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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↗

PubMed1979

A comparative study of O'nyong nyong virus with Chikungunya virus and plaque variants.

Two plaque variants of Chikungunya (CHIK) virus were serologically compared with O'nyong nyong (ONN) virus in order to elucidate the reported one way antigenic relationships between the two viruses. Three different hypotheses are examined and evidence is shown to support one of them. Comparison of some biological properties of the viruses showed ONN to be distinct in some respects. All viruses and variants were found to replicate in Anopheles gambiae cells.

Arboviruses↗

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↗

PubMed1977

Contrasting effects of rabbit and human platelets on chikungunya virus infectivity.

Chikungunya virus infectivity was markedly stabilized in the presence of washed suspensions of human platelets but rapidly disappeared in similar preparations of rabbit platelets. Supernatant fluids collected from human platelets had some stabilizing effect on chikungunya virus over a 6-day incubation period at 37 degrees C. Rabbit platelet supernatant fluid had no virus-stabilizing effect, nor did it demonstrate any capacity to inactivate virus as compared to whole rabbit platelet preparations. Thin-section election microscopy demonstrated that chikungunya virus formed an associated with human platelets by becoming entrapped in platelet aggregates; during this process some of the platelets appeared to have undergone degranulation and lysis. Rabbit platelets exposed to chikungunya virus for 24 h demonstrated a considerable amount of platelet degranulation and lysis but virus was not visualized either in association with platelet membranes or within phagocytic vacuoles in the platelet cytoplasm. Human platelets, which appear to be more stable under these incubation conditions, may protect chikungunya virus infectivity from heat inactivation by surrounding viruses with large platelet aggregates whereas rabbit platelets, which appear to be more fragile, do not afford this type of protection. Thus, chikungunya virus in the presence of rabbit platelets may become inactivated by heat or may become bound irreversibly to membranes in such a fashion that infectivity assay and electron microscopy techniques may prove to be too insensitive for detection of virus.

Animals↗

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↗

PubMed2027

Production of Viral Particles from a Chikungunya Virus Infectious Clone.

Chikungunya virus (CHIKV) is a positive-sense single-stranded RNA virus, which poses challenges for its study and genetic manipulation. Because direct mutagenesis of viral RNA genomes is technically impractical, reverse genetics systems are essential tools for investigating viral biology. To enable such approaches, infectious clones containing a full-length cDNA copy of the viral genome are constructed. The cDNA is positioned under the control of a bacteriophage RNA polymerase promoter, allowing commercial RNA polymerases to use the linearized plasmid as a template for the in vitro transcription of full-length viral genomic RNA (gRNA). Importantly, positive-sense viral genomes serve as mRNAs for the translation of viral proteins in a cellular environment, meaning that these transcripts contain all the information required to initiate viral replication. Following transfection into permissive cultured cells, viral proteins are expressed, enabling genome replication and, ultimately, the recovery of infectious particles from the cell supernatant. Here, we describe a detailed procedure for generating CHIKV particles through plasmid linearization, in vitro transcription, and subsequent RNA transfection.

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↗

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

Detection and genomic characterization of a travel-associated ECSA lineage chikungunya virus infection in Mexico.

BACKGROUND: In 2013, chikungunya virus (CHIKV), a re-emerging Aedes-borne virus, was introduced into the Americas. This led to synchronous epidemics across the region associated mainly with the Asian lineage, which eventually subsided. Resurgent outbreaks have been recorded since, principally in South America, largely driven by the East-Central-South-African (ECSA) lineage. In 2025, more than 300,000 CHIKV suspected cases were reported in Brazil and Cuba. CASE SUMMARY: In November 2025, a healthy adult male traveling from Cuba arrived in Merida, Mexico, and shortly after presented febrile symptoms consistent with an arboviral infection. CHIKV infection was diagnosed by RT-qPCR. Though the infection was mild, the patient developed a rash on the abdomen and neck that persisted for up to a month, with further inflammation of the joints of the left leg. Phylogenetic analysis of the viral genome indicated placement within the ECSA lineage, clustering with other contemporaneous virus genomes sampled from Brazil that belong to a recently described clade II within the country, in which viral genomes from Cuba also cluster. CONCLUSION: We identify a travel-associated ECSA lineage CHIKV case in Mexico. This viral lineage has not previously been detected in the country. This finding highlights the risk for subsequent local transmission and is consistent with reports of the presence of this lineage in Cuba. Ten years since the last CHIKV epidemic in Mexico, strengthened surveillance is required to anticipate potential local outbreaks within the region.

ECSA↗

PubMed1979

Production of temperature-sensitive and pathogenic virus from Aedes albopictus cells (Singh) persistently infected with Chikungunya virus.

When A. albopictus, clone C6/36, cells were infected with chikungunya (CHIK) virus, high virus yield accompanied by a cytopathic effect in the acute stage of infection was followed by a relatively low yield of virus over a long period of time. Virus produced from persistently infected cultures became gradually of smaller plaque size and more temperature-sensitive; however, such virus still retained pathogenicity for suckling mice even after one year of infection. When the persistently infected cells were subcultured, a dissociation was observed between the time course of cell growth and that of virus production, suggesting some intracellular mechanisms that turn off virus production. The greater part of the interference against CHIK virus by the culture medium of the persistently infected cells appeared to be mediated by the infective virus in the medium. The infective virus was easily removed from the persistently infected cells either by subculture or by cloning in the presence of anti-CHIK serum, yielding cured cultures or virus-negative clones.

Aedes↗

PubMed2025

Chikungunya virus in Thailand (2020-2023): Epidemiology, clinical features, and genomic insights.

Chikungunya virus (CHIKV) caused significant outbreaks in Thailand during 2008-2009 and 2018-2020. Despite the COVID-19 pandemic, CHIKV continued to circulate; however, data on its epidemiological, clinical, and genetic characteristics during and after this period remains limited. This study investigated CHIKV infections in Thailand from March 2020 to December 2023. Serum samples (n = 1,264) were collected from patients with suspected CHIKV infection at 14 hospitals across five provinces in central, eastern, and northeastern Thailand. Samples were tested by RT-qPCR and IgM fluorescence immunoassay. CHIKV infection was confirmed in 50.5% (638/1,264) of cases. Infections occurred across all age groups, with the highest prevalence among individuals aged ≥56 years. Clinical symptoms significantly associated with infection included myalgia, arthralgia, rash, and conjunctivitis. Rash was more frequently in individuals aged ≤15 years and was significantly associated with lower viral loads. Arthralgia was more common among older adults and was linked to later illness onset. Myalgia was least frequently reported in younger patients. Thirty-eight complete coding sequences of our Thai CHIKV strains were analyzed in phylogenetic and time-scaled trees alongside 186 global strains and 109 ECSA-IOL strains from GenBank, respectively. Genome analysis revealed that CHIKV strains circulating in Thailand during 2020-2023 belonged to the East/Central/South African-Indian Ocean lineage (ECSA-IOL). These strains did not evolve from earlier ECSA-IOL variants that carried the E1-A226V mutation, which was previously detected in Thailand. Instead, all isolates carried E1-K211E and E2-V264A, along with E1-226A, likely introduced from the Indian subcontinent around 2016-2017. This introduction triggered a major outbreak between late 2018 and 2020, followed by sustained transmission. The 2020-2023 Thai strains exhibited high genetic similarity to those from neighboring countries, with multiple nonsynonymous mutations suggesting ongoing viral adaptation. Understanding CHIKV epidemiology, clinical features, and evolution supports improved surveillance, diagnostics, and public health interventions.

Humans↗

PubMed2026

Autochthonous chikungunya virus (CHIKV) outbreak in the province of Modena, Emilia-Romagna region, Italy, August to October 2025: epidemiology, clinical features and virological findings.

Between 10 August and 31 October 2025, 343 cases (306 confirmed and 37 probable) of symptomatic autochthonous chikungunya virus (CHIKV) infection were notified in eight municipalities in the province of Modena, Emilia-Romagna region, northern Italy. The infection was diagnosed by detection of CHIKV RNA in blood and urine samples, and by detection of IgM antibodies against CHIKV. Most common symptoms were arthralgia (n = 326) and fever (n = 317). No fatalities were reported. Chikungunya virus RNA was detected in 39 (14.8%) of 263 pools of Aedes albopictus mosquitoes, thereby confirming local vector-borne transmission. Sequences from 11 case samples and two mosquito pools were whole genome sequenced. The viral strain belonged to the East/Central/South African (ECSA) lineage 2 and was closely related to the strains circulating in Reunion Island in 2024-25. The public health response included rapid vector control measures, reinforced epidemiological surveillance and multidisciplinary coordination between public health authorities and clinicians, laboratories and entomologists. This was one of the largest autochthonous CHIKV outbreaks ever recorded in a temperate European region. It highlights the critical importance of integrated, multidisciplinary preparedness and response for arboviral threats in non-endemic areas.

Humans↗

PubMed2026

Unraveling the epidemiological and dispersal dynamics of the 2024-2025 chikungunya virus epidemic on Réunion Island.

Réunion Island experienced a massive chikungunya virus epidemic in 2024-2025, with >54,000 confirmed cases. This is the second major chikungunya epidemic on the island, following the first one that peaked 20 years ago. It has been asserted that this new outbreak finds its origin in a single introduction event into the island, offering an opportunity to exploit viral genomic data to understand the epidemiological and dispersal dynamics of the introduced transmission chain. We sequenced >3,000 viral genomes collected during the epidemic. Harnessing this genomic dataset, we used several phylogeographic and phylodynamic approaches to unravel the paths taken by the transmission chain and the external factors that might have impacted its dispersal and epidemiological dynamics on the island. Our analyses highlight a dispersal pattern in line with a gravity-model dynamic with viral transition events being more frequent from and toward more populated areas. Our analyses reveal that the transmission chain was overall spatially intermixed, with frequent exchanges among residential areas. In addition, we show that the temporal dynamic and intensity of the epidemic were associated with climatic variables, namely temperature and precipitation. Our results also show that in theory, the population immunity-resulting from this epidemic and the previous one (2005-2006)-could be sufficient to explain on its own the decrease in the transmission rate that led to the end of the epidemic. While a short-term resurgence cannot be excluded, the risk of a large-scale circulation of the virus in the human population appears therefore relatively limited in the upcoming seasons.

Reunion↗

PubMed1979

Characterization of two Chikungunya virus variants.

The stability of virulence and plaque size of two variants of Chikungunya virus (genus Alphavirus) were examined. Mouse pathogenicity did not coincide with infective virus levels in the brain. An increase in the average survival times of mice receiving a lethal dose of the variant which allowed prolonged survival at high doses and harvested late after infection was observed. Studies in Vero cells suggested that the number of infective virus particles produced per cell was lower with the small plaque variant, though these cells were selective for this clone. On the other hand suckling mice or antisera favoured a more virulent large plaque variant.

Animals↗

PubMed2025

Microbiological Investigations for Chikungunya Virus in Children With Acute Encephalitis Syndrome in a Non-Outbreak Setting in Southern India.

Chikungunya virus (CHIKV) is an emerging cause of acute encephalitis syndrome (AES) in India, with limited data on its role in childhood AES in southern India. We systematically evaluated children with AES in southern India during a non-epidemic period for CHIKV. Serum and cerebrospinal fluid (CSF) samples were tested for CHIKV using IgM ELISA and real-time reverse transcriptase PCR. Amplicon sequencing was performed on PCR-positive samples. Clinical and laboratory features were compared between children with and without CSF CHIKV positivity (PCR/IgM antibodies). Of 376 children with AES, 20 (5.3%) had positive CHIKV tests. Co-infections were common, particularly with scrub typhus. Children presented with diverse symptoms affecting various organ systems. Neurological manifestations included meningism, seizures, cerebellar signs, behavioral abnormalities, cranial nerve involvement, involuntary movements, and hemiparesis/hemiplegia. Children with CSF CHIKV positivity showed more focal neurological deficits and transaminitis, and less musculoskeletal symptoms. Sequencing confirmation of CHIKV was made in all patients with positive CHIKV PCR, revealing a close relationship with 2016 Kenyan and Indian strains, albeit in a different clade within the East/Central/South African genotype. Along with important mutations known to impact CHIKV infectivity, four novel amino acid substitutions were detected in envelope protein coding regions. Our findings underscore the importance of routine and comprehensive CHIKV testing for children with AES, irrespective of season/outbreak. The high rate of co-infections warrants further research. Continued genomic surveillance is essential to monitor emerging mutations with epidemic potential, increased severity and the risk of neurological disease.

Humans↗

PubMed2027

Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.

This protocol provides a comprehensive, step-by-step workflow for whole-genome sequencing of Chikungunya virus (CHIKV) using an amplicon-based strategy optimized for Oxford Nanopore Technologies (ONT) platforms. The procedure includes detailed instructions for sample handling, viral RNA extraction, quality control, cDNA synthesis, multiplex PCR amplification, library preparation, sequencing, and primary bioinformatic processing. The protocol is designed to maximize reproducibility across laboratories and is suitable for genomic surveillance applications, including outbreak investigation and molecular epidemiology, even when working with low-to-moderate viral loads.

Chikungunya virus↗

PubMed1975

Isolation of chikungunya virus contaminating an Aedes albopictus cell line.

An Aedes albopictus cell line was found contaminated with structures morphologically compatible with an alphavirus. Rapid isolation of a cytopathic virus was effected by combining sonication, concentration with Aquacide II-r, rate zonal sedimentation and subsequent plating of fractions on Vero cells under agar overlay. The virus caused neithedeath nor disease on inoculation into infant and adult mice. It produced a c.p.e. in Vero and BHK 21 cells, and multiplied in Singh's Aedes aegypti cells. The virus was identified serologically as chikungunya by complement-fixation and plaque reduction netralization test. Virus was not detected in a single attempt by these methods in the American Type Culture Collection A. albopicturs line. The presence of chikungunya virus in A. albopictus cells is not easily recognized and may complicate interpretation of experimental results.

Aedes↗

PubMed1979

Effects of tannic acid and its related compounds upon Chikungunya virus.

The present report describes not only the effects of tannic acid (TA; belonging to hydrolyzable tannins) and its related compounds upon the infectivity of Chikungunya virus (CHIKV) but also the mechanism involved in this phenomenon. Our data show that TA inactivates CHIKV in vitro. Since the inactivating effect turned out to be pH-dependent and was suppressed by bovine serum albumin, it is most probable that the virus-inactivating capacity of TA is attributable to its preferential binding to proteins of virus particles. Examination on the virus-inactivating capacities of some TA-related compounds and comparison of their structures indicated that the active site of TA and its analogues might be the phenolic hydroxyl groups in their molecules. It seems that the active groups interact with the proteins of virus particles, resulting in a reduction or loss of viral infectivity. Discussion is made on the specificity of the actions of tannins and the possibility of application thereof to chemicals which are useful to investigate the nature and properties of viral proteins.

Animals↗