Vanessa Herder

Bhanja virus (BHAV) is a tick-borne bandavirus (Family Phenuiviridae) with a broad geographic distribution and documented neuroinvasive capacity, yet its molecular biology remains poorly understood. Within the genus Bandavirus, the non-structural protein NSs functions as the primary antagonist of innate immune responses, although mechanistic details for BHAV remain unknown. We established a reverse genetics platform for BHAV by combining virion RNA sequencing with terminal untranslated region mapping, enabling generation of recombinant viruses and systematic investigation of viral determinants. Using this system, we characterized recombinant BHAV replication in mammalian and arthropod cell lines and demonstrated that interferon competence is a critical determinant of viral replication in mammalian cells. Notably, we observed substantial amino acid divergence within the NSs protein across geographically distinct BHAV isolates, despite higher conservation of other viral proteins. To investigate the functional significance of this variation, we generated recombinant viruses expressing heterologous NSs proteins from African and European isolates. Viruses expressing NSs from ibAr2709 or R1819 isolates exhibited enhanced capacity to suppress interferon-beta induction compared to the prototype IG690 strain, correlating with increased viral protein accumulation in interferon-competent cells. Mechanistic studies revealed that BHAV NSs proteins inhibit interferon induction upstream of IRF3, with ibAr2709 and R1819 NSs showing selective inhibition of TBK1 phosphorylation. However, unlike highly pathogenic bandaviruses such as severe fever with thrombocytopenia syndrome virus (SFTSV), BHAV NSs proteins exhibit comparatively weak antagonism of downstream interferon signalling. In vivo studies using interferon alpha/beta receptor-deficient mice demonstrated that NSs sequence variation influences viral replication in splenic tissue without substantially altering disease phenotype. Together, these findings establish BHAV reverse genetics tools for future investigation and reveal how naturally-occurring NSs divergence modulates innate immune antagonism and viral fitness while maintaining an overall attenuated disease phenotype.

Coronaviruses genomes are enriched in suboptimal A- and U-ending codons, which are typically associated with reduced translation efficiency due to limited cognate tRNA availability. How coronavirus efficiently express their proteins despite this limitation remains unclear. By analyzing their codon usage, we identify four tRNA modifications—inosine (I), queuosine (Q), 5-methylcarboxymethyluridine/ 5-methylcarboxymethyl-2-thiouridine (mcm ⁵ U/mcm ⁵ s ² U), and 5-methylcytidine/ 5-formylcytidine (m ⁵ C/f ⁵ C)—as essential for decoding their suboptimal codons. Notably, SARS-CoV-2 and HCoV-OC43 infections, representing severe and mild human infections, respectively, reprogram these modifications to favor viral protein synthesis. Mechanistically, this reprogramming was driven by altered expression of the corresponding tRNA modifying enzymes. Since both viruses induced DNA damage and oxidative stress—known to similarly alter Q, mcm ⁵ U/mcm ⁵ s ² U, and m ⁵ C/f ⁵ C modifications to favor expression of stress response proteins—our findings support that coronavirus genomes have adapted to the tRNA modification landscape under stress conditions. Overall, coronaviruses orchestrate a codon-specific reprogramming of the host tRNA modification landscape, highlighting a conserved strategy that optimizes translation efficiency and represents a promising target for pan-coronavirus antiviral therapy development.

Adeno-associated viruses (AAVs) are common vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector–human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.

Avian influenza H5N1 clade 2.3.4.4b viruses caused a global panzootic and, unexpectedly, widespread outbreaks in dairy cattle, therefore representing a pandemic threat. To inform control strategies, it is critical to determine whether the potential to adapt to bovine cells is a general feature of H5N1 viruses, is specific to viruses of clade 2.3.4.4b, or narrowly restricted to some genotypes within this clade. Using a large panel of recombinant viruses representing >60 years of H5N1 history and other IAVs for comparison, we demonstrate replicative fitness in bovine cells is: (i) highly variable across 2.3.4.4b genotypes, (ii) limited in viruses predating the global expansion of this clade, (iii) determined by the internal gene cassette, and (iv) not restricted to udder epithelial cells. Mutations in the PB2 polymerase subunit emerge as key determinants of adaptation, although their phenotypic effects are context dependent. Bovine B3.13 and some avian genotypes exhibit enhanced modulation of bovine interferon-induced antiviral responses, determined by at least PB2, nucleoprotein, and the non-structural protein NS1. Our results highlight the polygenic nature of IAV host range, and reveal that the replication fitness in bovine cells, and likely their potential to adapt to cattle, varies greatly during the evolutionary trajectory of H5N1 viruses.

Lung structural cells form barriers against pathogens and trigger immune responses following infections. This leads to the recruitment of innate and adaptive immune cells some of which remain within the lung and contribute to enhanced pathogen control following subsequent infections. There is growing evidence that structural cells also display long-term changes following infection. Here we investigate long-term changes to mouse lung epithelial cells, fibroblasts, and endothelial cells following influenza virus infection finding that all three cell types maintain an imprint of the infection, particularly in genes linked to communication with T cells. MHCI and MHCII proteins continue to be expressed at higher levels in both differentiated epithelial cells and progenitor populations and several differentially expressed genes are downstream of the transcription factor, SpiB, a known orchestrator of antigen presentation. Lung epithelial cells from influenza-infected mice display functional changes, more rapidly controlling influenza virus than cells from naïve animals. This rapid anti-viral response and increased expression of molecules required to communicate with T cells demonstrates sustained and enhanced functions following infection. These data suggest lung structural cells display characteristics of immune memory which could affect outcomes that are protective in the context of infection or pathogenic in chronic inflammatory disorders.

Natural language processing (NLP), a branch of artificial intelligence that focuses on the interaction between computers and human language, has potential in advancing veterinary pathology through its ability to source knowledge efficiently from vast data sets, generate high-quality text rapidly, and enhance data searchability. This review explores the applications of NLP in veterinary pathology, emphasizing its potential role in diagnostics, training pathologists, and research. NLP might offer many advantages, such as accuracy, speed, and cost reduction, especially for routine tasks including text summarization and report generation. These benefits make NLP a promising technology for achieving precision, adding value, and driving innovation in health care. However, caution is warranted, as NLP models may introduce biases and errors due to the quality of the data they are trained on, have limitations in interpreting nuanced or context-specific information, and lead to private data leakage. Furthermore, the multifaceted nature of veterinary pathology data may require specifically trained and expert-validated algorithms for accurate interpretation. To ensure the credibility and validity of research findings, pathologists must critically evaluate and complement obtained outputs with human expertise and judgment. This article highlights the transformative potential of NLP in veterinary pathology, underscores the importance of integrating this technology into the field for enhanced diagnostic accuracy and research advancements, and gives real-life examples from pathologists for pathologists, which illustrate how NLP can be applied in veterinary pathology.

SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform. Here we generated a panel of recombinant viruses carrying different spike proteins from 27 variants circulating between 2020 and 2024 in the same genomic background. We then assessed several of their phenotypic traits both in vitro and in vivo. We found distinct phenotypic trajectories of spike among and between variants circulating before and after the emergence of Omicron variants. Spike of post-Omicron variants maintained enhanced tropism for the nasal epithelium and large airways but displayed, over time, several phenotypic traits typical of the pre-Omicron variants. Hence, spike with phenotypic features of both pre- and post-Omicron variants may continue to emerge in the future.

Postmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTDs), including coronavirus disease 2019 (COVID-19), but there are minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. In this study, we used histology and high-dimensional imaging to characterize fatal lung disease in Malawian adults with (n = 9) and without (n = 7) COVID-19, and we generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved COVID-19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in US, European and Asian cohorts, by type I/III interferon (IFN) responses, particularly in blood-derived monocytes, and in the Malawian cohort, by response to IFN-γ in lung-resident macrophages. HIV status had minimal impact on histology or immunopathology. Our study provides a data resource and highlights the importance of studying the cellular mechanisms of disease in underrepresented populations, indicating shared and distinct targets for treatment.

COVID-19 is characterized by a broad range of symptoms and disease trajectories. Understanding the correlation between clinical biomarkers and lung pathology during acute COVID-19 is necessary to understand its diverse pathogenesis and inform more effective treatments. Here, we present an integrated analysis of longitudinal clinical parameters, peripheral blood markers, and lung pathology in 142 Brazilian patients hospitalized with COVID-19. We identified core clinical and peripheral blood signatures differentiating disease progression between patients who recovered from severe disease compared with those who succumbed to the disease. Signatures were heterogeneous among fatal cases yet clustered into two patient groups: “early death” (15 days). Progression to early death was characterized systemically and in lung histopathological samples by rapid endothelial and myeloid activation and the presence of thrombi associated with SARS-CoV-2 ⁺ macrophages. In contrast, progression to late death was associated with fibrosis, apoptosis, and SARS-CoV-2 ⁺ epithelial cells in postmortem lung tissue. In late death cases, cytotoxicity, interferon, and T helper 17 (T _H 17) signatures were only detectable in the peripheral blood after 2 weeks of hospitalization. Progression to recovery was associated with higher lymphocyte counts, T _H 2 responses, and anti-inflammatory–mediated responses. By integrating antemortem longitudinal blood signatures and spatial single-cell lung signatures from postmortem lung samples, we defined clinical parameters that could be used to help predict COVID-19 outcomes.