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1.
Sci Transl Med ; 16(745): eadj4685, 2024 May.
Article in English | MEDLINE | ID: mdl-38691617

ABSTRACT

Current seasonal influenza virus vaccines induce responses primarily against immunodominant but highly plastic epitopes in the globular head of the hemagglutinin (HA) glycoprotein. Because of viral antigenic drift at these sites, vaccines need to be updated and readministered annually. To increase the breadth of influenza vaccine-mediated protection, we developed an antigenically complex mixture of recombinant HAs designed to redirect immune responses to more conserved domains of the protein. Vaccine-induced antibodies were disproportionally redistributed to the more conserved stalk of the HA without hindering, and in some cases improving, antibody responses against the head domain. These improved responses led to increased protection against homologous and heterologous viral challenges in both mice and ferrets compared with conventional vaccine approaches. Thus, antigenically complex protein mixtures can at least partially overcome HA head domain antigenic immunodominance and may represent a step toward a more universal influenza vaccine.


Subject(s)
Ferrets , Hemagglutinin Glycoproteins, Influenza Virus , Influenza Vaccines , Vaccination , Animals , Influenza Vaccines/immunology , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Orthomyxoviridae Infections/prevention & control , Orthomyxoviridae Infections/immunology , Mice , Antibodies, Viral/immunology , Humans , Influenza, Human/prevention & control , Influenza, Human/immunology , Antigens, Viral/immunology , Female , Mice, Inbred BALB C
2.
Front Immunol ; 15: 1404121, 2024.
Article in English | MEDLINE | ID: mdl-38720900

ABSTRACT

Pharmacodynamic assessment of T-cell-based cancer immunotherapies often focus on detecting rare circulating T-cell populations. The therapy-induced immune cells in blood-derived clinical samples are often present in very low frequencies and with the currently available T-cell analytical assays, amplification of the cells of interest prior to analysis is often required. Current approaches aiming to enrich antigen-specific T cells from human Peripheral Blood Mononuclear Cells (PBMCs) depend on in vitro culturing in presence of their cognate peptides and cytokines. In the present work, we improved a standard, publicly available protocol for T-cell immune analyses based on the in vitro expansion of T cells. We used PBMCs from healthy subjects and well-described viral antigens as a model system for optimizing the experimental procedures and conditions. Using the standard protocol, we first demonstrated significant enrichment of antigen-specific T cells, even when their starting frequency ex vivo was low. Importantly, this amplification occurred with high specificity, with no or neglectable enrichment of irrelevant T-cell clones being observed in the cultures. Testing of modified culturing timelines suggested that the protocol can be adjusted accordingly to allow for greater cell yield with strong preservation of the functionality of antigen-specific T cells. Overall, our work has led to the refinement of a standard protocol for in vitro stimulation of antigen-specific T cells and highlighted its reliability and reproducibility. We envision that the optimized protocol could be applied for longitudinal monitoring of rare blood-circulating T cells in scenarios with limited sample material.


Subject(s)
T-Lymphocytes , Humans , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Antigens, Viral/immunology , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Cells, Cultured , Cancer Vaccines/immunology
3.
J Med Virol ; 96(5): e29657, 2024 May.
Article in English | MEDLINE | ID: mdl-38727035

ABSTRACT

The H1N1pdm09 virus has been a persistent threat to public health since the 2009 pandemic. Particularly, since the relaxation of COVID-19 pandemic mitigation measures, the influenza virus and SARS-CoV-2 have been concurrently prevalent worldwide. To determine the antigenic evolution pattern of H1N1pdm09 and develop preventive countermeasures, we collected influenza sequence data and immunological data to establish a new antigenic evolution analysis framework. A machine learning model (XGBoost, accuracy = 0.86, area under the receiver operating characteristic curve = 0.89) was constructed using epitopes, physicochemical properties, receptor binding sites, and glycosylation sites as features to predict the antigenic similarity relationships between influenza strains. An antigenic correlation network was constructed, and the Markov clustering algorithm was used to identify antigenic clusters. Subsequently, the antigenic evolution pattern of H1N1pdm09 was analyzed at the global and regional scales across three continents. We found that H1N1pdm09 evolved into around five antigenic clusters between 2009 and 2023 and that their antigenic evolution trajectories were characterized by cocirculation of multiple clusters, low-level persistence of former dominant clusters, and local heterogeneity of cluster circulations. Furthermore, compared with the seasonal H1N1 virus, the potential cluster-transition determining sites of H1N1pdm09 were restricted to epitopes Sa and Sb. This study demonstrated the effectiveness of machine learning methods for characterizing antigenic evolution of viruses, developed a specific model to rapidly identify H1N1pdm09 antigenic variants, and elucidated their evolutionary patterns. Our findings may provide valuable support for the implementation of effective surveillance strategies and targeted prevention efforts to mitigate the impact of H1N1pdm09.


Subject(s)
Antigens, Viral , Influenza A Virus, H1N1 Subtype , Influenza, Human , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Humans , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Influenza, Human/virology , Influenza, Human/immunology , Antigens, Viral/genetics , Antigens, Viral/immunology , Machine Learning , Evolution, Molecular , Epitopes/genetics , Epitopes/immunology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , COVID-19/immunology , Pandemics/prevention & control , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/immunology , SARS-CoV-2/genetics , SARS-CoV-2/immunology
4.
Nat Commun ; 15(1): 3833, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38714654

ABSTRACT

Antigenic characterization of circulating influenza A virus (IAV) isolates is routinely assessed by using the hemagglutination inhibition (HI) assays for surveillance purposes. It is also used to determine the need for annual influenza vaccine updates as well as for pandemic preparedness. Performing antigenic characterization of IAV on a global scale is confronted with high costs, animal availability, and other practical challenges. Here we present a machine learning model that accurately predicts (normalized) outputs of HI assays involving circulating human IAV H3N2 viruses, using their hemagglutinin subunit 1 (HA1) sequences and associated metadata. Each season, the model learns an updated nonlinear mapping of genetic to antigenic changes using data from past seasons only. The model accurately distinguishes antigenic variants from non-variants and adaptively characterizes seasonal dynamics of HA1 sites having the strongest influence on antigenic change. Antigenic predictions produced by the model can aid influenza surveillance, public health management, and vaccine strain selection activities.


Subject(s)
Antigens, Viral , Hemagglutinin Glycoproteins, Influenza Virus , Influenza A Virus, H3N2 Subtype , Influenza, Human , Machine Learning , Seasons , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Humans , Influenza, Human/immunology , Influenza, Human/virology , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Antigens, Viral/immunology , Antigens, Viral/genetics , Hemagglutination Inhibition Tests , Antigenic Variation/genetics , Influenza Vaccines/immunology
5.
Viruses ; 16(5)2024 05 15.
Article in English | MEDLINE | ID: mdl-38793663

ABSTRACT

Marek's disease (MD), caused by gallid alphaherpesvirus 2 (GaAHV2) or Marek's disease herpesvirus (MDV), is a devastating disease in chickens characterized by the development of lymphomas throughout the body. Vaccine strains used against MD include gallid alphaherpesvirus 3 (GaAHV3), a non-oncogenic chicken alphaherpesvirus homologous to MDV, and homologous meleagrid alphaherpesvirus 1 (MeAHV1) or turkey herpesvirus (HVT). Previous work has shown most of the MDV gC produced during in vitro passage is secreted into the media of infected cells although the predicted protein contains a transmembrane domain. We formerly identified two alternatively spliced gC mRNAs that are secreted during MDV replication in vitro, termed gC104 and gC145 based on the size of the intron removed for each UL44 (gC) transcript. Since gC is conserved within the Alphaherpesvirinae subfamily, we hypothesized GaAHV3 (strain 301B/1) and HVT also secrete gC due to mRNA splicing. To address this, we collected media from 301B/1- and HVT-infected cell cultures and used Western blot analyses and determined that both 301B/1 and HVT produced secreted gC. Next, we extracted RNAs from 301B/1- and HVT-infected cell cultures and chicken feather follicle epithelial (FFE) skin cells. RT-PCR analyses confirmed one splicing variant for 301B/1 gC (gC104) and two variants for HVT gC (gC104 and gC145). Interestingly, the splicing between all three viruses was remarkably conserved. Further analysis of predicted and validated mRNA splicing donor, branch point (BP), and acceptor sites suggested single nucleotide polymorphisms (SNPs) within the 301B/1 UL44 transcript sequence resulted in no gC145 being produced. However, modification of the 301B/1 gC145 donor, BP, and acceptor sites to the MDV UL44 sequences did not result in gC145 mRNA splice variant, suggesting mRNA splicing is more complex than originally hypothesized. In all, our results show that mRNA splicing of avian herpesviruses is conserved and this information may be important in developing the next generation of MD vaccines or therapies to block transmission.


Subject(s)
Chickens , RNA Splicing , Viral Envelope Proteins , Animals , Chickens/virology , Viral Envelope Proteins/genetics , Viral Envelope Proteins/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Marek Disease/virology , Mardivirus/genetics , Mardivirus/physiology , Viral Proteins/genetics , Viral Proteins/metabolism , Herpesvirus 2, Gallid/genetics , Alternative Splicing , Antigens, Viral
6.
Viruses ; 16(5)2024 05 16.
Article in English | MEDLINE | ID: mdl-38793674

ABSTRACT

The Nipah virus (NiV) and the Hendra virus (HeV) are highly pathogenic zoonotic diseases that can cause fatal infections in humans and animals. Early detection is critical for the control of NiV and HeV infections. We present the development of two antigen-detection ELISAs (AgELISAs) using the henipavirus-receptor EphrinB2 and monoclonal antibodies (mAbs) to detect NiV and HeV. The NiV AgELISA detected only NiV, whereas the NiV/HeV AgELISA detected both NiV and HeV. The diagnostic specificities of the NiV AgELISA and the NiV/HeV AgELISA were 100% and 97.8%, respectively. Both assays were specific for henipaviruses and showed no cross-reactivity with other viruses. The AgELISAs detected NiV antigen in experimental pig nasal wash samples taken at 4 days post-infection. With the combination of both AgELISAs, NiV can be differentiated from HeV. Complementing other henipavirus detection methods, these two newly developed AgELISAs can rapidly detect NiV and HeV in a large number of samples and are suitable for use in remote areas where other tests are not available.


Subject(s)
Antibodies, Monoclonal , Antibodies, Viral , Enzyme-Linked Immunosorbent Assay , Ephrin-B2 , Hendra Virus , Henipavirus Infections , Nipah Virus , Hendra Virus/immunology , Animals , Nipah Virus/immunology , Antibodies, Monoclonal/immunology , Enzyme-Linked Immunosorbent Assay/methods , Ephrin-B2/metabolism , Ephrin-B2/immunology , Henipavirus Infections/diagnosis , Henipavirus Infections/virology , Henipavirus Infections/immunology , Antibodies, Viral/immunology , Swine , Humans , Sensitivity and Specificity , Receptors, Virus/metabolism , Antigens, Viral/immunology
7.
Front Immunol ; 15: 1373656, 2024.
Article in English | MEDLINE | ID: mdl-38742108

ABSTRACT

African swine fever virus (ASFV) is one of the most complex viruses. ASFV is a serious threat to the global swine industry because no commercial vaccines against this virus are currently available except in Vietnam. Moreover, ASFV is highly stable in the environment and can survive in water, feed, and aerosols for a long time. ASFV is transmitted through the digestive and respiratory tract. Mucosal immunity is the first line of defense against ASFV. Saccharomyces cerevisiae (SC), which has been certified by the U.S. Food and Drug Administration and has a generally recognized as safe status in the food industry, was used for oral immunization in this study. ASFV antigens were effectively expressed in recombinant SC strains with high DNA copy numbers and stable growth though surface display technology and chromosome engineering (δ-integration). The recombinant SC strains containing eight ASFV antigens-KP177R, E183L, E199L, CP204L, E248R, EP402R, B602L, and B646L- induced strong humoral and mucosal immune responses in mice. There was no antigenic competition, and these antigens induced Th1 and Th2 cellular immune responses. Therefore, the oral immunization strategy using recombinant SC strains containing multiple ASFV antigens demonstrate potential for future testing in swine, including challenge studies to evaluate its efficacy as a vaccine against ASFV.


Subject(s)
African Swine Fever Virus , African Swine Fever , Antigens, Viral , Immunization , Saccharomyces cerevisiae , Viral Vaccines , Animals , African Swine Fever Virus/immunology , African Swine Fever Virus/genetics , Saccharomyces cerevisiae/immunology , Saccharomyces cerevisiae/genetics , Administration, Oral , Mice , Viral Vaccines/immunology , Viral Vaccines/administration & dosage , Antigens, Viral/immunology , African Swine Fever/immunology , African Swine Fever/prevention & control , Swine , Immunity, Mucosal , Antibodies, Viral/blood , Antibodies, Viral/immunology , Mice, Inbred BALB C , Female , Immunity, Humoral
8.
Nat Commun ; 15(1): 4171, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38755147

ABSTRACT

Human Ebola virus (EBOV) outbreaks caused by persistent EBOV infection raises questions on the role of zoonotic spillover in filovirus epidemiology. To characterise filovirus zoonotic exposure, we collected cross-sectional serum samples from bushmeat hunters (n = 498) in Macenta Prefecture Guinea, adjacent to the index site of the 2013 EBOV-Makona spillover event. We identified distinct immune signatures (20/498, 4.0%) to multiple EBOV antigens (GP, NP, VP40) using stepwise ELISA and Western blot analysis and, live EBOV neutralisation (5/20; 25%). Using comparative serological data from PCR-confirmed survivors of the 2013-2016 EBOV outbreak, we demonstrated that most signatures (15/20) were not plausibly explained by prior EBOV-Makona exposure. Subsequent data-driven modelling of EBOV immunological outcomes to remote-sensing environmental data also revealed consistent associations with intact closed canopy forest. Together our findings suggest exposure to other closely related filoviruses prior to the 2013-2016 West Africa epidemic and highlight future surveillance priorities.


Subject(s)
Antibodies, Viral , Ebolavirus , Hemorrhagic Fever, Ebola , Humans , Animals , Guinea/epidemiology , Ebolavirus/immunology , Ebolavirus/isolation & purification , Hemorrhagic Fever, Ebola/epidemiology , Hemorrhagic Fever, Ebola/immunology , Hemorrhagic Fever, Ebola/virology , Hemorrhagic Fever, Ebola/blood , Hemorrhagic Fever, Ebola/transmission , Adult , Male , Antibodies, Viral/blood , Antibodies, Viral/immunology , Middle Aged , Zoonoses/virology , Zoonoses/epidemiology , Zoonoses/transmission , Female , Cross-Sectional Studies , Disease Outbreaks , Young Adult , Aged , Enzyme-Linked Immunosorbent Assay , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Viral Zoonoses/virology , Antigens, Viral/immunology
9.
J Med Virol ; 96(5): e29681, 2024 May.
Article in English | MEDLINE | ID: mdl-38773815

ABSTRACT

Rotavirus gastroenteritis is accountable for an estimated 128 500 deaths among children younger than 5 years worldwide, and the majority occur in low-income countries. Although the clinical trials of rotavirus vaccines in Bangladesh revealed a significant reduction of severe rotavirus disease by around 50%, the vaccines are not yet included in the routine immunization program. The present study was designed to provide data on rotavirus diarrhea with clinical profiles and genotypes before (2017-2019) and during the COVID-19 pandemic period (2020-2021). Fecal samples were collected from 2% of the diarrheal patients at icddr,b Dhaka hospital of all ages between January 2017 and December 2021 and were tested for VP6 rotavirus antigen using ELISA. The clinical manifestations such as fever, duration of diarrhea and hospitalization, number of stools, and dehydration and so on were collected from the surveillance database (n = 3127). Of the positive samples, 10% were randomly selected for genotyping using Sanger sequencing method. A total of 12 705 fecal samples were screened for rotavirus A antigen by enzyme immunoassay. Overall, 3369 (27%) were rotavirus antigen-positive, of whom children <2 years had the highest prevalence (88.6%). The risk of rotavirus A infection was 4.2 times higher in winter than in summer. Overall, G3P[8] was the most prominent genotype (45.3%), followed by G1P[8] (32.1%), G9P[8] (6.8%), and G2P[4] (6.1%). The other unusual combinations, such as G1P[4], G1P[6], G2P[6], G3P[4], G3P[6], and G9P[6], were also present. Genetic analysis on Bangladeshi strains revealed that the selection pressure (dN/dS) was estimated as <1. The number of hospital visits showed a 37% drop during the COVID-19 pandemic relative to the years before the pandemic. Conversely, there was a notable increase in the rate of rotavirus positivity during the pandemic (34%, p < 0.00) compared to the period before COVID-19 (23%). Among the various clinical symptoms, only the occurrence of watery stool significantly increased during the pandemic. The G2P[4] strain showed a sudden rise (19%) in 2020, which then declined in 2021. In the same year, G1P[8] was more prevalent than G3P[8] (40% vs. 38%, respectively). The remaining genotypes were negligible and did not exhibit much fluctuation. This study reveals that the rotavirus burden remained high during the COVID-19 prepandemic and pandemic in Bangladesh. Considering the lack of antigenic variations between the circulating and vaccine-targeted strains, integrating the vaccine into the national immunization program could reduce the prevalence of the disease, the number of hospitalizations, and the severity of cases.


Subject(s)
COVID-19 , Feces , Genotype , Rotavirus Infections , Rotavirus , Humans , Bangladesh/epidemiology , Rotavirus/genetics , Rotavirus/isolation & purification , Rotavirus/classification , Rotavirus Infections/epidemiology , Rotavirus Infections/virology , Child, Preschool , Infant , COVID-19/epidemiology , COVID-19/virology , COVID-19/prevention & control , Feces/virology , Female , Male , Child , Diarrhea/virology , Diarrhea/epidemiology , Adolescent , Adult , Antigens, Viral/genetics , Infant, Newborn , Gastroenteritis/epidemiology , Gastroenteritis/virology , Young Adult , Prevalence , SARS-CoV-2/genetics , SARS-CoV-2/classification , Middle Aged , Seasons
10.
ACS Nano ; 18(19): 12235-12260, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38696217

ABSTRACT

Variants of coronavirus porcine epidemic diarrhea virus (PEDV) frequently emerge, causing an incomplete match between the vaccine and variant strains, which affects vaccine efficacy. Designing vaccines with rapidly replaceable antigens and high efficacy is a promising strategy for the prevention of infection with PEDV variant strains. In our study, three different types of self-assembled nanoparticles (nps) targeting receptor-binding N-terminal domain (NTD) and C-terminal domain (CTD) of S1 protein, named NTDnps, CTDnps, and NTD/CTDnps, were constructed and evaluated as vaccine candidates against PEDV. NTDnps and CTDnps vaccines mediated significantly higher neutralizing antibody (NAb) titers than NTD and CTD recombinant proteins in mice. The NTD/CTDnps in varying ratios elicited significantly higher NAb titers when compared with NTDnps and CTDnps alone. The NTD/CTDnps (3:1) elicited NAb with titers up to 92.92% of those induced by the commercial vaccine. Piglets immunized with NTD/CTDnps (3:1) achieved a passive immune protection rate of 83.33% of that induced by the commercial vaccine. NTD/CTDnps (3:1) enhanced the capacity of mononuclear macrophages and dendritic cells to take up and present antigens by activating major histocompatibility complex I and II molecules to stimulate humoral and cellular immunity. These data reveal that a combination of S1-NTD and S1-CTD antigens targeting double receptor-binding domains strengthens the protective immunity of nanoparticle vaccines against PEDV. Our findings will provide a promising vaccine candidate against PEDV.


Subject(s)
Nanoparticles , Porcine epidemic diarrhea virus , Viral Vaccines , Porcine epidemic diarrhea virus/immunology , Animals , Nanoparticles/chemistry , Swine , Mice , Viral Vaccines/immunology , Coronavirus Infections/prevention & control , Coronavirus Infections/immunology , Mice, Inbred BALB C , Antigens, Viral/immunology , Antigens, Viral/chemistry , Antibodies, Neutralizing/immunology , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/chemistry , Protein Domains/immunology , Female , Nanovaccines
11.
Nat Commun ; 15(1): 4035, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38740742

ABSTRACT

Rapid and accurate detection of respiratory virus aerosols is highlighted for virus surveillance and infection control. Here, we report a wireless immunoassay technology for fast (within 10 min), on-site (wireless and battery-free), and sensitive (limit of detection down to fg/L) detection of virus antigens in aerosols. The wireless immunoassay leverages the immuno-responsive hydrogel-modulated radio frequency resonant sensor to capture and amplify the recognition of virus antigen, and flexible readout network to transduce the immuno bindings into electrical signals. The wireless immunoassay achieves simultaneous detection of respiratory viruses such as severe acute respiratory syndrome coronavirus 2, influenza A H1N1 virus, and respiratory syncytial virus for community infection surveillance. Direct detection of unpretreated clinical samples further demonstrates high accuracy for diagnosis of respiratory virus infection. This work provides a sensitive and accurate immunoassay technology for on-site virus detection and disease diagnosis compatible with wearable integration.


Subject(s)
Hydrogels , Influenza A Virus, H1N1 Subtype , SARS-CoV-2 , Wireless Technology , Immunoassay/methods , Immunoassay/instrumentation , Humans , Hydrogels/chemistry , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Wireless Technology/instrumentation , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H1N1 Subtype/isolation & purification , Aerosols , COVID-19/diagnosis , COVID-19/virology , COVID-19/immunology , Antigens, Viral/immunology , Antigens, Viral/analysis , Respiratory Syncytial Viruses/immunology , Respiratory Syncytial Viruses/isolation & purification , Limit of Detection
12.
Elife ; 122024 May 28.
Article in English | MEDLINE | ID: mdl-38805550

ABSTRACT

Human H3N2 influenza viruses are subject to rapid antigenic evolution which translates into frequent updates of the composition of seasonal influenza vaccines. Despite these updates, the effectiveness of influenza vaccines against H3N2-associated disease is suboptimal. Seasonal influenza vaccines primarily induce hemagglutinin-specific antibody responses. However, antibodies directed against influenza neuraminidase (NA) also contribute to protection. Here, we analysed the antigenic diversity of a panel of N2 NAs derived from human H3N2 viruses that circulated between 2009 and 2017. The antigenic breadth of these NAs was determined based on the NA inhibition (NAI) of a broad panel of ferret and mouse immune sera that were raised by infection and recombinant N2 NA immunisation. This assessment allowed us to distinguish at least four antigenic groups in the N2 NAs derived from human H3N2 viruses that circulated between 2009 and 2017. Computational analysis further revealed that the amino acid residues in N2 NA that have a major impact on susceptibility to NAI by immune sera are in proximity of the catalytic site. Finally, a machine learning method was developed that allowed to accurately predict the impact of mutations that are present in our N2 NA panel on NAI. These findings have important implications for the renewed interest to develop improved influenza vaccines based on the inclusion of a protective NA antigen formulation.


Two proteins, the hemagglutinin and the neuraminidase, protrude from the surface of the influenza virus. Their detection by the immune system allows the host organism to mount defences against the viral threat. The virus evolves in response to this pressure, which manifests as changes in the appearance of its hemagglutinin and neuraminidase. This process, known as antigenic drift, leads to the proteins evading detection. It is also why flu vaccines require frequent updates, as they rely on 'training' the immune system to recognise the most important strains in circulation ­ primarily by exposing it to appropriate versions of hemagglutinin. While the antigenic drift of hemagglutinin has been extensively studied, much less is known about how the neuraminidase accumulates mutations, and how these affect the immune response. To investigate this question, Catani et al. selected 43 genetically distant neuraminidases from human viral samples isolated between 2009 and 2017. Statistical analyses were applied to define their relatedness, revealing that a group of closely related neuraminidases predominated from 2009 to 2015, before they were being taken over by a second group. A third group, which was identified in viruses isolated in 2013, was remarkably close to the neuraminidase of strains that circulated in the late 1990s. The fourth and final group of neuraminidases was derived from influenza viruses that normally circulate in pigs but can also occasionally infect humans. Next, Catani et al. examined the immune response that these 43 neuraminidases could elicit in mice, as well as in ferrets ­ the animal most traditionally used in influenza research. This allowed them to pinpoint which changes in the neuraminidase sequences were important to escape recognition by the host. Data obtained from the two model species were comparable, suggesting that these experiments could be conducted on mice going forward, which are easier to work with than ferrets. Finally, Catani et al. used machine learning to build a computational model that could predict how strongly the immune system would respond to a specific neuraminidase variant. These findings could help guide the development of new vaccines that include neuraminidases tailored to best prime and train the immune system against a larger variety of strains. This may aid the development of 'supra-seasonal' vaccines that protect against a broad range of influenza viruses, reducing the need for yearly updates.


Subject(s)
Antigens, Viral , Ferrets , Influenza A Virus, H3N2 Subtype , Influenza, Human , Neuraminidase , Neuraminidase/immunology , Neuraminidase/genetics , Influenza A Virus, H3N2 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/enzymology , Humans , Animals , Antigens, Viral/immunology , Antigens, Viral/genetics , Mice , Influenza, Human/prevention & control , Influenza, Human/immunology , Influenza, Human/virology , Antibodies, Viral/immunology , Influenza Vaccines/immunology , Antigenic Variation , Viral Proteins/immunology , Viral Proteins/genetics , Viral Proteins/chemistry , Orthomyxoviridae Infections/prevention & control , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/virology
13.
Arch Virol ; 169(6): 131, 2024 May 31.
Article in English | MEDLINE | ID: mdl-38819530

ABSTRACT

Noroviruses (NoVs) are the chief cause of acute viral gastroenteritis worldwide. By employing the major capsid protein VP1 of a GII.6 NoV strain as an immunogen, we generated two monoclonal antibodies (mAbs) with wide-spectrum binding activities against NoV genogroup II (GII) VP1 proteins. One mAb (10G7) could bind to native and denatured GII-specific VP1 proteins. The other mAb (10F2) could bind to all tested native GII VP1 proteins, but not to denatured GII.3, GII.4, GII.7, or GII.17 VP1 proteins. Using GII.6/GII.4 fusion proteins, the mAb 10F2 binding region was confirmed to be located in the C-terminal P1 domain. An enzyme-linked immunosorbent assay based on peptides covering the P domain did not detect any binding. Using a panel of VP1 proteins with swapped regions, deletions, and mutations, the mAb 10F2 binding region was determined to be located between residues 496 and 513. However, the residue(s) responsible for its varied binding affinity for different denatured GII VP1 proteins remain to be identified. In summary, two NoV GII-specific cross-reactive mAbs were generated, and their binding regions were determined. Our results might facilitate the detection and immunogenic study of NoVs.


Subject(s)
Antibodies, Monoclonal , Antibodies, Viral , Capsid Proteins , Epitopes , Norovirus , Norovirus/genetics , Norovirus/immunology , Antibodies, Monoclonal/immunology , Capsid Proteins/immunology , Capsid Proteins/genetics , Capsid Proteins/chemistry , Epitopes/immunology , Epitopes/genetics , Antibodies, Viral/immunology , Animals , Antigens, Viral/immunology , Antigens, Viral/genetics , Mice , Humans , Caliciviridae Infections/virology , Caliciviridae Infections/immunology , Mice, Inbred BALB C , Epitope Mapping , Cross Reactions
14.
J Nanobiotechnology ; 22(1): 295, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38807131

ABSTRACT

The signal sequence played a crucial role in the efficacy of mRNA vaccines against virus pandemic by influencing antigen translation. However, limited research had been conducted to compare and analyze the specific mechanisms involved. In this study, a novel approach was introduced by substituting the signal sequence of the mRNA antigen to enhance its immune response. Computational simulations demonstrated that various signal peptides differed in their binding capacities with the signal recognition particle (SRP) 54 M subunit, which positively correlated with antigen translation efficiency. Our data revealed that the signal sequences of tPA and IL-6-modified receptor binding domain (RBD) mRNA vaccines sequentially led to higher antigen expression and elicited more robust humoral and cellular immune protection against the SARS-CoV-2 compared to the original signal sequence. By highlighting the importance of the signal sequence, this research provided a foundational and safe approach for ongoing modifications in signal sequence-antigen design, aiming to optimize the efficacy of mRNA vaccines.


Subject(s)
Protein Sorting Signals , SARS-CoV-2 , mRNA Vaccines , Animals , Mice , SARS-CoV-2/immunology , COVID-19/prevention & control , COVID-19/immunology , Mice, Inbred BALB C , RNA, Messenger/genetics , COVID-19 Vaccines/immunology , Female , Humans , Antigens, Viral/immunology , Antigens, Viral/genetics , Antigens, Viral/chemistry , Antibodies, Viral/immunology , Immunity, Humoral , Vaccines, Synthetic/immunology , Immunity, Cellular
16.
Viruses ; 16(5)2024 04 24.
Article in English | MEDLINE | ID: mdl-38793544

ABSTRACT

The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.


Subject(s)
Antigens, Viral , COVID-19 , Coronavirus Nucleocapsid Proteins , Phosphoproteins , SARS-CoV-2 , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Humans , Coronavirus Nucleocapsid Proteins/immunology , Coronavirus Nucleocapsid Proteins/genetics , COVID-19/diagnosis , COVID-19/immunology , COVID-19/virology , Antigens, Viral/immunology , Antigens, Viral/genetics , Phosphoproteins/immunology , Phosphoproteins/genetics , Enzyme-Linked Immunosorbent Assay/methods , Enzyme-Linked Immunosorbent Assay/standards , COVID-19 Serological Testing/methods , COVID-19 Serological Testing/standards , Antibodies, Viral/immunology , Antibodies, Monoclonal/immunology , Computational Biology/methods , Mutation , Animals
17.
Viruses ; 16(5)2024 04 23.
Article in English | MEDLINE | ID: mdl-38793539

ABSTRACT

With the continuous spread of new SARS-CoV-2 variants of concern (VOCs), the monitoring of diagnostic test performances is mandatory. We evaluated the changes in antigen diagnostic tests' (ADTs) accuracy along the Delta to Omicron VOCs transition, exploring the N protein mutations possibly affecting ADT sensitivity and assessing the best sampling site for the diagnosis of Omicron infections. In total, 5175 subjects were enrolled from 1 October 2021 to 15 July 2022. The inclusion criteria were SARS-CoV-2 ADT combined with a same-day RT-PCR swab test. For the sampling site analysis, 61 patients were prospectively recruited during the Omicron period for nasal and oral swab analyses by RT-PCR. Next-Generation Sequencing data were obtained to evaluate the different sublineages. Using RT-PCR as a reference, 387 subjects resulted in becoming infected and the overall sensitivity of the ADT decreased from 63% in the Delta period to 33% in the Omicron period. This decrease was highly statistically significant (p < 0.001), and no decrease in viral load was detected at the RNA level. The nasal site presented a significantly higher viral load than the oral site during the Omicron wave. The reduced detection rate of Omicron infections by ADT should be considered in the global testing strategy to preserve accurate diagnoses across the changing SARS-CoV-2 variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Sensitivity and Specificity , Humans , SARS-CoV-2/immunology , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/virology , COVID-19/immunology , Male , Viral Load , Female , Antigens, Viral/immunology , COVID-19 Serological Testing/methods , Mutation , Middle Aged , Adult , Prospective Studies , RNA, Viral/genetics , Aged
18.
Front Immunol ; 15: 1360140, 2024.
Article in English | MEDLINE | ID: mdl-38711513

ABSTRACT

Introduction: Modified Vaccinia Virus Ankara (MVA) is a safe vaccine vector inducing long- lasting and potent immune responses. MVA-mediated CD8+T cell responses are optimally induced, if both, direct- and cross-presentation of viral or recombinant antigens by dendritic cells are contributing. Methods: To improve the adaptive immune responses, we investigated the role of the purinergic receptor P2X7 (P2RX7) in MVA-infected feeder cells as a modulator of cross-presentation by non-infected dendritic cells. The infected feeder cells serve as source of antigen and provide signals that help to attract dendritic cells for antigen take up and to license these cells for cross-presentation. Results: We demonstrate that presence of an active P2RX7 in major histocompatibility complex (MHC) class I (MHCI) mismatched feeder cells significantly enhanced MVA-mediated antigen cross-presentation. This was partly regulated by P2RX7-specific processes, such as the increased availability of extracellular particles as well as the altered cellular energy metabolism by mitochondria in the feeder cells. Furthermore, functional P2RX7 in feeder cells resulted in a delayed but also prolonged antigen expression after infection. Discussion: We conclude that a combination of the above mentioned P2RX7-depending processes leads to significantly increased T cell activation via cross- presentation of MVA-derived antigens. To this day, P2RX7 has been mostly investigated in regards to neuroinflammatory diseases and cancer progression. However, we report for the first time the crucial role of P2RX7 for antigen- specific T cell immunity in a viral infection model.


Subject(s)
Cross-Priming , Dendritic Cells , Genetic Vectors , Receptors, Purinergic P2X7 , Vaccinia virus , Animals , Humans , Mice , Antigen Presentation/immunology , Antigens, Viral/immunology , CD8-Positive T-Lymphocytes/immunology , Cross-Priming/immunology , Dendritic Cells/immunology , Dendritic Cells/metabolism , Mice, Inbred C57BL , Receptors, Purinergic P2X7/immunology , Receptors, Purinergic P2X7/metabolism , Vaccinia virus/immunology
19.
Methods Mol Biol ; 2808: 247-264, 2024.
Article in English | MEDLINE | ID: mdl-38743375

ABSTRACT

Measles IgG avidity assays determine the overall strength of molecular binding between measles-specific IgG antibodies and measles virus antigens. Avidity results can distinguish recent from distant measles virus infections. Individuals who are immunologically naïve to measles virus develop low-avidity antibodies upon measles virus infection or first-time vaccination. Within 4-6 months, antibodies mature to high avidity. Measles avidity assays are most useful in the context of measles elimination. In such settings, avidity and epidemiological and clinical information are used to classify measles breakthrough infections for control and surveillance purposes and to assist in case confirmation when other laboratory results are inconclusive or nonexistent. We present a highly accurate end-titer measles avidity assay that delivers results based on IgG quality (avidity) that are independent of IgG concentration.


Subject(s)
Antibodies, Viral , Antibody Affinity , Immunoglobulin G , Measles virus , Measles , Antibody Affinity/immunology , Immunoglobulin G/immunology , Humans , Antibodies, Viral/immunology , Measles virus/immunology , Measles/immunology , Measles/virology , Antigens, Viral/immunology , Enzyme-Linked Immunosorbent Assay/methods
20.
Microb Pathog ; 191: 106669, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38697231

ABSTRACT

African swine fever (ASF) is a lethal disease caused by ASF virus (ASFV), severely impacting the global swine industry. Though nuclear acid-based detection methods are reliable, they are laboratory-dependent. In this study, we developed a device-independent, user friendly and cost-effective quantum dots based immunochromatographic strip (QDs-ICS) with high specificity and sensitivity for the rapid and on-site detection of ASFV antigen. For the preparation of the QDs-ICS, we generated a monoclonal antibody (mAb) mAb-8G8 and polyclonal antibody (pAb) against ASFV-p72 protein. The pAb was labelled with QDs to be used as the detection probe and the mAb-8G8 was coated on the nitrocellulose membrane as the test line. Our results proved that the strip displayed no cross-reactivity with other swine viruses and detection limit of the QDs-ICS was down to 1 ng/mL for the ASFV-p72 protein with great reproducibility. The strip also exhibited high stability with a storage period up to 12 months under room temperature. Twenty blind samples and one hundred clinical samples were examined by the QDs-ICS, conventional PCR and real-time PCR method, respectively. Results showed that the agreement rate between the QDs-ICS and PCR method was 100%, and the agreement rate between the strip and real-time PCR was 94%. The novel QDs-ICS developed here would be an effective tool for on-site detection of ASFV.


Subject(s)
African Swine Fever Virus , African Swine Fever , Antibodies, Monoclonal , Antibodies, Viral , Antigens, Viral , Chromatography, Affinity , Quantum Dots , Sensitivity and Specificity , African Swine Fever Virus/isolation & purification , African Swine Fever Virus/immunology , African Swine Fever Virus/genetics , Animals , African Swine Fever/diagnosis , African Swine Fever/virology , African Swine Fever/immunology , Swine , Antibodies, Monoclonal/immunology , Antibodies, Viral/immunology , Chromatography, Affinity/methods , Antigens, Viral/analysis , Antigens, Viral/immunology , Reproducibility of Results , Reagent Strips
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