Accelerating antiviral drug discovery: lessons from COVID-19

Nature Reviews Drug Discovery, Год журнала: 2023, Номер 22(7), С. 585 - 603

Опубликована: Май 12, 2023

Язык: Английский

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Fitness effects of mutations to SARS-CoV-2 proteins

Virus Evolution, Год журнала: 2023, Номер 9(2)

Опубликована: Июль 1, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here, develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

Язык: Английский

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Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Апрель 21, 2023

Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across world and effectively evaded immune responses, its viral fitness in cell animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent genomes is challenging because length genome (~30 kb). Here, we present a plasmid-based assembly rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons single ligation reaction with >80% efficiency. Fully sequenced stocks can be generated 1 3 weeks, respectively. By testing series naturally occurring well Delta-Omicron chimeric replicons, show nonstructural protein 6 harbors critical attenuating mutations, which dampen RNA replication reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study reveals deficits function underlying attenuation.

Язык: Английский

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Programmable Macrophage Vesicle Based Bionic Self‐Adjuvanting Vaccine for Immunization against Monkeypox Virus

Advanced Science, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 8, 2024

The emergence of monkeypox has become a global health threat after the COVID-19 pandemic. Due to lack available specifically treatment against MPV, developing an vaccine is thus most prospective and urgent strategy. Herein, programmable macrophage vesicle based bionic self-adjuvanting (AM@AEvs-PB) first developed for defending virus (MPV). Based on MPV-related antigen-stimulated macrophage-derived vesicles, nanovaccine constructed by loading mature virion (MV)-related intracellular protein (A29L/M1R) simultaneously modifying with enveloped (EV) antigen (B6R), enabling them effectively promote presentation enhance adaptive immune through self-adjuvant Owing synergistic properties coloaded MV EV in defensing activation ratio antigen-presenting cells nearly four times than that single same dose, resulting stronger immunity host. Notably, intramuscular injection uptake AM@AEvs-PB demonstrated vigorous immune-protective effects mouse challenge attempt, offering promising strategy pre-clinical development.

Язык: Английский

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Fitness effects of mutations to SARS-CoV-2 proteins

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 31, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino-acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

Язык: Английский

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SARS-CoV-2 ORF8 Protein Induces Endoplasmic Reticulum Stress-like Responses and Facilitates Virus Replication by Triggering Calnexin: an Unbiased Study

Journal of Virology, Год журнала: 2023, Номер 97(3)

Опубликована: Март 6, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for worldwide disease 2019 (COVID-19) pandemic. The novel SARS-CoV-2 ORF8 protein not highly homologous with known proteins, including accessory proteins of other coronaviruses. contains a 15-amino-acid signal peptide in N terminus that localizes mature to endoplasmic reticulum. Oligomannose-type glycosylation has been identified at N78 site. Here, unbiased molecular functions are also demonstrated. Via an immunoglobulin-like fold glycan-independent manner, both exogenous and endogenous interacts human calnexin HSPA5. key ORF8-binding sites Calnexin HSPA5 indicated on globular domain core substrate-binding domain, respectively. induces species-dependent reticulum stress-like responses cells exclusively via IRE1 branch, intensive PDIA4 upregulation, increases stress-responding effectors, CHOP, EDEM DERL3. overexpression facilitates replication. Both replication induced by have shown result from triggering switch. Thus, serves as unique virulence gene SARS-CoV-2, potentially contributing COVID-19-specific and/or human-specific pathogenesis. IMPORTANCE Although basically regarded homolog SARS-CoV, their genomic structure majority genes being homologous, SARS-CoV distinct. shows little homology or host thus special SARS-CoV-2. function clearly until now. Our results reveal characteristics demonstrate it rapidly generated but controllable virus mouse cells, providing explanation superficially vivo discrepancy between SARS-CoV-2-infected patients mouse.

Язык: Английский

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Virological characteristics correlating with SARS-CoV-2 spike protein fusogenicity

Frontiers in Virology, Год журнала: 2024, Номер 4

Опубликована: Март 14, 2024

Introduction The severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike (S) protein is essential in mediating membrane fusion of the virus with target cells. Several reports demonstrated that SARS-CoV-2 S fusogenicity reportedly closely associated intrinsic pathogenicity determined using hamster models. However, association between and other virological parameters remains elusive. Methods In this study, we investigated (e.g., S1/S2 cleavage efficiency, plaque size, pseudoviral infectivity, pseudovirus entry viral replication kinetics) eleven previous variants concern (VOCs) interest (VOIs) correlating fusogenicity. Results discussion was found to be strongly correlated efficiency size formed by clinical isolates. less kinetics. Taken together, our results suggest could potential indicators predict newly emerged variants.

Язык: Английский

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AZD3152 neutralizes SARS-CoV-2 historical and contemporary variants and is protective in hamsters and well tolerated in adults

Science Translational Medicine, Год журнала: 2024, Номер 16(753)

Опубликована: Июнь 26, 2024

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in variants that can escape neutralization by therapeutic antibodies. Here, we describe AZD3152, a SARS-CoV-2–neutralizing monoclonal antibody designed to provide improved potency and coverage against emerging variants. AZD3152 binds the back left shoulder SARS-CoV-2 spike protein receptor binding domain prevents interaction with human angiotensin-converting enzyme receptor. potently neutralized broad panel pseudovirus variants, including currently dominant Omicron variant JN.1 but reduced XBB subvariants containing F456L. In vitro studies confirmed F456L resistance additionally identified T415I K458E as mutations. Syrian hamster challenge model, prophylactic administration protected hamsters from weight loss inflammation-related lung pathologies viral load. phase 1 sentinel safety cohort ongoing SUPERNOVA study ( ClinicalTrials.gov : NCT05648110), single 600-mg intramuscular injection AZD5156 (containing 300 mg each cilgavimab) was well tolerated adults through day 91. Observed serum concentrations 91 were similar those observed cilgavimab consistent predictions for AZD7442, combination tixagevimab, population pharmacokinetic model. On basis its characteristics, is predicted durable protection symptomatic disease 2019 caused susceptible such JN.1, humans.

Язык: Английский

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Examining the feasibility of replacing ORF3a with fluorescent genes to construct SARS-CoV-2 reporter viruses

Journal of General Virology, Год журнала: 2025, Номер 106(2)

Опубликована: Фев. 12, 2025

The SARS-CoV-2 genome encodes at least nine accessory proteins, including innate immune antagonist and putative viroporin ORF3a. ORF3a plays a role in many stages of the viral replication cycle, modulation. We constructed two recombinant (r)SARS-CoV-2 viruses which gene was replaced with mScarlet (mS) or mNeonGreen (mNG), denoted as rSARS-CoV-2-Δ3a-mS rSARS-CoV-2-Δ3a-mNG, respectively. rSARS-CoV-2-Δ3a-mNG generated fluorescent signal after infection both A549-ACE-2-TMPRSS2 (AAT) Vero-E6-TMPRSS2 (VTN) cells, unlike rSARS-CoV-2-Δ3a-mS. mS protein could be detected immunologically VTN but not AAT indicating expression non-fluorescent protein. analysis transcriptomes infected cells by nanopore direct RNA sequencing (dRNAseq) revealed that level transcript below limit detection cells. virus found to genetically stable acquired partial deletions during sequential passaging creating rSARS-CoV-2-Δ3a-ΔmS. deletion removes chromophore coding sequence, this may explain presence rSARS-CoV-2-Δ3a-ΔmS all replicated lower titre produced smaller plaques than parental rSARS-CoV-2-S-D614G. Interestingly, higher titres larger plaque sizes This suggested insertion sequence contributed attenuation. In comparison rSARS-CoV-2, showed increased sensitivity pre-treatment IFN-α did exhibit dose-dependent increase Janus kinase-signal transducer activator transcription signalling pathway inhibitor, ruxolitinib. conclusion, replacement those reporter proteins attenuated its ability effectively evade response vitro.

Язык: Английский

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Molecular Farming for Immunization: Current Advances and Future Prospects in Plant-Produced Vaccines

Vaccines, Год журнала: 2025, Номер 13(2), С. 191 - 191

Опубликована: Фев. 15, 2025

Using plants as bioreactors, molecular farming has emerged a versatile and sustainable platform for producing recombinant vaccines, therapeutic proteins, industrial enzymes, nutraceuticals. This innovative approach leverages the unique advantages of plants, including scalability, cost-effectiveness, reduced risk contamination with human pathogens. Recent advancements in gene editing, transient expression systems, nanoparticle-based delivery technologies have significantly enhanced efficiency versatility plant-based systems. Particularly vaccine development, demonstrated its potential notable successes such Medicago's Covifenz COVID-19, illustrating capacity platforms to address global health emergencies rapidly. Furthermore, edible vaccines opened new avenues mainly settings low resources where cold chain used conventional logistics is challenge. However, optimization protein yield stability, complexity purification processes, regulatory hurdles are some challenges that still remain. review discusses current status development using operational mechanisms plant platforms, major applications prevention infectious diseases, developments, nanoparticle-mediated cancer vaccines. The discussion will also touch on ethical considerations, framework, future trends respect transformative plant-derived ensuring greater accessibility cost-effectiveness vaccination. field holds great promise disease area and, indeed, personalized medicine biopharmaceuticals near future.

Язык: Английский

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