Biology subjects

Ross, T. M.

Publications and source records attributed to Ross, T. M..

14 recordsLinked to original sources

bioRxiv2025

Antigenic Mapping of H2 Influenza Viruses recognized by Ferret and Human Sera and Predicting Antigenically Significant Sites

Influenza viruses cause hundreds of thousands of infections globally every year. In the past century, seasonal influenza viruses have included H1N1, H2N2 and H3N2 strains. H2N2 influenza viruses circulated in the human population between 1957-1968. Previously, our group demonstrated a lack of H2N2 influenza virus immunity in individuals born after 1968, as well as the effectiveness of hemagglutinin (HA) based vaccines for multiple influenza virus subtypes. In this study, H2 antigenic maps and radial graphs were generated using previously published data from H2 HA vaccinations of ferrets and seasonal influenza vaccinations of humans. The antigenic maps revealed a stark difference in clustering of HA antigens between the ferrets and humans, and the radial graphs showed specific antigen recognition varies greatly between different influenza preimmune ferrets. These maps also revealed the significant impact that different pre-existing immunities have on antigenic recognition and clustering of antigens after vaccine boost. From these data, we predicted two possible antigenically significant sites containing various mutations that have not been previously reported and showed that one of these sites is relevant using mouse anti-sera. ImportanceH2N2 influenza viruses have caused at least one known pandemic in humans and are poised to cause future pandemics. Investigating the antigenic diversity of H2 HA proteins provides valuable data for designing and understanding the performance of current and future vaccines. Data evaluating the difference in antigen recognition across species and pre-existing immunity can be used to predict antigenically significant sites and evaluate the impact of H1 and H3 infection and immune imprinting on H2 vaccine immunogenicity. This information can direct future studies when both extrapolating animal data to human studies and creating next generation vaccines. Contrasting the relationships between new, contemporary and ancestral H2 HA antigens by antigenic cartography is imperative for identifying new variants of concern and updating vaccine formulations.

microbiology↗

bioRxiv2025

Intranasal administration of split-inactivated influenza virus vaccine mixed with a novel adjuvant elicits protective antibodies against seasonal influenza viruses.

Seasonal influenza remains a persistent global health concern, and despite the availability of vaccines, there are both limitations in vaccine effectiveness and needle-associated hesitancy that reduce vaccine uptake. To address these challenges, this study evaluated the intranasal delivery of Fluzone, a commercially licensed split-inactivated influenza vaccine, formulated with or without adjuvant. Mice were vaccinated intranasally with Fluzone alone or combined with either Infectimune, a cationic lipid nanoparticle adjuvant, or TRAC478, a synthetic dual toll-like receptor liposome adjuvant containing TLR4 and TLR7/8 agonists. In immunologically naive mice, a higher inoculation volume was more effective at eliciting protective antibody responses even though the same dose of vaccine antigen was used for vaccination. Fluzone mixed with adjuvant enhanced hemagglutination-inhibition (HAI) titers and all mice were protected against influenza virus challenge. Mice with pre-existing anti-influenza virus immunity that was elicited by prior infection with historical influenza strains had modest antibody responses and full protection following immunization with unadjuvanted vaccine. However, the inclusion of an adjuvant with Fluzone significantly raised HAI titers and HA- specific IgG levels. Pre-immune mice vaccinated with Fluzone mixed with either adjuvant had low to undetectable viral lung titers following challenge. Overall, intranasally delivered split-inactivated influenza vaccines paired with a mucosal adjuvant is a promising strategy to enhance vaccine effectiveness.

immunology↗

bioRxiv2024

Generation of antigen-specific paired heavy-light chain antibody sequences using large language models

The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize existing antibodies and generate antibody sequences in a target-agnostic manner. In this work, we present MAGE (Monoclonal Antibody GEnerator), a sequence-based Protein Language Model (PLM) fine-tuned for the task of generating paired human variable heavy and light chain antibody sequences against targets of interest. We show that MAGE can generate novel and diverse antibody sequences with experimentally validated binding specificity against SARS-CoV-2, an emerging avian influenza H5N1, and respiratory syncytial virus A (RSV-A). MAGE represents a first-in-class model capable of designing human antibodies against multiple targets with no starting template.

bioinformatics↗

bioRxiv2024

A Single Dose of Inactivated Influenza Virus Vaccine Expressing COBRA Hemagglutinin Elicits Broadly-Reactive and Long-Lasting Protection

Influenza virus infections present a pervasive global health concern resulting in millions of hospitalizations and thousands of fatalities annually. To address the influenza antigenic variation, the computationally optimized broadly reactive antigen (COBRA) methodology was used to design influenza hemagglutinin (HA) or neuraminidase (NA) for universal influenza vaccine candidates. In this study, whole inactivated virus (WIV) or split inactivated virus (SIV) vaccine formulations expressing either the H1 COBRA HA or H3 COBRA HA were formulated with or without an adjuvant and tested in ferrets with pre-existing anti-influenza immunity. A single dose of the COBRA-WIV vaccine elicited a robust and broadly reactive antibody response against H1N1 and H3N2 influenza viruses. In contrast, the COBRA-SIV elicited antibodies that recognized fewer viruses, but with R-DOATP, its specificity was expanded. Vaccinated ferrets were protected against morbidity and mortality following challenge with A/California/07/2009 at 14 weeks post-vaccination with reduced viral shedding post-infection compared to the naive mock-vaccinated ferrets. However, the COBRA-IIVs did not block the viral transmission to naive ferrets. The contact infection induced less severe disease and delayed viral shedding than direct infection. Overall, the COBRA HA WIV or the COBRA HA SIV plus R-DOTAP elicited broadly reactive antibodies with long-term protection against viral challenge and reduced viral transmission following a single dose of vaccine in ferrets pre-immune to historical H1N1 and H3N2 influenza viruses. IMPORTANCEA next-generation influenza virus vaccine aims to provide broadly reactive protection against various drifted influenza strains. COBRA HA-based vaccines elicit broadly-reactive antibodies following two or three vaccinations. However, people are administered a single vaccination of current commercial influenza virus vaccines. In this study, ferrets with pre-existing anti-influenza immunity were administered a single shot COBRA-WIV that elicited long-lasting, broadly-reactive antibodies that protected ferrets against pdmH1N1 viral challenge. This is the first study describing the immune responses elicited by COBRA-IIV vaccines in ferrets that protected ferrets 14 weeks post-vaccination.

immunology↗

bioRxiv2024

Delay of innate immune responses following influenza B virus infection affects the development of robust antibody response in ferrets

Due to its natural influenza susceptibility, clinical signs, transmission, and similar sialic acid residue distribution, the ferret is the primary animal model for human influenza research. Antibodies generated following infection of ferrets with human influenza viruses are used in surveillance to detect antigenic drift and cross-reactivity with vaccine viruses and circulating strains. Inoculation of ferrets, with over 1500 human clinical influenza isolates (1998-2019) resulted in lower antibody responses (HI<1:160) to 86% (387/448) influenza B viruses (IBV) compared to 2.7% (30/1094) influenza A viruses (IAV). In this directed analysis, we show that the immune responses in ferrets inoculated with IBV (B/Victoria or B/Yamagata lineage) were delayed and reduced compared to IAV (A/H1pdm09 or A/H3N2). Analysis of innate gene expression in the ferret upper respiratory tract and peripheral blood indicated that IAV generated a strong inflammatory response, including an early activation of the interferon (IFN) response; whereas IBV elicited a delayed and reduced response. Serum levels of cytokines, chemokines, and IFNs were all much higher following IAV-infection than IBV-infection in ferrets. Pro-Inflammatory (MCP-1, MIP-1B, TNFA), IFN (IFNB, IFNG), TH1/TH2 (IP-10, IL-2), and T-effector (IL-12p40) proteins were significantly higher in sera of IAV-infected than IBV-infected ferrets over twenty-eight days following challenge. Serum levels of Type-I/II/III IFNs were detected following IAV-infection throughout the 28-day period and Type-III IFN was only detected by day 28 for IBV. An early increase in IFN-lambda levels corresponded to gene expression following IAV-infection. Reduced innate immune responses detected following IBV-infection reflected the subsequent delayed and reduced serum antibodies. Differences in serum antibody responses by IBV were not observed in antibody secreting cells in the spleen or peripheral blood. These findings help in understanding the antibody responses in humans following IBV vaccination or infection and consideration of potential addition of innate immunomodulators to overcome low responses. AUTHOR SUMMARYThe ferret is the primary animal model for human influenza research. Using a ferret model, we studied the differences in both innate and adaptive immune responses following infection with influenza A and B viruses. Antibodies generated following infection of ferrets is used for surveillance assays to detect antigenic drift and cross-reactivity with vaccine viruses and circulating influenza strains. Influenza A virus (IAV) infection of ferrets to generate these reagents resulted in a strong antibody response, but Influenza B virus (IBV) infection generated weak antibody responses. In this study using influenza-infected ferrets, we found that IAV resulted in an early activation of the interferon and pro-inflammatory response, whereas IBV showed a delay and reduction in these responses. Serum levels of interferons and other cytokines or chemokines were much higher in ferrets following IAV infection. These reduced innate responses were reflected the subsequent delayed and reduced antibody responses to IBV in the sera. These findings may help in understanding low antibody responses in humans following influenza B vaccination and infection and may warrant the use of innate immunomodulators to overcome these weak responses.

microbiology↗

bioRxiv2022

The effect of waning on antibody levels and memory B cell recall following SARS-CoV-2 infection or vaccination

As of March 2022, there have been over 450 million reported SARS-CoV-2 cases worldwide, and more than 4 billion people have received their primary series of a COVID-19 vaccine. In order to longitudinally track SARS-CoV-2 antibody levels in people after vaccination or infection, a large-scale COVID-19 sero-surveillance progam entitled SPARTA (SeroPrevalence and Respiratory Tract Assessment) was established early in the pandemic. Anti-RBD antibody levels were tracked in more than 1,000 people. There was no significant decrease in antibody levels during the first 14 months after infection in unvaccinated participants, however, significant waning of antibody levels was observed following vaccination, regardless of previous infection status. Moreover, participants who were pre-immune to SARS-CoV-2 prior to vaccination seroconverted to significantly higher antibody levels, and antibodies were maintained at significantly higher levels than in previously infected, unvaccinated participants. This pattern was entirely due to differences in the magnitude of the initial seroconversion event, and the rate of antibody waning was not significantly different based on the pre-immune status. Participants who received a third (booster) dose of an mRNA vaccine not only increased their anti-RBD antibody levels [~]14-fold, but they also had [~]3 times more anti-RBD antibodies compared to the peak of their antibody levels after receiving their primary vaccine series. In order to ascertain whether the presence of serum antibodies is important for long-term seroprotection, PBMCs from 13 participants who lost all detectable circulating antibodies after vaccination or infection were differentiated into memory cells in vitro. There was a significant recall of memory B cells in the absence of serum antibodies in 70% of the vaccinated participants, but not in any of the infected participants. Therefore, there is a strong connection between anti-RBD antibody levels and the effectiveness of memory B cell recall.

immunology↗

bioRxiv2021

The pre-existing human antibody repertoire to computationally optimized influenza H1 hemagglutinin vaccines

The computationally optimized broadly reactive antigen (COBRA) approach has previously been used to generate hemagglutinin (HA) immunogens for several influenza subtypes that expand vaccine-elicited antibody breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA antigens. Cross-reactivity between wild type HA and H1 COBRA HA proteins were observed at both the oligoclonal B cell level and for a subset of isolated monoclonal antibodies (mAbs). The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 head and stem domains, and the majority of the mAbs had HAI and neutralizing activity against pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had HAI and neutralizing activity against a pre-pandemic H1 strain. One mAb, P1-05, targets the stem region of H1 HA proteins, but does not compete with known stem-targeting H1 mAbs. We determined that mAb P1-05 recognizes a recently discovered membrane proximal epitope on HA, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by P1-05. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA- reactive B cells that target head, central stalk, and anchor epitopes, and demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes. SignificanceInfluenza imposes significant human and economic costs every year. The current seasonal vaccine elicits primarily strain-specific antibodies, and year to year vaccine effectiveness is variable. The COBRA approach could provide longer protection and obviate the requirement for annual vaccination. Whereas COBRA HAs have previously been evaluated in animal models, the pre-existing COBRA HA-reactive human B cell population has yet to be elucidated, and is important to identify specific B cells that may be recalled by H1 HA COBRA vaccination. This work demonstrates that seasonally vaccinated individuals possess a functional B cell population targeting both head and stem domains that could be recalled with COBRA HA immunogens.

immunology↗

bioRxiv2021

Formulation of Dry Powders of Vaccines Containing MF59 or AddaVax by Thin-Film Freeze-Drying

Oil-in-water (O/W) nanoemulsion-based vaccine adjuvants such as MF59(R) are often used in seasonal and pandemic influenza vaccines. However, vaccines containing nanoemulsions require cold chain for storage and are sensitive to accidental freezing. We explored the feasibility of developing dry powders of vaccines adjuvanted with MF59 or AddaVax, a preclinical grade nanoemulsion that has the same composition and droplet size as MF59, by thin-film freeze-drying (TFFD). AddaVax alone was successfully converted from a liquid to dry powders by TFFD using trehalose as a stabilizing agent while maintaining the droplet size distribution of the AddaVax when reconstituted, whereas subjecting the same AddaVax composition to conventional shelf freeze-drying led to significant aggregation or fusion. TFFD was then applied to convert liquid AddaVax-adjuvanted vaccines containing either model antigens such as ovalbumin and lysozyme, mono-, bi-, and tri-valent recombinant hemagglutinin (rHA) protein-based H1 and/or H3 (universal) influenza vaccine candidates, as well as the MF59-containing Fluad(R) Quadrivalent influenza vaccine to dry powders. Antigens, stabilizing agents, and buffer showed different effects on the physical properties of the vaccines (e.g., mean particle size and particle size distribution) after subjected to TFFD, but the integrity and hemagglutination activity of the rHA antigens did not significantly change and the immunogenicity of reconstituted influenza vaccine candidates was preserved when evaluated in BALB/c mice. The vaccine dry powder was not sensititve to repeated freezing-and-thawing, in contrast to its liquid counterpart. It is concluded that TFFD can be applied to convert vaccines containing MF59 or an nanoemulsion with the same composition and droplet size as MF59 from liquid to dry powders while maintaining the immunogencity of the vaccines, and it may be used to prepare dry powders of multivalent universal influenza vaccines.

pharmacology and toxicology↗

bioRxiv2021

Functional characterization of SARS-CoV-2 vaccine elicited antibodies in immunologically naive and pre-immune humans

As the COVID-19 pandemic continues, the authorization of vaccines for emergency use has been crucial in slowing down the rate of infection and transmission of the SARS-CoV-2 virus that causes COVID-19. In order to investigate the longitudinal serological responses to SARS-CoV-2 natural infection and vaccination, a large-scale, multi-year serosurveillance program entitled SPARTA (SARS SeroPrevalence and Respiratory Tract Assessment) was initiated at 4 locations in the U.S. The serological assay presented here measuring IgG binding to the SARS-CoV-2 receptor binding domain (RBD) detected antibodies elicited by SARS-CoV-2 infection or vaccination with a 95.5% sensitivity and a 95.9% specificity. We used this assay to screen more than 3100 participants and selected 20 previously infected pre-immune and 32 immunologically naive participants to analyze their antibody binding to RBD and viral neutralization (VN) responses following vaccination with two doses of either the Pfizer-BioNTech BNT162b2 or the Moderna mRNA-1273 vaccine. Vaccination not only elicited a more robust immune reaction than natural infection, but the level of neutralizing and anti-RBD antibody binding after vaccination is also significantly higher in pre-immune participants compared to immunologically naive participants (p<0.0033). Furthermore, the administration of the second vaccination did not further increase the neutralizing or binding antibody levels in pre-immune participants (p=0.69). However, ~46% of the immunologically naive participants required both vaccinations to seroconvert.

immunology↗

bioRxiv2021

Sex disparities in influenza: a multiscale network analysis

Sex differences in the pathogenesis of infectious diseases due to differential immune responses between females and males have been well documented for multiple pathogens. However, the molecular mechanism underlying the observed sex differences in influenza virus infection remains poorly understood. In this study, we used a network-based approach to characterize the blood transcriptome collected over the course of infection with influenza A virus from female and male ferrets to dissect sex-biased gene expression. We identified significant differences in the temporal dynamics and regulation of immune responses between females and males. Our results elucidate sex-differentiated pathways involved in the unfolded protein response (UPR), lipid metabolism, and inflammatory responses, including a female-biased IRE1/XBP1 activation and male-biased crosstalk between metabolic reprogramming and IL-1 and AP-1 pathways. Overall, our study provides molecular insights into sex differences in transcriptional regulation of immune responses and contributes to a better understanding of sex bias in influenza pathogenesis.

systems biology↗

bioRxiv2021

Broadly Reactive H2 Hemagglutinin Vaccines Elicit Cross-Reactive Antibodies in Ferrets Pre-Immune to Seasonal Influenza A Viruses

Influenza vaccines have traditionally been tested in naive mice and ferrets. However, humans are first exposed to influenza viruses within the first few years of their lives. Therefore, there is a pressing need to test influenza virus vaccines in animal models that have been previously exposed to influenza viruses before being vaccinated. In this manuscript, previously described H2 computationally optimized broadly reactive antigen (COBRA) HA vaccines (Z1, Z5) were tested in influenza virus pre-immune ferret models. Ferrets were infected with historical, seasonal influenza viruses to establish pre-immunity. These pre-immune ferrets were then vaccinated with either COBRA H2 HA recombinant proteins or WT H2 HA recombinant proteins in a prime-boost regimen. A set of naive pre-immune or non pre-immune ferrets were also vaccinated to control of the effects of the multiple different pre-immunities. All of the ferrets were then challenged with a swine H2N3 influenza virus. Ferrets with pre-existing immune responses influenced recombinant H2 HA elicited antibodies following vaccination as measured by HAI and classical neutralization assays. Having both H3N2 and H1N1 immunological memory regardless of the order of exposure significantly decreased viral nasal wash titers and completely protected all ferrets from both morbidity and mortality, including the mock vaccinated ferrets in the group. While the vast majority of the pre-immune ferrets were protected from both morbidity and mortality across all of the different pre-immunities, the Z1 COBRA HA vaccinated ferrets had significantly higher antibody titers and recognized the highest number H2 influenza viruses in a classical neutralization assay compared to the other H2 HA vaccines. ImportanceH1N1 and H3N2 influenza viruses have co-circulated in the human population since 1977. Nearly every human alive today has antibodies and memory B and T cells against these two subtypes of influenza viruses. H2N2 influenza viruses caused the 1957 global pandemic and people born after 1968 have never been exposed to H2 influenza viruses. It is quite likely that a future H2 influenza virus could transmit within the human population and start a new global pandemic, since the majority of people alive today are immunologically naive to viruses of this subtype. Therefore, an effective vaccine for H2 influenza viruses should be tested in an animal model with previous exposure to influenza viruses that have circulated in humans. Ferrets were infected with historical influenza A viruses to more accurately mimic the immune responses in people who have pre-existing immune responses to seasonal influenza viruses. In this study, pre-immune ferrets were vaccinated with WT and COBRA H2 recombinant HA proteins in order to examine the effects of pre-existing immunity to seasonal human influenza viruses have on the elicitation of broadly cross-reactive antibodies from heterologous vaccination.

immunology↗

bioRxiv2021

Hemagglutination Inhibition (HAI) Antibody Landscapes after Vaccination with diverse H7 hemagglutinin (HA) proteins

BackgroundA systemic evaluation of the antigenic differences of the H7 influenza hemagglutinin (HA) proteins, especially for the viruses isolated after 2016, are limited. The purpose of this study was to investigate the antigenic differences of major H7 strains with an ultimate aim to discover H7 HA proteins that can elicit protective receptor-blocking antibodies against co-circulating H7 influenza strains. MethodA panel of nine H7 influenza strains were selected from 3,633 H7 HA amino acid sequences identified over the past two decades (2000-2018). The sequences were expressed on the surface of virus like particles (VLPs) and used to vaccinate C57BL/6 mice. Serum samples were collected and tested for hemagglutination-inhibition (HAI) activity. The vaccinated mice were challenged with lethal dose of H7N9 virus, A/Anhui/1/2013. ResultsVLPs expressing the H7 HA antigens elicited broadly reactive antibodies each of the selected H7 HAs, except the A/Turkey/Italy/589/2000 (Italy/00) H7 HA. A putative glycosylation due to an A169T substitution in antigenic site B was identified as a unique antigenic profile of Italy/00. Introduction of the putative glycosylation site (H7 HA-A169T) significantly altered the antigenic profile of HA of the A/Anhui/1/2013 (H7N9) strain. ConclusionThis study identified key amino acid mutations that result in severe vaccine mismatches for future H7 epidemics. Future universal influenza vaccine candidates will need to focus on viral variants with these key mutations.

immunology↗

bioRxiv2020

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection

SARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of action in vivo is incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Thus, potently neutralizing mAbs require Fc effector functions for maximal therapeutic benefit during therapy to modulate protective immune responses and mitigate lung disease.

immunology↗

bioRxiv2019

High-resolution proteomics identifies potential new markers of Zika and dengue infections

Distinguishing between Zika and dengue virus infections is critical for treatment and anticipation of complications. However, existing biomarkers have high error rates. To identify new potential diagnostic signatures, we used next-generation proteomics to profile 122 serum samples from 62 Zika or dengue patients. We quantified >500 proteins and identified 26 proteins that were significantly differentially expressed. These proteins typically function in infection and wound healing, with several also linked to pregnancy and brain. Integrating machine learning approaches, we used 7 proteins to predict ZIKV infection correctly in 72% of the cases, outperforming other tools. The three most predictive proteins were Platelet Factor 4 Variant 1, Fibrinogen Alpha, and Gelsolin. Finally, we showed that temporal changes in protein signatures from the same patient can disambiguate some diagnoses and serve as indicators for past infections. Taken together, we demonstrate that serum proteomics can be highly valuable to diagnose even challenging samples.

systems biology↗