutes of Health funding, the Parker Institute for Cancer Immunotherapy, the Cancer Research Institute, and the Ressler Family Fund.

Source:

Children’s Hospital of Philadelphia

Journal reference:

Pan, Y., et al. (2023) IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. PNAS. doi.org/10.1073/pnas.2221116120.

Microbiology

Novel antibodies target human receptors to neutralize SARS-CoV-2 variants and future sarbecoviruses

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Neha MathurBy Neha MathurMay 17 2023Reviewed by Lily Ramsey, LLM

In a recent study published in the Nature Microbiology Journal, researchers generated six human monoclonal antibodies (mAbs) that prevented infection by all human angiotensin-converting enzyme 2 (ACE2) binding sarbecoviruses tested, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, Delta and Omicron.

They targeted the hACE2 epitope that binds to the SARS-CoV-2 spike (S) glycoprotein rather than targeting the S protein, which all previous therapeutic mAbs for SARS-CoV-2 targeted.

Study: Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Image Credit: paulista/Shutterstock.comStudy: Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Image Credit: paulista/Shutterstock.com

Background

The emergence of new variants of SARS-CoV-2, especially Omicron sublineages, made all therapeutic mAbs targeting SARS-CoV-2 S obsolete.

Any new S-targeting mAb therapy will also probably have limited utility because SARS-CoV-2 will continue to adapt to human antibodies. Ideally, mAbs developed in anticipation of future pandemics caused by sarbecoviruses should be resilient to mutations that arise in them.

About the study

In the present study, researchers developed hACE2-binding mAbs that blocked infection by pseudotypes of all tested sarbecoviruses at potencies matching SARS-CoV-2 S targeting therapeutic mAbs. The binding affinity of these mAbs to hACE2 was in the nanomolar to picomolar range.

To develop these mAbs, researchers used the KP and Av AlivaMab mouse strains that generate a human Kappa (κ) light chain and Kappa (κ) and Lambda (λ) light chains carrying antibodies, respectively.

They immunized these mice with monomeric and dimeric recombinant hACE2 extracellular domains. Fusion to the fraction, crystallizable (Fc) portion of human immunoglobulin G1 (IgG1) rendered them dimeric.

Further, the team generated hybridomas from mice using sera that inhibited SARS-CoV-2 pseudotyped viruses. They used enzyme-linked immunosorbent assay (ELISA) to screen hybridoma supernatants for hACE2-binding mAbs.

Furthermore, the researchers tested the ability of the six most potent mAbs to inhibit Wuhan-hu-1 S pseudotyped infection in Huh-7.5 target cells.

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The team purified chimeric mAbs from the hybridoma culture supernatants and used a SARS-CoV-2 pseudotype assay to reconfirm their antiviral activity. They also sequenced the human Fab variable regions, VH and VL.

The team cloned VH and VL domains from the six most potent chimeric human-mouse mAbs into a human IgG1 expression vector to generate fully human anti-hACE2 mAbs.

They used single-particle cryo-electron microscopy (cryo-EM) to delineate the structural basis for broad neutralization of anti-hACE2 mAbs.

Specifically, they determined the structure of soluble hACE2 bound to the antigen-binding fragment (Fab) of 05B04, one of the most potent mAbs unaffected by naturally occurring human ACE2 variations.

Finally, the researchers tested these hACE2 mAbs in an animal model and determined their pharmacokinetic behavior.

Results

The researchers identified 82 hybridomas expressing hACE2-binding mAbs, of which they selected ten based on their potency in inhibiting pseudotyped virus infection of Huh-7.5 cells.

These ten mAbs were 1C9H1, 4A12A4, 05B04, 2C12H3, 2F6A6, 2G7A1, 05D06, 05E10, 05G01 and 05H02. Four of the five mAbs from the KP AlivaMab mice, viz., 05B04, 05E10, 05G01, and 05D06, shared identical complementarity-determining regions (CDRs). Conversely, AV AlivaMab mice-derived mAbs were diverse.

While allosteric inhibition of hACE2 activity by the mAbs was theoretically feasible, such inhibition did not occur.

Also, the anti-hACE2 mAbs did not affect hACE2 internalization or recycling, suggesting that the anti-hACE2 mAbs would unlikely undergo accelerated target-dependent clearance from the circulation during in vivo use.

These two findings confirmed that these mAbs would not have harmful side effects based on their target specificity.

In addition, the anti-hACE2 mAbs showed favorable pharmacokinetics and no ill effects on the hACE2 knock-in mice. When used prophylactically in hACE2 knock-in mice, these mAbs conferred near-sterilizing protection against lung SARS-CoV-2 infection.

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Moreover, they presented a high genetic barrier to the acquisition of resistance by SARS-CoV-2.

The six anti-hACE2 mAbs also inhibited infection by pseudotyped SARS-CoV-2 variants, Delta, and Omicron, with similar potency, i.e., half maximal inhibitory concentration (IC50) values ranging between 8.2 ng ml−1 and 197 ng ml−1.

A cryo-EM structure of the 05B04-hACE2 complex at 3.3 Å resolution revealed a 05B04 Fab bound to the N-terminal helices of hACE2.

05B04-mediated inhibition of ACE2-binding sarbecoviruses through molecular mimicry of SARS-CoV-2 receptor-binding domain (RBD) interactions, providing high binding affinity to hACE2 despite the smaller binding footprint on hACE2.

None of the four most potent mAbs affected hACE2 enzymatic activity or induced the internalization of hACE2 localized on the host cell surface. Thus, based on their target specificity, these mAbs shall not have deleterious side effects.

Though these anti-ACE2 antibodies could effectively inhibit sarbecovirus infection in humans, the fact that the antibodies target a host receptor molecule rather than the SARS-CoV-2 S protein will necessitate their testing in terms of safety, efficacy, and pharmacological behavior in primate models before human clinical trials.

Conclusions

SARS-CoV-2 might evolve and start using receptors other than ACE2, creating another genetic hurdle to overcome for researchers working on the development of SARS-CoV-2 therapeutics.

However, the human anti-hACE2 mAbs engineered in this study showed exceptional breadth and potency in inhibiting infection by hACE2-utilizing sarbecoviruses.

Thus, they represent a long-term, ‘resistance-proof’ prophylaxis and treatment for SARS-CoV-2, even for future outbreaks of SARS-like coronaviruses.

In addition, these mAbs might prove particularly useful for susceptible patients like those with immunodeficiency and in which vaccine-induced protective immunity is unattainable or difficult to attain.

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Journal reference:
Microbiology

Novel assay based on hybrid DNA-RNA probe for detecting food contaminated with salmonella

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Apr 18 2023Reviewed by Lily Ramsey, LLM

A team of researchers have developed an easy-to-use colorimetric assay for the detection of food contaminated with salmonella. The assay is based on a novel nucleic acid probe that is cleaved by an RNase enzyme specific to the salmonella species. As the team report in the journal Angewandte Chemie, this specific enzymatic cleavage principle made it possible to build a sensitive but simple and portable test system using colloidal gold.

Novel assay based on hybrid DNA-RNA probe for detecting food contaminated with salmonella​​​​​​​

Image Credit: Angewandte Chemie

Consumption of food contaminated with Salmonella typhimurium, whether eggs, ground meat, or chicken, can lead to severe food poisoning. However, suspected cases of salmonella are usually only confirmed several days later, when the bacteria are detected in microbiology laboratories by growing them in culture. A team of researchers led by Yingfu Li, Tohid Didar, and Carlos Filipe of McMaster University in Hamilton, Canada, have now developed a novel test system based on a hybrid DNA-RNA probe that specifically and rapidly detects salmonella, without the need for microbiological diagnostics or expensive analytical equipment.

Using a multi-round selection process, the McMaster team uncovered an artificial DNA-RNA hybrid probe that is a substrate for a salmonella-specific form of an RNase H enzyme. Based on this highly specific enzymatic recognition, the team first developed a fluorescence-based assay on salmonella RNase H, and then extended the principle to a simple, portable salmonella assay based on a colloidal gold colorimetry.

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Colloidal gold is a common color reagent familiar to many of us from its use in SARS-CoV-2 antigen test strips. In a slight departure from this methodology, however, the team did not use a paper strip as the basis for their assay, but instead turned to plastic pipette tips, which are commonly used in the laboratory to measure specific amounts of liquids.

For the preparation of the colorimetric assay, the inner wall of a pipette tip was first coated with DNA-functionalized nanogold. A mixture of reagents composed of nanogold-DNA and the DNA-RNA probe were then sucked up into the pipette tip, causing a double layer of nanogold to form on the walls, because the DNA-RNA hybrid probe links both layers.

However, when the sample mixture contains salmonella, the upper layer is released thanks to the salmonella RNase H specifically cleaving the DNA-RNA linker probe. When the gold-containing solution is then drained onto an absorbent pad with a nylon membrane, a clear red spot indicates the presence of salmonella in the sample being tested. The team also tested the specificity of their system, finding it did not falsely detect the presence of other bacteria containing RNAse H.

The authors highlight that the test is not only much less complex than other methods for detecting salmonella, but also much faster. In contrast to other methods, only one hour of incubation in a pipette tip is required for highly sensitive detection of salmonella, for example, in ground beef. In the future, the team envision developing more nucleic acid probes which can specifically detect other infectious pathogens, for example coliform bacteria such as E. coli.

Source:

Wiley

Journal reference:

Li, J., et al. (2023). A Simple Colorimetric Au‐on‐Au Tip Sensor with a New Functional Nucleic Acid Probe for Food‐borne Pathogen Salmonella typhimurium. Angewandte Chemie International Edition. doi.org/10.1002/anie.202300828.

Microbiology

Relaxation of pandemic measures resulted in the surge of Strep A infections to above pre-COVID levels

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Reviewed by Emily Henderson, B.Sc.Apr 17 2023

New research from France shows that infections cause by Group A Streptococcus (GAS) fell by 80% as the first COVID lockdown took effect in March 2020 and stayed at low levels until March 2022, from which point they increased by 18% a month to rise well above pre-COVID levels.

The study is being presented at the European Congress of Clinical Microbiology & Infectious Diseases in Copenhagen, Denmark (15-18 April) and is by Dr Robert Cohen (Association Clinique et Thérapeutique Infantile du Val-de-Marne [ACTIV]), The French Ambulatory Paediatrics Association (AFPA) Paris (France), and Clinical Research Centre, Centre Hospitalier Intercommunal de Créteil – Créteil (France) and colleagues.

The authors analyzed non-invasive GAS infections in a network of non-emergency pediatricians between January 2018 and December 2022. Clinicians evaluating children aged 15 years old and younger for tonsillopharyngitis, perianal infections, paronychia/blistering dactylitis and scarlet fever (all can be caused by GAS) were invited to perform a rapid antigen detection test (RADT) to confirm the presence of GAS infection.

The primary outcome was the incidence of non-invasive GAS infections per 10,000 visits over time. Incidence rates were modeled, considering two important timepoints: March 2020 (first national lockdown in France) and March 2022 (mask-wearing in schools no longer mandatory).

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Over the study period, 125 pediatricians recorded 262,959 episodes of infectious diseases (118,035 children; median age 2.1 years). GAS-related illnesses represented 4.3% (n=11,701) of all infections. In March 2020, the incidence of GAS diseases decreased by around 80%. Between March 2020 and March 2022, the incidence remained low, with no significant trend (Figure). After March 2022, the incidence significantly increased (by 17% per month;), with similar patterns across all GAS-related diseases, reaching levels way above those seen pre-COVID (see figure)

The authors conclude: “COVID-19 mitigation measures had a major impact on the epidemiology of non-invasive GAS infections, and the relaxation of these measures was followed by a surge of GAS infections to above pre-pandemic levels.”

Dr Robert Cohen, ACTIV, and the French Ambulatory Paediatrics Association (AFPA) Paris, and Clinical Research Centre, Centre Hospitalier Intercommunal de Créteil – Créteil, France. E) [email protected]

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European Congress of Clinical Microbiology & Infectious Diseases

Microbiology

Nasal SARS-CoV-2 vaccine outperforms existing vaccines in preclinical trial

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Bhavana KunkalikarBy Bhavana KunkalikarApr 6 2023Reviewed by Benedette Cuffari, M.Sc.

In a recent study published in the journal Nature Microbiology, researchers assess the role of the live-attenuated vaccine (LAV) sCPD9 in inducing systemic and mucosal immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com

Study: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Image Credit: TopMicrobialStock / Shutterstock.com

Introduction

Coronavirus disease 2019 (COVID-19) vaccines, currently administered through the intramuscular route, effectively stimulate the production of neutralizing antibodies, effector and central memory T-cells, germinal center B-cells, long-lived plasma cells, and nasal-resident CD8+ T-cells. The intramuscular route has lower efficacy in promoting long-lasting mucosal immunoglobulin A (IgA) and IgG responses, as well as pulmonary tissue-resident memory cell responses.

Notably, mucosal antibodies are important in reducing viral infectivity and transmission at the site of entry. Tissue-resident memory cells have faster recall responses and can recognize cognate antigens earlier due to their local positioning.

About the study

In the present study, researchers compare the immune responses and preclinical efficacy of the Pfizer-BioNTech BNT162b2 messenger ribonucleic acid (mRNA) COVID-19 vaccine, adenovirus-vectored spike vaccine Ad2-spike, and LAV sCPD9 in Syrian hamsters.

The efficiency and mechanism of action of the evaluated vaccines were evaluated in a heterologous SARS-CoV-2 Delta variant challenge condition. To this end, Syrian hamsters received one vaccine dose and were exposed to the SARS-CoV-2 Delta variant 21 days after vaccination to evaluate its effectiveness. Hamsters were administered two vaccine doses 21 days apart and were later infected with the virus 14 days after booster administration.

Histopathology was used to examine challenged hamsters and determine any lung damage caused by infection. Single-cell RNA sequencing (scRNA-seq) was performed on lung specimens to establish a correlation between inflammation levels and cellular responses.

The humoral responses of hamsters were assessed by analyzing their sera collected before and after vaccination and determining their neutralizing ability against SARS-CoV-2 variants at different time points.

Results

All vaccinations protected hamsters from weight loss induced by SARS-CoV-2 infection. However, the vaccines did not provide complete protection against SARS-CoV-2 Delta infection after a single dose, as viral RNA was still present in the respiratory tract. The sCPD9 vaccine was the only tested vaccine that successfully reduced replicating viral titers to undetectable levels within two days post-challenge (dpc).

The overall efficacy of the SARS-CoV-2 vaccine was enhanced through prime-boost vaccination. Despite a significant reduction after prime-boost vaccination, all groups exhibited detectable viral RNA in oropharyngeal specimens and lungs. Nevertheless, sCPD9-based vaccination was more effective in decreasing viral RNA levels.

Vaccinated animals exhibited a significant reduction in replication-competent vial levels in their lungs two days post-challenge (dpc). Only the sCPD9 booster vaccine effectively reduced replicating virus proportions below the detection threshold, irrespective of whether the entire vaccination series was heterologous or homologous.

Furthermore, sCPD9 was highly effective in preventing inflammation and pneumonia after a single vaccination. This was demonstrated by the reduced levels of consolidated lung areas, along with lower scores for bronchitis, edema, and lung inflammation.

Animals with different vaccination schedules showed more significant bronchial hyperplasia. Prime-boost regimens showed a similar trend, with the mRNA vaccine displaying better histological outcomes with a homologous boost.

Homologous sCPD9 prime-boost vaccination offered better lung protection against inflammation. Both heterologous and homologous sCDP9 vaccinated hamsters exhibited reduced inflammation- and infection-related genes in their lung transcriptome.

Sera from sCPD9 vaccine recipients showed higher neutralization capacity against the ancestral SARS-CoV-2 variant B.1 compared to other groups. The sCPD9 sera effectively neutralized the Beta and Delta variants, as well as the Omicron BA.1 sublineage.

The neutralization capacity against Omicron BA.1 was reduced in all cohorts, with sCPD9 sera associated with significant neutralization. Neutralizing antibodies increased over time in all cohorts by five dpc due to challenge infection.

Hamsters that received the sCPD9 or mRNA vaccine, along with the prime-only vaccination, produced more neutralizing antibodies than those that only received the prime-only vaccination. Booster vaccination improved the serum neutralization capacity for various variants, with Omicron BA.1 exhibiting the highest neutralization evasion capacity among the tested variants.

Hamsters vaccinated with mRNA+sCDP9 and prime-boost sCDP9 produced notable IgG antibody responses against the SARS-CoV-2 spike, nucleocapsid protein, and open reading frame (ORF)-3a. Comparatively, hamsters vaccinated with prime-boost mRNA and Ad2 only exhibited IgG reactivity against the spike protein.

Conclusions

The study findings presented a comparison of vaccines across different platforms, including a novel LAV that provided better protection against SARS-CoV-2 infection than other types of COVID-19 vaccines. Importantly, these findings on enhanced immunity through heterologous prime-boost vaccination align with other recent studies that utilize systemic priming and intranasal boosting with Ad-2 vector or mRNA vaccines.

Anti-SARS-CoV-2 IgA levels in the nasal mucosa are significantly higher among sCPD9-vaccinated animals. Animals vaccinated with sCPD9 showed significant improvement in protection against virus replication, lung inflammation, and tissue damage. Animals that received sCPD9 had a broader antigen recognition, likely due to the key features of LAV.

Journal reference:
  • Nouailles, G., Adler, J. M., Pennitz, P., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology 1-15. doi:10.1038/s41564-023-01352-8
Microbiology

Live attenuated nasal vaccine elicits superior immunity to SARS-CoV-2 variants in hamsters

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Reviewed by Emily Henderson, B.Sc.Apr 4 2023

Since the beginning of the COVID-19 pandemic, researchers have been working on mucosal vaccines that can be administered through the nose. Now, scientists in Berlin have developed a live attenuated vaccine for the nose. In “Nature Microbiology”, they describe the special immune protection it induces.

Coronaviruses spread primarily through the air. When infected people speak, cough, sneeze or laugh, they expel droplets of saliva containing the virus. Other people then breathe in these airborne pathogens and become infected themselves. A research team in Berlin decided to try to fight the virus that causes COVID-19 where it first takes hold: the mucous membranes of the nose, mouth, throat, and lungs. To do so, the scientists developed a live attenuated SARS-CoV-2 vaccine that is administered through the nose. In the latest issue of the journal “Nature Microbiology“, the interdisciplinary team describes how this live attenuated vaccine confers better immunity than vaccines injected into muscle.

Already in the fall of last year, two nasal vaccination formulations were approved for use in India and China. These contain modified adenoviruses – which typically cause respiratory or gastrointestinal illnesses – that are self-attenuating, meaning they either replicate poorly or stop replicating altogether, and therefore never trigger disease. Other live nasal vaccines are currently undergoing development and testing around the world.

Protection at the site of infection

The benefits of a nasal vaccine go far beyond just providing an alternative for people afraid of needles. When a vaccine is injected, it infers immunity primarily in the blood and throughout the entire body. However, this means that the immune system only detects and combats coronaviruses relatively late on in an infection, as they enter the body via the mucous membranes of the upper respiratory tract. “It is here, therefore, that we need local immunity if we want to intercept a respiratory virus early on,” explains the study’s co-last author Dr. Jakob Trimpert, a veterinarian and research group leader at the Institute of Virology at Freie Universität Berlin.

“Nasal vaccines are far more effective in this regard than injected vaccines, which fail or struggle to reach the mucous membranes,” emphasizes Dr. Emanuel Wyler, another co-last author. He has been researching COVID-19 since the start of the pandemic as part of the RNA Biology and Posttranscriptional Regulation Lab, which is led by Professor Markus Landthaler at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center (MDC-BIMSB).

In an ideal scenario, a live intranasal vaccine stimulates the formation of the antibody immunoglobulin A (IgA) directly on site, thus preventing infection from occurring in the first place. IgA is the most common immunoglobin in the mucous membranes of the airways. It is able to neutralize pathogens by binding to them and preventing them from infecting respiratory tract cells. At the same time, the vaccine stimulates systemic immune responses that help provide effective overall protection from infection.

Memory T cells that reside in lung tissue play a similarly useful role to antibodies in the mucosa. These white blood cells remain in affected tissue long after an infection has passed and remember pathogens they have encountered before. Thanks to their location in the lungs, they can respond quickly to viruses that enter through the airways.” The co-first author draws attention to one of the observations the team made during their study: “We were able to show that prior intranasal vaccination results in the increased reactivation of these local memory cells in the event of a subsequent SARS-CoV-2 infection. Needless to say, we were particularly pleased with this result.”

Dr. Geraldine Nouailles, immunologist and research group leader at the Department of Pneumology, Respiratory Medicine, and Intensive Care Medicine at Charité

Local immunity impedes viral infection

The scientists tested the efficacy of the newly developed intranasal COVID-19 vaccine on hamster models that had been established by Trimpert and his team at Freie Universität Berlin at the beginning of the pandemic. These rodents are currently the most important non-transgenic model organisms for research into the novel coronavirus, as they can be infected with the same virus variants as humans and develop similar symptoms. They found that after two doses of the vaccine, the virus could no longer replicate in the model organism. “We witnessed strong activation of the immunological memory, and the mucous membranes were very well protected by the high concentration of antibodies,” Trimpert explains. The vaccine could therefore also significantly reduce the transmissibility of the virus.

In addition, the scientists compared the efficacy of the live attenuated vaccine with that of vaccines injected into the muscle. To do so, they vaccinated the hamsters either twice with the live vaccine, once with the mRNA and once with the live vaccine, or twice with an mRNA or adenovirus-based vaccine. Then, after the hamsters were infected with SARS-CoV-2, they used tissue samples from the nasal mucosa and lungs to see how strongly the virus was still able to attack the mucosal cells. They also determined the extent of the inflammatory response using single-cell sequencing. “The live attenuated vaccine performed better than the other vaccines in all parameters,” Wyler summarizes. This is probably due to the fact that the nasally administered vaccine builds up immunity directly at the viral entry site. In addition, the live vaccine contains all components of the virus – not just the spike protein, as is the case with the mRNA vaccines. While spike is indeed the virus’s most important antigen, the immune system can also recognize the virus from about 20 other proteins.

Better than conventional vaccines

The best protection against the SARS-CoV-2 was provided by double nasal vaccination, followed by the combination of a muscular injection of the mRNA vaccine and the subsequent nasal administration of the live attenuated vaccine. “This means the live vaccine could be particularly interesting as a booster,” says the study’s co-first author Julia Adler, a veterinarian and doctoral student at the Institute of Virology at Freie Universität Berlin.

The principle of live attenuated vaccines is old and is already used in measles and rubella vaccinations, for example. But in the past, scientists generated the attenuation by chance – sometimes waiting years for mutations to evolve that produced an attenuated virus. The Berlin researchers, on the other hand, were able to specifically alter the genetic code of the coronaviruses. “We wanted to prevent the attenuated viruses from mutating back into a more aggressive variant,” explains Dr. Dusan Kunec, a scientist at the Institute of Virology at Freie Universität Berlin and another co-last author of the study. “This makes our live vaccine entirely safe and means it can be tailored to new virus variants,” stresses Kunec, who was instrumental in developing the vaccine.

The next step is safety testing: The researchers are collaborating with RocketVax AG, a Swiss start-up based in Basel. The biotech company is developing the live attenuated SARS-CoV-2 vaccine and preparing a phase 1 clinical trial in humans. “We are thrilled to be at the forefront of developing and manufacturing the live attenuated SARS-CoV-2 vaccine as a nasal spray at RocketVax. Our goal is to rapidly scale-up production and advance clinical development towards market access to provide protection against post-COVID symptoms for all. We see great potential in the market for seasonal nasal vaccines”, says Dr. Vladimir Cmiljanovic, CEO of RocketVax.

The future will show which nasal vaccine will ultimately provide better protection. The manufacturers of the nasal adenovirus vaccines developed in India and China have not yet applied for approval in Europe. But one thing is clear to the scientists: since they are administered as nasal sprays or drops, nasal vaccines are a good option for use in places with limited access to trained medical staff. They are also inexpensive to produce and easy to store and transport. Last but not least, live attenuated vaccines such as this one have been proven to provide cross-protection against related viral strains, and thus presumably also against future SARS-CoV-2 variants.

Source:

Max Delbrück Center for Molecular Medicine in the Helmholtz Association

Journal reference:

Nouailles, G., et al. (2023). Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nature Microbiology. doi.org/10.1038/s41564-023-01352-8

Microbiology

Wayne State team discovers a simple technology to detect active TB infection antibodies

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Reviewed by Emily Henderson, B.Sc.Mar 13 2023

A team of faculty from Wayne State University has discovered new technology that will quickly and easily detect active Mycobacterium tuberculosis (TB) infection antibodies. Their work, “Discovery of Novel Transketolase Epitopes and the Development of IgG-Based Tuberculosis Serodiagnostics,” was published in a recent edition of Microbiology Spectrum, a journal published by the American Society for Microbiology. The team is led by Lobelia Samavati, M.D., professor in the Center for Molecular Medicine and Genetics in the School of Medicine. Samavati was joined by Jaya Talreja, Ph.D, and Changya Peng, research scientists in Wayne State’s Department of Internal Medicine.

TB remains a global health threat, with 10 million new cases and 1.7 million deaths annually. According to the latest World Health Organization report, TB is the 13th leading cause of death and the second leading infectious killer after COVID-19. Latent tuberculous infection (LTBI) is considered a reservoir for TB bacteria and subjects can progress to active TB. One-third of the world’s population is infected with TB and, on average, 5 to 10% of those infected with LTBI will develop active TB disease over the course of their lives, usually within the first five years after initial infection.

The gold standard tests to determine whether an infection is active TB are the sputum smear and culture tests. However, these methods require collecting sputum, which is time consuming, expensive, requires trained personnel and lacks sensitivity. The current conventional tests differentiating LTBI from uninfected controls -; such as tuberculin skin tests (TST) and/or interferongamma release assay (IGRA) -; do not differentiate between active TB infection and latent TB. Despite advances in rapid molecular techniques for TB diagnostics, there is an unmet need for a simple inexpensive point-of-care (POC), rapid non-sputum-based test.

Samavati’s research group has worked for more than 15 years to develop technology for detection of antibodies in various respiratory diseases. Her lab has developed a novel non-sputum based technology and has discovered several novel immune-epitopes that differentialy bind to specific immunoglobulin (IgG) in TB-infected subjects. The levels of epitope-specific IgG in seum can differentiate active TB from LTBI subjects, healthy contols and other respiratory diseases. This technology can be used as a simple serum assay non-sputum based serological POC- TB test, which is highly specific and sensitveto diffentiate active TB from LTBI.

“Previously, we developed a T7 phage antigen display platform and after immunoscreening of large sets of serum samples, identified 10 clones that differentially bind to serum antibody (IgG) of active TB patients differentiating TB from other respiratory diseases,” said Samavati. “One of these high-performance clones had homology to the Transketolase (TKT) enzyme of TB bacteria that is an essential enzyme required for the intracellular growth of the bacteria in a host. We hypothesized that abundance of IgG in sera against the identified novel neoantigen that we named as TKTµ may differentiate between active TB, LTBI and other non-TB granulomatous lung diseases such as sarcoidosis. We developed a novel direct Peptide ELISA test to quantify the levels of IgG in serum samples against TKTµ. We designed two additional overlapping M.tb TKT-peptide homologs with potential antigenicity corresponding to M.tb-specific transketolase (M.tb-TKT1 and M.tb-TKT3) and hence standardized three Peptide ELISA (TKTμ, M.tb TKT1 and M.tb TKT3) for the TB serodiagnosis.”

After development and standardization of a direct peptide ELISA for three peptides, the research team tested 292 subjects, and their TKT-peptide ELISA results show that TB patients have significantly higher levels of TKT-specific antibodies compared to patients who were healthy controls and with LTBI. The increased levels of TKT-specific antibodies is presumably associated with growing M.tb bacteria in active TB patients. TKT plays a key role in the switch from the dormancy to proliferative phase and TKT specific IgG may uncover the differences between active TB and LTBI. Thus, IgG-based serodiagnosis of TB with TKT-peptide ELISA is promising.

Currently, commercially available serological TB tests show poor sensitivity and specificity. The ELISA results obtained with the Wayne State team’s discovered TKT peptides yielded high specificity and sensitivity. Their results show that IgG antibodies against transketolase can discriminate active tuberculosis. 

Our TKT peptide ELISA test requires chemically synthesized TKT peptides to coat the wells in the ELISA plate, less than 100µl blood serum sample from patient, detection reagents and an ELISA plate reader. We are extremely enthusiastic about our technology and the fact that with a simple test we can differentiate active TB from LTBI and other respiratory diseases. We believe that our method and TKT peptide ELISA can fit the requirements of the World Health Organization and the Centers for Disease Control and Prevention as a POC screening method.”

Lobelia Samavati, M.D., Professor, Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University

The research team has applied a patent application on its technology and is actively seeking companies interested in investing.

This research was supported by the National Heart, Lung and Blood Institute of the National Institutes of Health, grant numbers 113508 and 148089. The Foundation for Innovative New Diagnostics (FIND, Geneva, Switzerland) provided TB and LTBI samples.

Source:

Wayne State University

Journal reference:

Talreja, J., et al. (2023). Discovery of Novel Transketolase Epitopes and the Development of IgG-Based Tuberculosis Serodiagnostics. Microbiology Spectrum. doi.org/10.1128/spectrum.03377-22.

Microbiology

Bacterial outer membrane vesicles: utility as vaccines and novel engineering approaches

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Dr. Sanchari Sinha Dutta, Ph.D.By Dr. Sanchari Sinha Dutta, Ph.D.Jan 3 2023Reviewed by Danielle Ellis, B.Sc.

In an article published in Frontiers in Microbiology, scientists have described the utility of gram-negative bacteria-derived outer membrane vesicles as vaccines and methods to expand their applications.

Study: Outer membrane vesicles: A bacterial-derived vaccination system. Image Credit: Maxx-Studio/Shutterstock
Study: Outer membrane vesicles: A bacterial-derived vaccination system. Image Credit: Maxx-Studio/Shutterstock

Background

Outer membrane vesicles (OMVs) are spherical lipid nanoparticles with a diameter of 20-300 nm. These vesicles are derived from the cell membrane of Gram-negative bacteria and are composed of bacterial proteins, lipids, nucleic acids, and other components.

OMVs derived from pathogenic or non-pathogenic bacteria play an essential role in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and maintaining bacterial fitness. However, as a non-replicative component, OMVs cannot induce disease pathogenesis independently.  

Bacterial proteins and glycans make OMVs a potent immunogenic component that can be used as adjuvants to induce host immune response. Because of this property, OMVs are considered potential candidates for vaccine development.

Isolation of OMVs

Gram-negative bacteria release OMVs during growth or in stressful conditions. However, such spontaneous OMVs are released in low quantities and, thus, cannot be used for large-scale vaccine production.

Several strategies have been developed to increase OMV production. Sonication, vortexing, or EDTA-mediated extraction have been applied to mechanically disrupt the bacterial membrane, leading to the release of OMVs.

OMVs extracted by EDTA closely relate to the native bacterial membrane and induce comparable immune responses. In contrast, sonication and vortexing increase the amount of non-membrane components in the final product, resulting in increased antigenicity and reduced safety.

Detergent-based extraction is another well-documented method that produces OMVs with reduced levels of lipopolysaccharides (LPS), which are bacterial toxins. Despite reducing the risk of toxicity, this process leads to the loss of many bacterial proteins and lipoproteins, which in turn results in the suppression of OMV-stimulated immune responses.

Manipulating certain bacterial genes can increase vesiculation and, thus, can produce high levels of genetically-modified OMVs. The genes encoding bacterial lipoproteins Lpp and NlpI and the outer membrane protein OmpA are the major targets for genetic manipulation.

Heterologous OMVs

Non-pathogenic bacterial strains can express heterologous proteins to reduce toxicity and improve the immunogenicity of OMVs.

A protein of interest can be fused with a bacterial transmembrane protein, and the resulting plasmid can be introduced into the bacterial strain, which will subsequently produce recombinant OMVs expressing the desired protein on the surface.

Another potential strategy for expressing heterologous proteins is glycoengineering of the LPS O antigen. Glycosylated OMVs can be produced by expressing the O antigen gene of a pathogen in a non-pathogenic O-antigen mutant strain of bacteria.

OMV-induced immune response

The pathogen-associated molecular patterns present on the OMV outer membrane activate the pattern recognition receptors on the host cells, leading to the activation of innate immune signaling and the release of proinflammatory cytokines. The engulfment of OMVs by innate immune cells induces adaptive immune responses.

LPS acts as an adjuvant to induce an effective host immune response to the bacterial antigen expressed on the OMV surface. However, overexpression of LPS can lead to overstimulation of immune responses and induction of systemic toxic shock. Detergent-based preparations or genetic manipulations can be used to reduce the level of highly reactive LPS on the OMV surface.

OMV-based vaccines

OMVs expressing desired antigens can be administered into the body through various routes, including oral/intranasal, intramuscular, subcutaneous, intraperitoneal, and intradermal. It has recently been shown that OMV expressing the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces robust immune responses in hamsters when administered intranasally.

Two clinically-approved OMV vaccines, VA-MENGOC-BC™ and Bexsero™, are currently available against the invasive N. meningitidis serogroup B strain. The PorA protein expressed by this bacterium is highly variable between strains. The OMVs derived from the meningitis-causing strain have been used successfully to develop vaccines against this particular bacterial strain.

Many OMV vaccines are currently under development. These vaccine candidates have been designed to target N. gonorrhoeae, Shigella spp., Salmonella spp., extraintestinal pathogenic E. coli (EXPEC), V. cholerae, M. tuberculosis, and non-typeable H. influenzae.    

Besides anti-bacterial vaccines, OMVs have been used to produce vaccines against viruses, including influenza virus and coronavirus. Tumor-targeted OMVs containing therapeutic siRNA or tumor antigens have also been developed as therapeutic cancer vaccines.

Journal reference: