ABSTRACT Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic infectious agent and causes animal and human illness of the central nervous system. Japanese encephalitis virus inflicts severe harm, yet even with an approved vaccine, prevention and control remain daunting, and the molecular mechanism underlying the virus-host interplay remains incompletely understood. In this study, we found that the host peroxiredoxin 1 (PRDX1) protein inhibits JEV replication. PRDX1 targets nonstructural protein 1 (NS1) of JEV and mediates its degradation via the proteasome and autophagy pathways, thus inhibiting viral replication. By targeting TRAF6, an E3 ligase, the PRDX1 protein catalyzes the ubiquitination of NS1, leading to its recognition by NDP52, a cargo receptor, along with lysosomal degradation. We also found that the JEV NS3 protein can target and degrade PRDX1 to decrease the antiviral function of PRDX1, which is a tactic by which viruses confront the host. In conclusion, these findings showed that selective autophagy has dual functions in the host and JEV: it can degrade viral proteins to inhibit viral replication and host antiviral proteins to promote viral replication. IMPORTANCE Japanese encephalitis virus (JEV) is a flavivirus capable of inducing human encephalitis and dysgenesis in gestating sows. It has an extraordinary ability to hijack cellular systems and evade defenses, establishing infection and spreading it throughout the body to cause disease. During viral infection, the host initiates several antiviral responses and activates various host-restricted factors to resist viral invasion. In this study, we identified PRDX1 as a novel host restrictor that inhibits viral multiplication by binding to TRAF6 (an E3 ubiquitin ligase) and NDP52 (a cargo receptor) to degrade nonstructural protein 1 (NS1) of JEV. We also found that JEV infection can downregulate intracellular PRDX1 expression via nonstructural protein 3 (NS3), thus promoting viral replication. These results revealed that the virus-host interaction is a complex and dynamic process in which viruses restrict and compete with each other.
ABSTRACT Orchidaceae is one of the largest plant families and includes species of major ornamental, economic, and ecological importance. Despite this diversity, the viruses associated with orchids remain poorly characterized. The growing availability of high-throughput sequencing data offers new opportunities to explore plant virus diversity across broad taxonomic scales. Here, we conducted a large-scale meta-analysis of orchid-associated viruses by reanalyzing 2,789 publicly available RNA-seq data sets representing 41 genera across 18 subtribes and five subfamilies. We identified sequences corresponding to 163 viruses, including 13 new associations with orchids. Notably, 117 sequences likely represent putative novel species, including tentative new genera within the families Benyviridae , Betaflexiviridae , Phenuiviridae , and Tymoviridae . This analysis also reveals patterns of virus co-occurrence within the orchid virome and uncovers links between viral taxa and orchid life forms. Overall, these findings greatly broaden the known diversity of orchid-associated viruses and offer a comprehensive global framework for understanding their composition, ecological interactions, and potential scope. IMPORTANCE Orchids are among the most diverse plant families, yet little is known about the viruses associated with them. Plant viruses pose significant risks to agriculture and may also threaten orchid conservation, particularly when infected plant material is moved through trade or cultivation. A comprehensive understanding of the orchid virome is therefore essential for improving virus detection, managing diseases, and producing virus-free planting material. In this study, we used large-scale analysis of publicly available RNA-seq data to identify viral sequences associated with orchid-derived transcriptomic data sets and to characterize the diversity of orchid-associated viruses. Our results substantially expand the catalog of viruses associated with Orchidaceae, revealing numerous previously undescribed viruses and candidate virus-orchid associations. By providing a global perspective on the Orchidaceae virome, this work highlights the power of data mining approaches for virus discovery and establishes a foundation for future studies on plant virus ecology, evolution, and surveillance.
ABSTRACT During the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), antibody-based therapies such as COVID-19 convalescent plasma (CCP) and monoclonal antibodies (mAbs) emerged rapidly. However, many CCP clinical trials failed to show consistent benefits, and mAbs lost effectiveness as new SARS-CoV-2 variants emerged. These studies consistently indicated that antibody therapies are effective when given very early in disease and in patients with delayed or suppressed immune responses. Intravenous immunoglobulin (IVIG), which is pooled IgGs from thousands of donors, has been explored as an additional source of anti-SARS-CoV-2 antibodies to treat acutely ill patients because IVIG was shown to prevent disease and death in animal models against variants even without neutralizing activity. As antibodies can also protect via Fc-mediated activation of innate immune effector functions, in this study, we compared the qualitative and quantitative properties of CCP and IVIG to determine if IVIG might serve as a clinical therapeutic alternative to CCP. We measured SARS-CoV-2 spike (S)- and nucleocapsid (N)- specific antibody-binding titers across variants and evaluated their ability to induce antibody-dependent effector functions. We found that IVIG and CCP had comparable binding and Fc-effector activity against ancestral SARS-CoV-2. Remarkably, IVIG manufactured before the emergence of XBB.1.5, JN.1, KP.2, XEC, and XFG demonstrated strong binding and Fc-effector activity against these newer variants. IMPORTANCE Despite the availabilities of vaccines for SARS-CoV-2 for most individuals, there remain vulnerable populations for which vaccination is ineffective. As the emergence of SARS-CoV-2 variants has rendered many monoclonal antibody therapies ineffective, there remains a need to understand the role of polyclonal antibody therapies for SARS-CoV-2, such as COVID-19 convalescent plasma (CCP) and intravenous immunoglobulin (IVIG). While CCP is variable and donor-dependent, IVIG is pooled from thousands of donors with a range of vaccine- and natural infection-derived antibody responses and may represent a consistent source of polyclonal antibodies. We compared high neutralizing antibody titer CCP, previously shown to be associated with reduced time to hospital discharge, with IVIG produced post-2021. We find that IVIG offers expanded antibody binding to SARS-CoV-2 variants, including those that emerged after the IVIG was collected, and enhanced induction of Fc-mediated innate immune effector functions, highlighting the potential utility of IVIG as an adjunct treatment of SARS-CoV-2. CLINICAL TRIALS This study is registered with ClinicalTrials.gov as NCT04524507 .
ABSTRACT Orbiviruses comprise numerous species and are transmitted by insect vectors. They are non-enveloped viruses with a multilayered capsid and a segmented double-stranded RNA (dsRNA) genome. Bluetongue virus (BTV), the prototype species of the genus Orbivirus , is a significant pathogen of livestock and is widely distributed throughout the world, causing serious periodic outbreaks with substantial economic consequences. Consequently, BTV has been extensively studied as a model orbivirus, resulting in a comprehensive understanding of its molecular epidemiology, genetics, biochemistry, structure, and replication cycle. This includes detailed insights into virus entry into host cells, synthesis of progeny viral components, assembly of new virions, and subsequent cell-to-cell transmission. This review summarizes the current literature on each of these aspects and discusses how this knowledge has been applied to develop novel vaccines against BTV and related orbiviruses. In addition, the review highlights important gaps in our understanding of virus replication within insect vectors, particularly Culicoides biting midges (gnats), at the molecular level. Addressing these gaps will provide valuable insights into orbivirus evolution, transmission, and the emergence of new viral strains.
ABSTRACT Norovirus is the leading cause of acute gastroenteritis, responsible for 685 million cases and 200,000 deaths annually. Wastewater-based epidemiology (WBE) enables not only global surveillance of dominant strains but also the detection of cryptic and emerging viral variants. An important question, however, is how to link genomic diversity to clinical impact and phenotypic traits of the strains detected in wastewater. In the Global Urban Wastewater Project, phylogenetically distinct norovirus GI.3 and GII.12 lineages were detected in wastewater from Cameroon. In this study, we characterized their host- and tissue-binding specificity and antigenic makeup in comparison with other GI.3 and GII.12 lineages using a luciferase immunoprecipitation system-based assay, alongside sequence analysis of the VP1 P2 subdomain. We observed intra-genotype variation among GI.3 variants. GI.3 Cameroon/2017 shared phenotypes with its closest reference strain (GI.3 Mexico/2016), and their histo-blood group antigen (HBGA)-binding profiles suggested a narrower susceptible population compared to other GI.3 lineages. Conversely, GII.12 strains showed no significant differences in HBGA binding, antigenic profiles, and tissue attachment. Together, these results reveal distinct patterns of phenotypic diversity between the two genotypes. While GI.3 variants exhibited lineage-specific traits, the GII.12 strains appeared phenotypically conserved across lineages. These findings highlight the feasibility and importance of integrating phenotypic analysis with WBE to assess potential public health risks posed by novel viral variants. IMPORTANCE While detection of norovirus through case-based surveillance is limited to variants causing symptomatic infection, wastewater-based epidemiology (WBE) allows for detection of cryptic and emerging variants. However, validation, such as phenotypic characterization, is needed to assess the clinical importance of a variant detected in WBE. In this study, we investigated the phenotypic traits of genetically distinct GI.3 and GII.12 lineages detected in wastewater from Cameroon. We utilized NanoLuc luciferase immunoprecipitation system (N-LIPS)-based assays to assess binding specificity and antigenicity. Compared to traditional methods involving virus isolation and virus-like particle production, N-LIPS-based assays are considerably less laborious and faster. This allows for rapid characterization of novel variants, making the timely assessment of phenotypic changes of such variants for outbreak or pandemic preparedness feasible. Finally, by integrating insights from phenotypic assays, we showed the possibility of expanding the public health value of wastewater surveillance in assessing the risk of novel viral variants.
