SEARCH · PubMed Health

Results for “Alphavirus”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

16 recordsLinked to original sources

PubMed2026

Quantitative Fluorescence Imaging of Alphavirus Infection for Antiviral Screenings.

Fluorescence microscopy offers a highly sensitive and versatile approach for investigating alphavirus infection at the cellular level. By combining fluorescently labeled viruses with quantitative image analysis, this method enables detailed spatial and temporal characterization of infection dynamics, including the detection of subtle differences in replication kinetics and cell-to-cell spread. A central aim of this protocol is its application in antiviral screening assays. Image-based quantification of fluorescence intensity provides a robust and reproducible means to assess the efficacy of antiviral compounds, allowing early and sensitive detection of inhibitory effects in infected cells. This facilitates the identification of promising antiviral hits and supports the evaluation of dose-dependent responses. The approach is also well-suited for comparative studies of different alphavirus strains or mutants, as variations in replication behavior and dissemination patterns become readily apparent. Its flexibility, compatibility with multiple cell lines, and straightforward integration into automated imaging platforms makes the method scalable and suitable for high-throughput screening campaigns. Overall, this protocol advances the discovery and evaluation of antiviral strategies. Given that several alphaviruses cause significant human and veterinary diseases, lack approved antiviral therapies, and continue to expand geographically with emerging outbreaks, the identification of novel antivirals remains an urgent priority. Therefore, this fluorescence-based workflow represents a valuable and timely contribution to modern alphavirus research.

Antiviral Agents↗

PubMed2025

Proximity interactome of alphavirus replicase component nsP3 includes proviral host factors eIF4G and AHNAK.

All positive-strand RNA viruses replicate their genomes in association with modified intracellular membranes, inducing either membrane invaginations termed spherules, or double-membrane vesicles. Alphaviruses encode four non-structural proteins nsP1-nsP4, all of which are essential for RNA replication and spherule formation. To understand the host factors associated with the replication complex, we fused the efficient biotin ligase miniTurbo with Semliki Forest virus (SFV) nsP3, which is located on the cytoplasmic surface of the spherules. We characterized the proximal proteome of nsP3 in three cell lines, including cells unable to form stress granules, and identified >300 host proteins constituting the microenvironment of nsP3. These included all the nsPs, as well as several previously characterized nsP3 binding proteins. However, the majority of the identified interactors had no previously identified roles in alphavirus replication, including 39 of the top 50 interacting proteins. The most prominent biological processes involving the proximal proteins were nucleic acid metabolism, translational regulation, cytoskeletal rearrangement and membrane remodeling. siRNA silencing confirmed six novel proviral factors, USP10, AHNAK, eIF4G1, SH3GL1, XAB2 and ANKRD17, which are associated with distinct cellular functions. All of these except SH3GL1 were also important for the replication of chikungunya virus. We discovered that the small molecule 4E1RCat, which inhibits the interaction between the canonical translation initiation factors eIF4G and eIF4E, exhibits antiviral activity against SFV. Since the same molecule was previously found to inhibit coronaviruses, this suggest the possibility that translation initiation factors could be considered as targets for broadly acting antivirals.

Viral Nonstructural Proteins↗

PubMed2025

Seroprevalence of Chikungunya and O'nyong-nyong Viruses in Senegal, West Africa.

Arthritogenic alphaviruses such as chikungunya (CHIKV) and o'nyong-nyong (ONNV) viruses have shown capacity to cause widespread epidemics, with recurrent and sporadic outbreaks occurring throughout sub-Saharan Africa. We analyzed the seroprevalence for CHIKV and ONNV in 470 non-febrile subjects from three regions in Senegal (Sindia, 2018; Thies, 2018; and Kedougou, 2022/2023) using retrospective samples. We assessed the presence of anti-CHIKV IgG and neutralizing antibody titers against CHIKV and ONNV via enzyme-linked immunosorbent assay (ELISA) and microneutralization tests, respectively, and determined risk factors of CHIKV and ONNV exposure by binary logistic regression. The overall alphavirus seroprevalence based on an anti-CHIKV virus like particle (VLP) IgG ELISA was 38.5%, with rates varying geographically: Kedougou (48.6%), Thies (31.9%), and Sindia (14.9%). Neutralizing antibody titers revealed CHIKV and ONNV seroprevalence rates of 7.4% and 9.8%, respectively, with significant variations by region and age group. Cross-reactivity analysis showed that 82.9% of CHIKV cases exhibited a neutralizing response to ONNV, while 71.7% of ONNV cases cross-neutralized CHIKV. Residents of Thies had significantly higher odds of CHIKV infection (aOR, 3.147; 95% CI: 1.164-8.510) while ONNV infection was more likely in Kedougou (aOR, 3.888; 95% CI: 1.319-11.466). Furthermore, older age (> 40 years) was a significant risk factor both CHIKV (aOR, 2.094; 95% CI: 0.846-5.185) and ONNV infection (aOR, 2.745; 95% CI: 1.212-6.216). Our study confirms the co-circulation of CHIKV and ONNV in Senegal, highlighting their geographic and demographic distribution. These findings underscore the need for continued surveillance, alphavirus testing, and tailored public health strategies to mitigate their impact in Senegal.

Humans↗

PubMed2026

Rasputin/G3BP mediates subversion of antiviral immunity by o'nyong-nyong virus in Anopheles coluzzii.

Cellular G3BP proteins are essential for alphavirus infection in both vertebrate and mosquito hosts, but the underlying mechanism of their proviral activity is poorly understood in any host. Whether the mosquito G3BP ortholog, Rasputin (Rin), interacts with host immunity to influence alphavirus infection has not been investigated, and anopheline mosquito interactions with arboviruses have been little studied. Here, we find that Rin silencing in Anopheles mosquitoes results in decreased ONNV infection levels, indicating a proviral activity for Anopheles Rin. We find that Rin function is required to maintain basal activity of the antiviral Imd and JAK/STAT pathways in uninfected mosquitoes. However, during ONNV infection, the control of the Imd pathway by Rin activity appears corrupted because Rin silencing leads to overexpression of the Imd positive regulator, Rel2. Thus, silencing of Rin both augments Rel2 transcript abundance and decreases ONNV load. Co-silencing of Rel2 with Rin restores normal ONNV infection levels, indicating that Rin activity is required to inhibit Imd function during ONNV infection, and which explains most of the Rin proviral phenotype. In addition, we show that the ONNV non-structural protein 3 (nsP3), which binds to Rin, strongly alters the pattern of Anopheles cellular protein partners interacting with Rin. In the presence of ONNV nsP3, 48 Rin-binding host proteins are unchanged but seven binding proteins are excluded and eight new cellular proteins bind Rin. The altered cellular protein partners are candidate host factors involved in viral subversion of Rin control over Imd activity. Overall, these results reveal a molecular mechanism in which ONNV, probably through nsP3, co-opts the normal Rin function for basal cellular immune activity by subverting the Imd antiviral pathway to promote infection. These results may be generalizable for Rin function during alphavirus infection of other mosquitoes, as well as for G3BP function in the mammalian host, and could offer a target for development of vector-based genetic control tools against arbovirus transmission.

Animals↗

PubMed2026

Transgene sequence codon optimization and composition determines replication competence of self-amplifying RNA.

Self-amplifying RNA (saRNA) is an emerging RNA therapeutic modality that can facilitate higher magnitude and more durable protein expression at substantially lower doses than nonreplicating mRNA. Unlike conventional messenger RNA (mRNA), alphavirus-derived saRNA must support a replicase-driven RNA amplification step in addition to translation, raising the possibility that transgene coding sequences impose sequence-level constraints on replication. Here, saRNA replication was found to be dependent on the codon composition of the transgene; multiple therapeutic transgenes were replication defective despite an intact Venezuelan Equine Encephalitis Virus (VEEV)-derived saRNA backbone. Replication defects were rescued by synonymous codon re-optimization of the same transgenes, indicating that nucleotide-level features of the coding sequence, rather than the encoded protein, govern replication competence. Comparative compositional analyses identified a distinct signature associated with productive replication, characterized by elevated GC (>53%) and GC3 (>63%) content, higher codon adaptation to human (>0.75), and reduced UpA (<43/kb) and UpU (<41/kb) dinucleotide density. Moreover, deliberate compositional perturbation of an otherwise replication-competent transgene shifted these features and abolished replication, supporting a causal and combinatorial role for sequence composition in defining saRNA replication outcome. These findings define an underappreciated constraint in saRNA therapeutics and motivate saRNA-specific payload design frameworks that incorporate alphavirus-associated compositional biases during transgene sequence optimization.

Codon↗

PubMed2026

O'nyong-nyong virus adaptive mutations in non-structural protein 1 and 3 enhance RNA replication and overcome FHL1 requirement.

Arthritogenic alphaviruses, like o'nyong-nyong virus (ONNV), cause debilitating musculoskeletal diseases and are geographically expanding. To predict their emergence, we seek to better understand evolutionary mechanisms that enable changes in virus tropism. Here, we identify adaptive mutations in the ONNV non-structural proteins (nsPs) that arose during cellular serial passaging and enabled ONNV to infect non-permissive Lunet cells. Using shotgun proteomics, we show that this human hepatoma cell line lacks the four-and-a-half-LIM domain protein 1 (FHL1), an essential host factor in ONNV RNA replication. Individual single nucleotide mutations in the nsP1 ring-aperture membrane-binding and oligomerization domain, the nsP3 macrodomain, and the nsP3 opal stop codon overcome FHL1 deficiency in Lunet cells by enhanced RNA replication. These findings demonstrate how subtle genomic changes in nsPs can profoundly influence alphavirus replication and tropism.

LIM Domain Proteins↗

PubMed2026

Cell type-dependent induction of type I interferon and PARP1 activation in astrocytes and neurons during chikungunya virus infection.

Chikungunya virus, a mosquito-borne alphavirus, causes fever, rash, arthritis, and neurological disorders. Its non-structural protein 3 harbors a macrodomain, a key neurovirulence factor that removes adenosine diphosphate ribose from ADP-ribosylated substrates. Notably, chikungunya virus infection results in distinct ADP-ribosylation patterns and non-structural protein 3 macrodomain-mediated replication dynamics in astrocytes and neurons. Understanding the connection between ADP-ribosylation and the activation of innate immunity, particularly interferon release, is key to elucidating how the cellular immunological state influences ADP-ribosylation, an understudied post-translational modification during viral infection. Here, murine astrocytic (C8-D1A) and neuronal (NSC-34) cells were infected with chikungunya virus to profile transcript and protein expression of innate immune mediators and type I IFNs. The role of PARP1 in global ADP-ribosylation patterns was assessed using PARP-specific inhibitors and genetic depletion approaches. Our investigations revealed that neuronal chikungunya virus infection induces ADP-ribosylation through PARP1 activation, driven by caspase-3-mediated apoptosis, without transcriptionally activating PARPs. In contrast, astrocytic infections showed minimal ADP-ribosylation despite transcriptional activation of interferon-stimulated PARPs. Neurons exhibited limited innate immune response gene transcriptional activity, whereas astrocytes demonstrated strong upregulation of genes essential for pattern recognition receptor activation, thus enhancing double-stranded RNA sensing and increasing type I interferon production during infection. We posit that PARP1 activation and type I IFN response differentially regulate ADP-ribosylation in chikungunya virus-infected neural cells in a cell type-dependent manner.IMPORTANCEChikungunya virus is an emergent mosquito-borne alphavirus increasingly associated with neurological infection and subsequent long-term disabilities. Its continued global spread and recurrent outbreaks underscore its significant pandemic potential and the urgent need for effective countermeasures. Chikungunya virus showcases distinct, cell-type dependent replication dynamics within astrocytes and neurons, two major permissive cerebral cell types. However, understanding of the immunological basis of such cell type-specific infection dynamics remains limited, yet is necessary to elucidate virus pathogenesis within the brain and thus identification of downstream drug targets. Our study characterized two distinctly activated innate immunological pathways in chikungunya virus-infected astrocytes versus neurons, thus significantly contributing to molecular understanding cell type-specific chikungunya virus neurovirulence on a molecular level.

Animals↗

PubMed2026

Development of a Real-Time Reverse Transcription Polymerase Chain Reaction Assay for Una Virus.

Una virus (UNAV) is an understudied alphavirus with the capacity to infect humans. Although it was discovered decades ago in South America, little is still known about this virus because accurate diagnostic tests are still needed. The first UNAV-specific real-time reverse transcription polymerase chain reaction (rRT-PCR) test is described in the present study. This assay targets the nonstructural protein 1 coding region and was designed from an alignment using all available UNAV sequences. The linear range of the UNAV rRT-PCR extended from 6.2 to 0.2 log10 copies/µL, with a lower limit of 95% detection of 2.0 copies/µL. The assay offered sensitive UNAV detection in contrived whole-blood samples. In addition, no amplification was observed in the assay when tested with genomic RNA from multiple closely related arboviruses. The UNAV rRT-PCR exhibits high sensitivity and specificity, which is critical for research into this virus in regions where multiple related alphaviruses co-circulate.

Journal Article↗

PubMed2027

Optimized Amplicon Strategy for Long-Read Sequencing of the Chikungunya Virus Genome.

Chikungunya virus (CHIKV) is a positive-sense RNA alphavirus transmitted to humans primarily by Aedes aegypti and Aedes albopictus mosquitoes. Its global circulation and significant public health impact underscore the need to better understand the molecular mechanisms driving CHIKV pathogenesis and transmission. Although robust molecular biology methods exist for CHIKV genome sequencing, a major limitation for surveillance and research is the inability to determine whether two nucleotide variations co-occur within the same viral genome when they are separated beyond the span of typical short-read designs. Here, we describe an optimized approach for processing CHIKV RNA samples that generates large amplicons suitable for long-read nanopore sequencing. This protocol enables amplification of the complete CHIKV genome in only two or three amplicons and facilitates detection of co-occurring nucleotide variations across 4-7.5 kb within the same molecule, thereby simplifying sequencing workflows and improving resolution in studies of viral evolution.

Chikungunya virus↗

PubMed2025

A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity.

Chikungunya is a mosquito-borne viral disease that causes fever and severe joint pain for which there is no direct acting drug treatments. Vinyl sulfone SGC-NSP2PRO-1 (3) was identified as a potent inhibitor of the nsP2 cysteine protease (nsP2pro) that reduced viral titer against infectious isolates of Chikungunya and other alphaviruses. The covalent warhead in 3 captured the active site C478 and inactivated nsP2pro with a kinact/Ki ratio of 5950 M-1 s-1. The vinyl sulfone 3 was inactive across a panel of 23 other cysteine proteases and demonstrated remarkable proteome-wide selectivity by two chemoproteomic methods. A negative control analog SGC-NSP2PRO-1N (4) retained the isoxazole core and covalent warhead but demonstrated > 100-fold decrease in enzyme inhibition. Both 3 and 4 were stable across a wide range of pH in solution and upon prolonged storage as solids. Vinyl sulfone 3 and its negative control 4 will find utility as high-quality chemical probes to study the role of the nsP2pro in cellular studies of alphaviral replication and virulence.

Chikungunya virus↗

PubMed2027

Overview of Chikungunya Virus Epidemiology, Biology, and Pathogenesis.

Chikungunya virus (CHIKV), an arthropod-borne alphavirus within the Togaviridae family, is transmitted primarily by Aedes aegypti and Aedes albopictus. The virus causes an acute febrile illness characterized by severe, often bilateral polyarthralgia, with potential progression to chronic musculoskeletal pain and rare systemic complications involving cardiovascular and neurological systems. CHIKV exhibits a spherical, enveloped virion (~70 nm) with T = 4 icosahedral symmetry, incorporating E1/E2 glycoprotein heterodimers that mediate receptor binding and membrane fusion. Its positive-sense RNA genome (~11.8 kb) encodes nonstructural proteins for replication and structural proteins for virion assembly. Replication occurs in cytoplasmic spherules, involving synthesis of genomic and subgenomic RNAs, followed by glycoprotein maturation and budding at the plasma membrane. Epidemiologically, CHIKV has expanded beyond Africa and Asia, with major outbreaks driven by adaptive mutations enhancing transmission via A. albopictus. Since introduction to the Americas in 2013, the global incidence remains high, with >180,000 confirmed cases reported in 2025. Preventive strategies rely on vector control and vaccination; VLP-based vaccines (e.g., Vimkunya) show promise, while live-attenuated formulations face safety concerns. No licensed antivirals exist; current management is supportive, though investigational therapies targeting viral replication and immune modulation are under development.

Chikungunya virus↗

PubMed2027

RT-RPA-Assisted CRISPR/Cas12a-Based Isothermal Detection of Chikungunya Virus.

Chikungunya virus (CHIKV) is transmitted through the bite of Aedes mosquitoes, specifically A. aegypti and A. albopictus. CHIKV belongs to the alphavirus with a positive-sense ssRNA genome of 11-12 kb size. The virus has been reported from various geographical regions across the globe. Chikungunya fever is an acute febrile illness, which, if left untreated, may develop into chronic arthralgia that may persist for several months or acute encephalitis syndrome. Therefore, early diagnosis of CHIKV is crucial to initiate prompt supportive treatment. Laboratory diagnosis of CHIKV typically relies on serological tests such as IgM antigen capture ELISA and molecular methods including RT-PCR or qRT-PCR. However, both these methods are not viable in peripheral settings. This chapter highlights recent advancements in molecular detection techniques for CHIKV, specifically isothermal detection methods that eliminate the requirement for complex instruments. The detection is facilitated by RT-RPA and CRISPR/Cas12a endonuclease. The assay offers advantages over existing methods such as rapid and early detection, and eliminates cross-over contamination, ultra-sensitivity, high specificity, and ease of result interpretation.

Chikungunya virus↗

PubMed2024

Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.

Accurate and rapid identification of viruses is crucial for an effective medical diagnosis when dealing with infections. Conventional methods, including DNA amplification techniques or lateral-flow assays, are constrained to a specific set of targets to search for. In this study, we introduce a novel tandem mass spectrometry proteotyping-based method that offers a universal approach for the identification of pathogenic viruses and other components, eliminating the need for a priori knowledge of the sample composition. Our protocol relies on a time and cost-efficient peptide sample preparation, followed by an analysis with liquid chromatography coupled to high-resolution tandem mass spectrometry. As a proof of concept, we first assessed our method on publicly available shotgun proteomics datasets obtained from virus preparations and fecal samples of infected individuals. Successful virus identification was achieved with 53 public datasets, spanning 23 distinct viral species. Furthermore, we illustrated the method's capability to discriminate closely related viruses within the same sample, using alphaviruses as an example. The clinical applicability of our method was demonstrated by the accurate detection of the vaccinia virus in spiked saliva, a matrix of paramount clinical significance due to its non-invasive and easily obtainable nature. This innovative approach represents a significant advancement in pathogen detection and paves the way for enhanced diagnostic capabilities.

Tandem Mass Spectrometry↗

PubMed2026

Identification and characterization of anti-chikungunya virus compounds using a biosafe toolkit.

Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus for which no specific antiviral therapy is currently available. During the large outbreak in Foshan, Guangdong Province, China, in July 2025, CHIKV rapidly spread to neighboring regions and caused more than 16,000 confirmed cases. In this study, the predominant outbreak strain of CHIKV was selected as the reference sequence to establish a panel of complementary biosafe tools for antiviral compound screening and mechanistic investigation. A virus replicon particle (VRP) system for CHIKV was first constructed and applied to compound library screening, resulting in the identification of three candidate antiviral compounds: MDL-12330A, bazedoxifene acetate, and anidulafungin. To further validate their antiviral activities and investigate their potential mechanisms, CHIKV functional evaluation systems were subsequently established, including vesicular stomatitis virus (VSV)- and murine leukemia virus (MLV)-based pseudovirus systems for viral entry, a replicon RNA system for post-entry replication-associated processes, a replication-defective nsP4 mutant replicon RNA system for primary translation, and a virus-like particle (VLP) system for viral particle assembly and budding assessment. Using these complementary systems, we systematically evaluated the antiviral profiles of the three candidate compounds across multiple stages of the CHIKV life cycle. This analysis revealed distinct stage-specific inhibitory patterns and provided insights into their potential antiviral mechanisms, which warrant validation using authentic CHIKV infection to assess their translational potential.

Chikungunya virus↗

PubMed2026

Ross River virus transmission, infection, and disease: two and a half decades of research progress-an updated cross-disciplinary review.

SUMMARYRoss River virus (RRV) causes the most mosquito-borne disease notifications in Australia and a considerable burden of non-fatal, yet frequently prolonged rheumatic illness across the Australia-Pacific region, reflected in thousands of notifications each year and notable economic and quality-of-life losses. Research on RRV spans multiple disciplines, encompassing viral genomics, immunopathology, transmission ecology, epidemiology, entomology, and environmental science. This review synthesizes two decades of cross-disciplinary investigations to present an integrated perspective on the biological, clinical, ecological, and environmental dimensions of RRV infection. By consolidating findings from diverse fields, the review enhances understanding of the complex factors influencing RRV transmission and disease outcomes throughout its endemic range.

Humans↗

PubMed2026

Multiplexed RT-LAMP Assays in Handheld Devices for In-Situ Detection of Chikungunya, Dengue, Mayaro, and Zika Viruses.

Mosquito-borne viruses pose a significant global health challenge, particularly in resource-limited settings where multiple viruses often cause illnesses with similar symptoms that require different treatment. We introduce the first 7-plex reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in a hand-held device capable of detecting the presence of Chikungunya virus (CHIKV), dengue virus serotypes (DENV 1-4), Mayaro virus (MAYV), and Zika virus (ZIKV) in a single test. If the result is positive from the single-plex device for the 7-plex assay, 3-plex and 4-plex devices are then used to identify the exact virus within a specimen. In-situ detection is achieved by integrating valve-enabled, paper-based sample preparation with fluorescence detection using a blue LED flashlight as a light source and a yellow plastic film as a filter, allowing visual discrimination between positive and negative samples by the naked eye or by recording images using a smart phone. The detection limits ranged from 2 genome equivalents (GE)/reaction (for ZIKV) to 92 GE/reaction (for DENV-3) across 7 types of viruses when 1 μL of viral RNA was used. We observed 90% overall agreement between the point-of-care (POC) device and lab-based reverse transcription polymerase chain reactions (RT-PCR) when blinded clinical specimens were tested. This assay and device have a potential to address critical surveillance gaps in endemic regions, enabling timely detection of multiple mosquito-borne viruses to guide appropriate clinical management and public health countermeasures in settings where laboratory resources are scarce.

Nucleic Acid Amplification Techniques↗