Rift Valley fever virus (RVFV) poses a continued threat to human health and animal husbandry. Two neutralizing and protective human monoclonal antibodies (mAbs), RVFV-268 and RVFV-379, exhibit similar affinities and epitope footprints on the Gn glycoprotein component of the RVFV Gn-Gc capsomeric lattice. Here, we define fine details of the biophysical determinants of Gn recognition used by RVFV human monoclonal antibodies through studying an antibody encoded by a set of recombined genes not previously identified in RVFV antibodies. We find that RVFV-379 exhibits a larger footprint than that observed for RVFV-268 and other antibodies targeting the same region, which involves major contributions of both the light and heavy chains. RVFV-379 also uses an oblique angle of approach towards the virion surface that contrasts with the perpendicular angle of engagement observed for some other potently neutralizing human mAbs. Further, consistent with amino acid sequence variation within and proximal to the RVFV-379 epitope, in vitro neutralization screening reveals a limited degree of neutralization breadth across prevalent RVFV strains, suggesting that RVFV has fewer functional constraints at this region of the virus envelope. By dissecting the molecular determinants of mAb recognition of Gn, this integrated analysis refines strategies needed for the rational design of vaccines that can elicit a potent and species-wide protective antibody immune response to this important re-emerging pathogen.

The first workshop dedicated to Lassa virus–specific correlates of protection (CoP) was held in 2024 and was convened by the Coalition for Epidemic Preparedness Innovations (CEPI). Experts from multiple disciplines reviewed existing knowledge and identified gaps in understanding Lassa virus- and vaccine-induced immune responses. Discussions covered key areas including epidemiology, immunogenicity, preclinical and clinical research, data science, and regulatory considerations, with the goal of pinpointing opportunities to discover CoP.

Ebola virus disease (EVD) is characterized by immune dysregulation and damaging hyperinflammation. We aimed to characterize the signaling pathways and regulatory mechanisms dysregulated during EVD. To avoid hyperinflammation, innate immune signaling is regulated by post-translational modifications (PTMs), including protein phosphorylation. Here, we show that the protein tyrosine phosphatase nonreceptor type 13 (PTPN13) negatively regulates Interferon (IFN)-β while also positively regulating the neutrophil chemoattractant CXCL1. Using vectors encoding IRF3 with mutations on phosphorylation sites, we identified Y292 on IRF3 as a PTPN13 target of dephosphorylation. Knockout of PTPN13 increased IRF3 phosphorylation and expression of IFNβ and IFN-stimulated genes (ISGs) following poly(I:C) stimulation. Intriguingly, depletion of PTPN13 during Ebola virus (EBOV) infection resulted in decreased IFNβ and ISG induction at later time points post-infection, which correlated with increased viral titers. We identified PTPN13-mediated dephosphorylation of the viral protein VP35 as one potential mechanism inhibiting virus replication. Additionally, the induction of inflammatory chemokines, including CXCL1, decreased in PTPN13 knockout cells late during EBOV infection. These effects could be explained by increased phosphorylation of the regulatory p85 subunit of PI3K. Dephosphorylation of p85 promotes its degradation, subsequently enhancing PI3K kinase activity and downstream signaling via AKT. Together, our study suggests that PTPN13 is involved in immune regulation and efficient antiviral responses by dephosphorylation of IRF3, EBOV-VP35 and PI3K-p85.

Antibody-dependent enhancement (ADE) of infection is a well-described phenomenon for several viruses, including dengue, Ebola, respiratory syncytial virus, and HIV. ADE occurs when virus-antibody complexes engage Fc receptors (FcRs) and virus-specific receptors, enhancing infection under conditions of incomplete neutralization. The Coronavirus Immunotherapeutic Consortium (CoVIC) assembled a comprehensive dataset of functional properties for over 400 mAbs, enabling direct comparison of neutralization, Fc-mediated functions, receptor binding, and infection of immune cells. Infection rates in most primary human immune cell types were low, with modest increases observed for some mAbs. In contrast, macrophages were more susceptible to SARS-CoV-2 and exhibited substantial ADE with select mAbs. ADE was completely inhibited by FcR blockade and significantly reduced by antibody-or ceftazidime-mediated blocking of angiotensin-converting enzyme 2 (ACE2). Neutralization potency did not correlate with ADE, as both strongly and weakly neutralizing antibodies induced enhancement. Instead, ADE magnitude depended on an antibody's ability to block spike protein binding to ACE2. Importantly, ADE resulted in productive infection with release of infectious virus. Evaluation of antibodies against the BA.1 (Omicron) variant revealed reduced or lost ADE for most mAbs, with increased ADE observed for several mAbs relative to the USA-WA1/2020 strain.

Several SARS-CoV-2 proteins have been shown to counteract the host innate immune response, mostly using in vitro protein expression, which may not fully reflect their role in the context of viral infection. In addition, while each viral protein was characterized in a different experimental system, its relative contribution to immunosuppression remains unclear. Here we used a SARS-CoV-2 bacterial artificial chromosome with en passant mutagenesis to recover a panel of 12 infectious recombinant SARS-CoV-2 viruses, each with mutations in either NSP1, NSP2, NSP3, NSP6, NSP12, NSP13, NSP14, NSP15, NSP16, ORF3a, ORF6, or ORF8. We used the interferon-stimulated response element (ISRE)-driven luciferase assay in 293T-ACE2/TMPRSS2 cells to test the panel, demonstrating that mutations in many proteins, especially in NSP1 and NSP15, increased the type I interferon response relative to the parental wild-type virus. RNA-seq analysis of mutant-virus infected Calu-3 cells showed that the mutations in NSP1 or NSP15 lead to higher expression of multiple genes involved in innate immune response, cytokine-mediated signaling, and regulation of lymphocyte proliferation. Furthermore, mutations in either NSP1 or NSP15 resulted in a greater maturation of human monocyte-derived dendritic cells in vitro. Infection of K18 hACE2 transgenic mice with either NSP1 or NSP15 mutated viruses demonstrated attenuated respiratory tract replication. Analysis of lung immune cells from infected mice by single-cell RNA-seq identified 15 populations of major myeloid and lymphoid cells with changes in the pattern of their activation associated with viral infection. The effects of mutations in NSP1 or NSP15 on these responses are consistent with differences in the immunosuppressive mechanisms utilized by the two proteins. Overall, these data demonstrate different and redundant mechanisms of innate immune antagonism by SARS-CoV-2 and suppression of activation of antigen-presenting cells and T and B lymphocytes mediated by multiple viral proteins.

ABSTRACT Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) nonstructural protein 1 (Nsp1) dampens the host immune response by shutting off host gene expression, a strategy that has remained evolutionary conserved among a diverse range of coronaviruses (CoVs). Residues important for SARS-CoV-2 Nsp1 mediated host shutoff have been incompletely defined. We have generated and characterized the ability of four Nsp1 mutants to inhibit host gene expression in both plasmid-based overexpression assays and utilized reverse genetic approaches to generate recombinant (r)SARS-CoV-2 expressing each Nsp1 mutant to investigate their impact on viral infection. Infection of K18-hACE2 transgenic mice with the rSARS-CoV-2 Nsp1 mutants resulted in reduced pathogenicity as determined by body weight maintenance and survival, attenuated viral replication in lung and nasal turbinate, distinct immune signatures in lung, and less severe lung pathology in comparison to wild-type (WT) virus-infected mice. Our data suggests amino acid residues in the C-terminal domain, in addition to the linker domain, of SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity as a result of their role in disrupting host gene expression. The reduced pathogenicity of rSARS-CoV-2 Nsp1 mutants highlights the potential for targeting Nsp1 for rational design of viral inhibitors and development of live-attenuated vaccine strategies as effective prophylactic and therapeutic treatments, respectively, to combat SARS-CoV-2 and possibly other CoV infections. IMPORTANCE To mitigate the ongoing public health threat posed by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) and prepare for future coronavirus (CoV) outbreaks, there is an urgent need for effective prophylactic and therapeutic strategies, including vaccines and antivirals. The nonstructural protein 1 (Nsp1) is a conserved CoV virulence factor that suppresses host gene expression and disrupts immune responses. However, the contribution of specific Nsp1 residues to CoV pathogenesis remains unclear. Here, we identify residues within the C-terminal and linker regions of Nsp1 as critical determinants of SARS-CoV-2 pathogenicity in vivo . These findings advance our understanding of CoV host shutoff mechanisms and support Nsp1 as a promising target for the development of live-attenuated vaccines and antiviral therapeutics.

In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.

The first-ever recent Marburg virus (MARV) outbreak in Tanzania and recent emergences in Rwanda, Ghana and Equatorial Guinea underscore the importance of therapeutic or vaccine development against the virus, for which none are approved. mRNA vaccines were proven successful in a pandemic-response to severe acute respiratory syndrome coronavirus-2, making it an appealing platform to target pathogenic emerging viruses. Here, we develop 1-methyl-pseudouridine-modified mRNA vaccines formulated in lipid nanoparticles (LNP) targeting the glycoproteins (GP) of MARV and the closely-related Ravn virus (RAVV). Vaccination of female guinea pigs elicits robust binding and neutralizing antibodies and confers complete protection against homologous and heterologous virus replication, disease and death. Characterization of antibody responses identifies disparities in the binding and functional profiles between the two viruses and regions in GP that are broadly reactive. The glycan cap is highlighted as an immunoreactive site for orthomarburgviruses, inducing antibody responses that are virus dependent. Profiling the antibody responses against the two viruses provides insight into how antigenic differences may affect the response towards conserved GP regions, which would otherwise be predicted to be cross-reactive, and has implications for the future design of broadly protective vaccines. The results support the use of mRNA-LNPs against pathogens of high consequence.

Ebola virus (EBOV) causes a severe human disease with high lethality. Pathogenesis of EBOV disease is characterized by a paradoxical combination of hyperinflammation and immunosuppression. EBOV has a single envelope glycoprotein (GP), which is a type I transmembrane protein with strong immunomodulatory effects. GP contains a conserved immunosuppressive domain (ISD) with a high similarity to ISDs of envelope proteins retroviruses. To investigate the effects of ISD, a set of 17 EBOV viral-like particle (VLP) constructs containing the entire EBOV nucleoprotein, VP40, and GP with single alanine or glycine substitutions in each position of ISD was generated and tested in human peripheral blood mononuclear cells (PBMCs). Wild-type VLPs induced inflammatory responses; however, when added to pre-stimulated cells, they reduced inflammation, thus exerting immunosuppressive properties. Substitution of lysine at ISD position 5 (Lys-5) increased anti-inflammatory properties by reducing proliferative responses of VLPs and also reducing nuclear factor of activated T-cells 1 (NFAT1) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation. In contrast, substitution of tryptophan at position 14 (Trp-14) increased both the pro-inflammatory and the proliferative responses and the adhesion of VLP-infected human monocytes to microvascular endothelial cells. Thus, the ISD N- and C-termini have pro- and anti-inflammatory properties, respectively, suggesting their unique implications in the EBOV pathogenesis. Furthermore, the immunomodulating effects of ISD were also mediated by shed GP, which is abundant in the medium. These data may be useful for the development of treatments for diseases caused by EBOV by targeting the ISD.IMPORTANCEOur data suggest that the ISD N-terminus plays a role in activating immune cells and pro-inflammatory response. In contrast, the C-terminus of ISD downregulates the pro-inflammatory response through the reduction of NF-kB and NFAT activities. The data also show that EBOV GP increases the adhesion of monocytes to endothelial cells, and the effect is inhibited by the ISD C-terminus. Moreover, the data demonstrate that the immunomodulating effects of ISD are mediated not only by the virus-associated GP but also by the shed GP, which is abundant in the medium. Pathogenesis of the disease caused by EBOV is characterized by hyperinflammation and some features of immunosuppression, which could in part be affected by the complex effects of the ISD. These data indicate that targeting the ISD may be considered for the development of treatments for the disease caused by EBOV.

Although virus-like particle (VLP) vaccines were shown to be effective against several viruses, their advantage over vaccines that include envelope protein only is not completely clear, particularly for mRNA-encoded VLPs. We conducted a side-by-side comparison of the immunogenicity and protective efficacy of mRNA vaccines encoding the Marburg virus (MARV) full-length glycoprotein (GP) delivered alone or as a VLP. Electron microscopy confirmed VLP formation when MARV GP and matrix protein VP40 were coexpressed. We vaccinated guinea pigs with a 2-component mRNA vaccine encoding GP and VP40 (VLP) or GP alone. At the highest dose, both vaccines protected fully, although the VLP vaccine elicited a slightly lower humoral response than did the GP-only mRNA vaccine. However, at low doses, GP-only mRNA conferred 100% protection, whereas the VLP vaccine conferred only partial protection. In mice, VLP mRNA induced a moderate preference for GP-specific CD8+ T cell responses, whereas the GP-only mRNA somewhat favored CD4+ T cell responses. Guinea pig whole-blood RNA-Seq revealed that the VLP vaccine downregulated genes associated with various biological and metabolic processes, including the NF-κB signaling pathway, whereas the GP-only vaccine upregulated IFN signaling. Overall, the VLP mRNA vaccine was less immunogenic and protective, whereas the GP-only mRNA vaccine conferred robust protection with a dose of as little as 1 μg in guinea pigs.

Ebola virus (EBOV) replication is regulated by the host protein phosphatases, PP1 and PP2A, which dephosphorylate the transcriptional cofactor of EBOV polymerase VP30. The PP1-targeting compound 1E7-03 induces VP30 phosphorylation and inhibits EBOV infection. Here, we investigate the broader role of PP1 in EBOV replication and transcription, including its interaction with nucleoprotein (NP). When EBOV-infected cells were continuously treated with 1E7-03, the NP E619K mutation was found and selected for further analysis. The NP E619K mutation moderately reduced the EBOV minigenome transcription, which was restored by the treatment with 1E7-03. Proteomics, immunoprecipitation, dimerization, split NanoBit, and colocalization analyses indicated that NP interacts with PP1 and that NP E619K mutations enhanced this binding. Treatment with 1E7-03 dissociated PP1-NP complex, but enhanced NP dimerization, which was more pronounced for NP E619K mutant. Mutation and deletion analyses pointed to several potential PP1-binding sites in NP that were located in the moderately disordered NP regions. When NP was co-expressed with VP24 and VP35, formation of EBOV capsids was impaired with NP E619K mutation. Treatment with 1E7-03 restored the capsid formation by the NP E619K mutant but inhibited capsids formed by WT NP. Our findings suggest that PP1 binds to NP and that this binding might regulate NP dimerization and capsid formation. Collectively, our results point to a new role for PP1 in EBOV replication, in which NP binding to PP1 may facilitate viral transcription by delaying capsid formation and EBOV replication.

The Coronavirus Immunotherapeutic Consortium (CoVIC) conducted side-by-side comparisons of over 400 anti-SARS-CoV-2 spike therapeutic antibody candidates contributed by large and small companies as well as academic groups on multiple continents. Nine reference labs analyzed antibody features, including in vivo protection in a mouse model of infection, spike protein affinity, high-resolution epitope binning, ACE-2 binding blockage, structures, and neutralization of pseudovirus and authentic virus infection, to build a publicly accessible dataset in the database CoVIC-DB. High-throughput, high-resolution binning of CoVIC antibodies defines a broad and predictive landscape of antibody epitopes on the SARS-CoV-2 spike protein and identifies features associated with durable potency against multiple SARS-CoV-2 variants of concern and high in vivo efficacy. Results of the CoVIC studies provide a guide for selecting effective and durable antibody therapeutics and for immunogen design as well as providing a framework for rapid response to future viral disease outbreaks.

Prevention of severe COVID-19 disease by SARS-CoV-2 in high-risk patients, such as immuno-compromised individuals, can be achieved by administration of antibody prophylaxis, but producing antibodies can be costly. Plant expression platforms allow substantial lower production costs compared to traditional bio-manufacturing platforms depending on mammalian cells in bioreactors. In this study, we describe the expression, production and purification of the originally human COVA2-15 antibody in plants. Our plant-produced mAbs demonstrated comparable neutralizing activity with COVA2-15 produced in mammalian cells. Furthermore, they exhibited similar capacity to prevent SARS-CoV-2 infection in a hamster model. To further enhance these biosimilars, we performed three glyco- and protein engineering techniques. First, to increase antibody half-life, we introduced YTE-mutation in the Fc tail; second, optimization of N-linked glycosylation by the addition of a C-terminal ER-retention motif (HDEL), and finally; production of mAb in plant production lines lacking β-1,2-xylosyltransferase and α-1,3-fucosyltransferase activities (FX-KO). These engineered biosimilars exhibited optimized glycosylation, enhanced phagocytosis and NK cell activation capacity compared to conventional plant-produced S15 and M15 biosimilars, in some cases outperforming mammalian cell produced COVA2-15. These engineered antibodies hold great potential for enhancing in vivo efficacy of mAb treatment against COVID-19 and provide a platform for the development of antibodies against other emerging viruses in a cost-effective manner.

The rodent-borne Andes virus (ANDV) causes a severe disease in humans. We developed an ANDV mRNA vaccine based on the M segment of the viral genome, either with regular uridine (U-mRNA) or N1-methylpseudouridine (m1Ψ-mRNA). Female mice immunized by m1Ψ-mRNA developed slightly greater germinal center (GC) responses than U-mRNA-immunized mice. Single cell RNA and BCR sequencing of the GC B cells revealed similar levels of activation, except an additional cluster of cells exhibiting interferon response in animals vaccinated with U-mRNA but not m1Ψ-mRNA. Similar immunoglobulin class-switching and somatic hypermutations were observed in response to the vaccines. Female Syrian hamsters were immunized via a prime–boost regimen with two doses of each vaccine. The titers of glycoprotein-binding antibodies were greater for U-mRNA construct than for m1Ψ-mRNA construct; however, the titers of ANDV-neutralizing antibodies were similar. Vaccinated animals were challenged with a lethal dose of ANDV, along with a naïve control group. All control animals and two animals vaccinated with a lower dose of m1Ψ-mRNA succumbed to infection whereas other vaccinated animals survived without evidence of virus replication. The data demonstrate the development of a protective vaccine against ANDV and the lack of a substantial effect of m1Ψ modification on immunogenicity and protection in rodents.

The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq), we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryoelectron microscopy (cryo-EM) structure of 54043-5 bound to the prefusion S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses in vitro, including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Antibodies to Ebola virus glycoprotein (EBOV GP) represent an important correlate of the vaccine efficiency and infection survival. Both neutralization and some of the Fc-mediated effects are known to contribute the protection conferred by antibodies of various epitope specificities. At the same time, the role of the complement system remains unclear. Here, we compare complement activation by two groups of representative monoclonal antibodies (mAbs) interacting with the glycan cap (GC) or the membrane-proximal external region (MPER) of GP. Binding of GC-specific mAbs to GP induces complement-dependent cytotoxicity (CDC) in the GP-expressing cell line via C3 deposition on GP in contrast to MPER-specific mAbs. In the mouse model of EBOV infection, depletion of the complement system leads to an impairment of protection exerted by one of the GC-specific, but not MPER-specific mAbs. Our data suggest that activation of the complement system represents an important mechanism of antiviral protection by GC antibodies.

Abstract ID 92941Poster Board 546Ebola virus (EBOV), a negative-sense RNA virus, is zoonotic pathogen that causes severe hemorrhagic fever with high case fatality rates in humans. EBOV disease outbreaks have been occurring since 1976. The largest outbreaks took place in West African in 2014 and resulted in over 28,000 cases and 11,000 deaths. There have been advances in the development of EBOV vaccines and monoclonal antibodies. However, no antiviral drugs are yet approved, especially for the treatment of pan-filovirus infections. EBOV transcription requires viral VP30 and VP35 proteins, which, according to our recently conducted global proteomic study (1), are phosphorylated in the EBOV virions. Phosphorylation of VP35 on Thr-210 regulated EBOV transcriptional activity and VP35 interaction with EBOV-NP (1). Host protein phosphatases, PP1 and PP2A were shown to facilitate EBOV transcription and replication (2,3). Our unpublished observations indicate that NP E619K mutant binds stronger to PP1 and that binding compromises formation of EBOV capsid. Thus, targeting PP1 might be a valuable approach for EBOV inhibition. Recent high throughout screen conducted in Mathieu Bollen’s laboratory at KULeuven identified several gold-containing compounds including FDA approved Auranofin among 400,000 compounds that were screened for PP1 as target. Here we tested the effect of Auranofin and chloro-gold compounds on EBOV transcription and replication and NP interaction with VP35. Auranofin inhibited EBOV minigenome (IC50 = 0.5 μM) and also potently inhibited EBOV and MARV replication in Vero E6 cells at submicromolar concentrations. Compared to chloro-gold compound, Auranofin showed at least 10-times better efficacy and also less toxicity. To determine the mechanism of Auranofin action, we investigated its effect on the NP-VP35 and NP-NP interactions using split NanoBiT assay. Auranofin potently inhibited NP binding to VP35 in split NanoBiT (IC50 = 3 μM) comparing to chloro-gold (IC50 = 12 μM). Auranofin demonstrated low cytotoxicity (IC50>300 μM) in 293T cells that were used for the split NanoBiT. Auranofin also showed potent inhibition of NP-NP interaction in split NanoBiT (IC50 = 1 μM) comparing to chloro-gold (IC50 = 3 μM). Taken together, our study suggests that Auranofin may serve as EBOV inhibitor by targeting EBOV NP-VP35 and NP-NP interactions. As Auranofin is approved for human use for rheumatoid arthritis, it is feasibly can be further tested as an inhibitor for EBOV and MARV infectionsReferences1Ivanov A, … Bukreyev A, Nekhai S. 2020. Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription. Cell Mol Life Sci 77:2579–2603.2Ilinykh PA, … Nekhai S, Bukreyev A. 2014. Role of protein phosphatase 1 in dephosphorylation of Ebola virus VP30 protein and its targeting for the inhibition of viral transcription. J Biol Chem 289:22723–38.3Kruse T, … Nilsson J, Becker S. 2018. The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30. Mol Cell 69:136–145 e6Acknowledgements: We thank Dr. Mathieu Bollen for sharing screening data, Dr. Elke Mühlberger for providing the EBOV minigenome, and Dr. Yoshihiro Kawaoka for providing the plasmids expressing EBOV NP, VP35, L, VP30, and the T7 polymerase. This project was supported by the NIH Research Grants U19AI109664, 5U54MD007597, 2R01HL125005 and P30AI117970