Medawar Building for Pathogen Research

For individuals with hepatitis B virus (HBV), hepatitis B surface antigen (HBsAg) loss is associated with substantially decreased risk of liver-related morbidity and mortality. In recent years, many determinants of HBsAg loss have been investigated in several studies involving persons with chronic HBV infection living with and without HIV. The purpose of this review is to summarize factors that could help predict HBsAg loss in persons with HIV (PWH). Rates of HBsAg loss can be higher in PWH with HBV compared to those without HIV, which has been partially attributed to immune reconstitution after starting antiretroviral therapy. In recent years, quantitative HBsAg (qHBsAg) levels were identified as the most important single serum marker predicting HBsAg loss. Other viral markers, such as hepatitis B core-related antigen, circulating HBV RNA, and immunological markers (i.e., quantitative hepatitis B core antibody, assessment of HBV-specific immune responses, peripheral blood mononuclear cells phenotypes), might also help predict HBsAg loss in PWH with HBV, particularly for certain sub-populations. Low qHBsAg before or fast qHBsAg declines after initiating potent anti-HBV therapy has been identified as the most reliable predicting serum marker. Other markers might be useful in certain sub-populations and clinical situations.

We provide an overview of Monte Carlo algorithms based on Markovian stochastic dynamics of interacting and reacting many-particle systems not in thermal equilibrium. These agent-based simulations are an effective way of introducing students to current research without requiring much prior knowledge or experience. By starting from the direct visualization of the data, students can gain immediate insight into emerging macroscopic features of a complex system and subsequently apply more sophisticated data analysis to quantitatively characterize its rich dynamical properties, both in the stationary and transient regimes. We utilize simulations of reaction–diffusion systems, stochastic models for population dynamics and epidemic spreading, to exemplify how interdisciplinary computational research can be effectively utilized in bottom-up undergraduate and graduate education through learning by doing. We also give helpful hints for the practical implementation of Monte Carlo algorithms, provide sample codes, explain some typical data analysis tools, and describe various potential error sources, pitfalls, and tips for avoiding them.

Abstract COVID-19 vaccines were updated to address immune escape from variants of concern (VOC). We explored the impact of ancestral/BA.1 bivalent mRNA booster vaccination (Autumn 2022) on peripheral and nasal antibody and T-cell responses to SARS-CoV-2 in 133 healthcare workers, building on previous longitudinal vaccination studies. We demonstrate that maintenance of antibody and T-cell responses up to eighteen months following the third vaccine is at least partially driven by intercurrent infection. Boosting with the bivalent vaccine increases the breadth of circulating and nasal antibodies to spike, which waned over time but was still detectable six months post-dose. T-cell responses are well maintained and highly cross-reactive to VOCs irrespective of booster vaccination. Vaccination strongly boosted nasal IgG, but this was short-lived compared to circulating antibodies. Overall, ongoing COVID-19 vaccination provides benefit, boosting immunity in individuals who have not been recently infected, but new strategies may be needed to provide longer-term nasal immunity.

Filopodia, microspikes and cytonemes are implicated in sensing the environment and in dissemination of morphogens, organelles and pathogens across tissues. Their major structural component is parallel bundles of actin filaments that assemble from the cell membrane. Whilst the length of filopodia is central to their function, it is not known how their lengths are determined by actin bundle dynamics. Here, we identified a set of monoclonal antibodies that lengthen filopodia-like structures formed in a cell-free reconstitution system, and used them to uncover a key molecular switch governing length regulation. Using immunolabelling, enzyme-linked immunosorbent assays, immunoprecipitation and immunoblock experiments, we identified four antibodies that lengthen actin bundles by selectively binding the open DNase 1-binding loop (D-loop) of actin filaments. The antibodies inhibit actin disassembly and their effects can be alleviated by providing additional actin or cofilin. This work indicates that maintaining an open state of the actin filament D-loop is a mechanism of generating long filopodia-like actin bundles.

CD4+ T cells have been established as central orchestrators of cellular and humoral immune responses to infection or vaccination. However, the need for CD4+ T cell help to generate primary CD8+ T cell responses is variable depending on the infectious agent or vaccine and yet consistently required for the recall of CD8+ T cell memory responses or antibody responses. Given the deployment of new vaccine platforms such as nucleoside-modified mRNA vaccines, we sought to elucidate the requirement for CD4+ T cell help in the induction of cellular and antibody responses to mRNA and adenovirus (Ad)-vectored vaccines against SARS-CoV-2. Using antibody-mediated depletion of CD4+ T cells in a mouse immunization model, we observed that CD4+ T cell help was dispensable for both primary and secondary CD8+ T cell responses to the BNT162b2 and mRNA-1273 mRNA vaccines but required for the AZD1222 Ad-vectored vaccine. Nonetheless, CD4+ T cell help was needed by both mRNA and Ad-vectored vaccine platforms for the generation of antibodies, demonstrating the centrality of CD4+ T cells in vaccine-induced protective immunity against SARS-CoV-2. Ultimately, this highlights the shared and distinct regulation of humoral and cellular responses induced by these vaccine platforms.

Abstract Analysis of viral genetic data has previously revealed distinct within-host population structures in both untreated and interferon-treated chronic hepatitis C virus (HCV) infections. While multiple subpopulations persisted during the infection, each subpopulation was observed only intermittently. However, it was unknown whether similar patterns were also present after Direct Acting Antiviral (DAA) treatment, where viral populations were often assumed to go through narrow bottlenecks. Here we tested for the maintenance of population structure after DAA treatment failure. We analysed whole-genome next-generation sequencing data generated from a randomised study using DAAs (the BOSON study). We focused on samples collected from patients (N=84) who did not achieve sustained virological response (i.e. treatment failure) and had sequenced virus from multiple timepoints. For each individual, we tracked concordance in nucleotide variant frequencies through time. Using a sliding window approach, we applied sequenced-based and tree-based clustering algorithms across the entire HCV genome. Finally, we reconstructed viral haplotypes and estimated lineage specific within-host divergence rates from the haplotype phylogenies. Distinct viral subpopulations were maintained among a high proportion of individuals post DAA treatment failure. Using maximum likelihood modelling and model comparison, we found an overdispersion of viral evolutionary rates among individuals, and significant differences in evolutionary rates between lineages within individuals. These results suggest the virus is compartmentalised within individuals, with the varying evolutionary rates due to different viral replication rates or different selection pressures. We propose lineage awareness in future analyses of HCV evolution and infections to avoid conflating patterns from distinct lineages, and to recognise the likely existence of unsampled subpopulations.

Abstract Membrane-binding adaptor protein Sorting nexin 9 (SNX9) contributes to viral uptake and inflammation and is associated with worse outcomes in several cancers. It is involved in endocytosis of epidermal growth factor receptors, β1-integrin and membrane type 1 matrix metalloprotease and in mitochondrial-derived vesicles. Its BAR-PX domain binds phosphatidylinositol phosphates (PIPs) and its SH3 domain interacts with dynamin and N-WASP to stimulate Arp2/3 complex actin polymerization during vesicle scission. Recent complexities have arisen in SNX9’s lipid specificity and its involvement both endocytic and filopodial membrane topologies. Here we use biolayer interferometry, cell-free reconstitution and superresolution microscopy to analyse the activities of SNX9. We find that more SNX9 binds membranes that contain PI(4,5)P2 and PI(3)P compared with PI(3,4)P2, despite having similar affinity, suggesting SNX9 can assemble into different macromolecular arrangements depending on the composition. Actin assembly requires the wider protein and lipid network provided by PX-BAR and SH3 interactions. 3D direct stochastic optical reconstruction microscopy on filopodia-like reconstitutions shows that SNX9 and related protein Transducer of Cdc42 activation-1 (TOCA-1) are competent to form both tubular and plaque-like organizations with the actin machinery. Finally, using cryo-electron tomography we show that SNX9 assembles both branched and bundled actin filaments demonstrating its multifunctional nature.

The One Health approach, which integrates the health of humans, animals, plants, and ecosystems at various levels, is crucial for addressing interconnected health threats. This is complemented by the advent of mRNA vaccines, which have revolutionized disease prevention. They offer broad-spectrum effectiveness and can be rapidly customized to target specific pathogens. Their utility extends beyond human medicine, showing potential in veterinary practices to control diseases and reduce the risk of zoonotic transmissions. This review place mRNA vaccines and One Health in the context of tick-borne diseases. The potential of these vaccines to confer cross-species immunity is significant, potentially disrupting zoonotic disease transmission cycles and protecting the health of both humans and animals, while reducing tick populations, infestations and circulation of pathogens. The development and application of mRNA vaccines for tick and tick-borne pathogens represent a comprehensive strategy in global health, fostering a healthier ecosystem for all species in our interconnected world.

The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called ‘FLip’ mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.