Chikungunya seroprevalence, force of infection, and prevalence of chronic disability after infection in endemic and epidemic settings: a systematic review, meta-analysis, and modelling study

Chikungunya virus and other emerging arthritogenic alphaviruses

Arthritogenic alphaviruses are arboviruses (arthropod-borne viruses) that are genetically and serologically related positive-strand RNA viruses and cause epidemics on a global scale. They are transmitted by mosquitoes and cause diseases in humans that are mainly characterized by fever and often debilitating, sometimes chronic polyarthralgia. At present, approved treatments or vaccines are not available for most arthritogenic alphaviruses, and recently licensed vaccines against chikungunya virus are awaiting implementation in endemic areas. Most arthritogenic alphaviruses are currently limited to specific geographic areas due to vector distributions and availability of amplifying hosts, but they pose a substantial risk of emergence in other regions. The exception is chikungunya virus, which has emerged repeatedly from Africa, established sustained and efficient transmission in urban areas (including in temperate climates) and has caused major epidemics across the world. In this Review, we highlight recent advances in our understanding of the transmission cycles of arthritogenic alphaviruses, their vectors, epidemiology, transmission dynamics, evolution, pathophysiology and immune responses. We also outline strategies and countermeasures to anticipate and mitigate the impact of arthritogenic alphaviruses on human health.

Transcriptomic analysis of chronic chikungunya in the Reunionese CHIKGene cohort uncovers a shift in gene expression more than 10 years after infection

AIM

In 2005-2006, a chikungunya epidemic of unprecedented magnitude hit Reunion Island, which raised a public health concern through the substantial proportions of long-lasting manifestations. To understand the pathophysiology underlying chronic chikungunya (CC), we designed the CHIKGene cohort study and collected blood samples from 133 subjects diagnosed with CC and from 86 control individuals that had recovered within 3 months, 12-to-15 years after exposure.

METHODS

We conducted bulk RNAseq analysis on peripheral blood mononuclear cells to find differentially expressed genes (DEGs), gene set enrichment analysis (GSEA) and gene ontologies to uncover top-level enriched terms associated with DEGs, and weighted gene correlation network analysis (WGCNA) to elucidate underlying cellular processes.

RESULTS

Among 1549 DEGs, gene expression analysis identified 10 top genes including NR4A2 and TRIM58 (upregulated in CC), IGHG3 and IGHV3-49 (downregulated in CC) linked to immune regulation, OSBP2 (upregulated in CC) and SEMA6B (downregulated in CC) linked to neuronal homeostasis and axon guidance, respectively. GSEA and WGCNA unveiled cellular processes such as "Metabolism of RNA" and "Cell Cycle".

CONCLUSIONS

This study uncovers a shift in gene expression of CC subjects. IGHG3 and IGHV3-49 gene shut-offs spotlight the importance of neutralizing antibodies against chikungunya virus in the progression to chronic disease. Human diseases associations highlight connections to rheumatoid arthritis, nervous and cardiac systems. GSEA and WGCNA bounce the hypotheses of a persistent viral reservoir or an increased susceptibility to RNA viral pathogens with new onset infections. Together, our findings might offer potential targets for therapeutic options aimed at alleviating chronic chikungunya.

Modeling the impact of vaccine campaigns on the epidemic transmission dynamics of chikungunya virus outbreaks

A licensed chikungunya vaccine now exists; however, it remains unclear whether it could be deployed during outbreaks to reduce the health burden. We used an epidemic in Paraguay as a case study. We conducted a seroprevalence study and used models to reconstruct epidemic transmission dynamics, providing a framework to assess the theoretical impact of a vaccine had it been available. We estimated that 33.0% (95% confidence interval (CI) 30.1-36.0%) of the population became infected during the outbreak. Of these individuals, 6.3% (95% CI 5.8-6.9%) were detected by the surveillance system, with a mean infection fatality ratio of 0.013% (95% CI 0.012-0.014%). A disease-blocking vaccine with 75% efficacy deployed in 40% of individuals aged ≥12 years over a 3-month period would have prevented 34,200 (95% CI 30,900-38,000) cases, representing 23% of all cases, and 73 (95% CI 66-81) deaths. If the vaccine also leads to infection blocking, 88% of cases would have been averted. These findings suggest that the vaccine is an important new tool to control outbreaks.

Long-term persistence of serum IgM antibodies against chikungunya virus in patients with chronic arthralgia

BACKGROUND

Anti-Chikungunya virus (CHIKV) IgM antibodies may persist for months after infection in some individuals, but the evidence is limited, and their exact duration remains unknown.

OBJECTIVE

This study aimed to determine the duration for which anti-CHIKV IgM antibodies remain detectable following acute infection.

METHODS

A commercial ELISA was used to assess the frequency of anti-CHIKV IgM antibody detection over time in 145 longitudinal serum samples obtained from 45 laboratory-confirmed chikungunya patients in Brazil (two to six samples per patient).

RESULTS

Among samples obtained within seven days post-symptom onset (DPSO), 13% (6/45) were IgM-positive. Between 10 and 120 DPSO, 100% (62/62) of samples were positive. Positivity rates for samples collected between 121 - 720, 721-900, 901-1,080, 1,081-1,260, and > 1,260 DPSO were 62% (5/8), 35% (6/17), 12% (1/8), 33% (1/3) and 50% (1/2), respectively. Notably, among 21 patients who developed chronic arthralgia and had at least one sample collected > 720 DPSO, 7 (33%) still had detectable anti-CHIKV IgM. This suggests that approximately one-third of chikungunya patients with chronic arthralgia may maintain anti-CHIKV IgM for over two years following acute disease.

CONCLUSIONS

Our findings indicate that anti-CHIKV IgM antibodies can persist substantially longer than typically observed for acute RNA virus infections. This has significant implications for chikungunya diagnosis and surveillance. Further research is needed to determine whether long-term IgM persistence also occurs in patients without chronic chikungunya symptoms.

Deep mutationally scanned CHIKV E3/E2 virus library maps viral amino acid preferences and predicts viral escape mutants of neutralizing CHIKV antibodies

As outbreaks of chikungunya virus (CHIKV), a mosquito-borne alphavirus, continue to present public health challenges, additional research is needed to generate protective and safe vaccines and effective therapeutics. Prior research established a role for antibodies in mediating protection against CHIKV infection, and the early appearance of CHIKV-specific IgG or IgG neutralizing antibodies protects against progression to chronic CHIKV disease in humans. However, the importance of epitope specificity for these protective antibodies and how skewed responses contribute to the development of acute and chronic CHIKV-associated joint disease remains poorly understood. Here, we describe the deep mutational scanning of one of the dominant targets of neutralizing antibodies during CHIKV infection, the E3/E2 (also known as p62) glycoprotein complex, to simultaneously test thousands of p62 mutants against selective pressures of interest in a high throughput manner. Characterization of the virus library revealed achievement of high diversity while also selecting out nonfunctional virus variants. Furthermore, this study provides evidence that this virus library system can comprehensively map sites critical for the neutralization function of antibodies of both known and unknown p62 domain specificities.IMPORTANCEChikungunya virus (CHIKV) is a mosquito-borne alphavirus of global health concern that causes debilitating acute and chronic joint disease. Prior studies established a critical role for antibodies in protection against CHIKV infection. Here, we describe the generation of a high-throughput, functional virus library capable of identifying critical functional sites for anti-viral antibodies. This new tool can be used to better understand antibody responses associated with distinct CHIKV infection outcomes and could contribute to the development of efficacious vaccines and antibody-based therapeutics.

Current and future advances in practice: arboviral arthritides

Arboviral arthritides are a group of viral infections affecting the musculoskeletal system. Mosquitoes are vectors for some of the arboviral febrile diseases such as due to chikungunya, dengue and Zika viruses, which constitute a major proportion of arboviral arthritide syndromes in humans. They have gained epidemiological importance as the natural habitats of these mosquitoes are in the vicinity of human dwellings. Chikungunya virus infection frequently leads to post-infectious chronic musculoskeletal syndromes including erosive inflammatory arthritis, which resembles RA. Clinical features of the chronic phase result from the chronic persistence of the virus in certain tissues after the acute infection has resolved. In addition, the triggering of autoimmunity has also been implicated in musculoskeletal syndromes. Due to the diversity of clinical presentations and overlapping features with other viral illnesses and inflammatory arthritides, diagnosis and management are challenging. Poor prognostic factors for predicting evolution to chronic arthritides are not well delineated. There is no universal agreement regarding when to start immunomodulatory agents and the duration of such therapy. The lack of specific antiviral agents adds to the complexity of the situation. A live-attenuated vaccine has been recently approved by the US Food and Drug Administration for the prevention of chikungunya virus infection. This review discusses the musculoskeletal syndromes related to arboviral infections, with a major focus on chikungunya virus-related arthritis to provide practical guidance to clinicians involved in managing patients with chikungunya and its sequelae.

Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections

Global risk maps are an important tool for assessing the global threat of mosquito and tick-transmitted arboviral diseases. Public health officials increasingly rely on risk maps to understand the drivers of transmission, forecast spread, identify gaps in surveillance, estimate disease burden, and target and evaluate the impact of interventions. Here, we describe how current approaches to mapping arboviral diseases have become unnecessarily siloed, ignoring the strengths and weaknesses of different data types and methods. This places limits on data and model output comparability, uncertainty estimation and generalisation that limit the answers they can provide to some of the most pressing questions in arbovirus control. We argue for a new generation of risk mapping models that jointly infer risk from multiple data types. We outline how this can be achieved conceptually and show how this new framework creates opportunities to better integrate epidemiological understanding and uncertainty quantification. We advocate for more co-development of risk maps among modellers and end-users to better enable risk maps to inform public health decisions. Prospective validation of risk maps for specific applications can inform further targeted data collection and subsequent model refinement in an iterative manner. If the expanding use of arbovirus risk maps for control is to continue, methods must develop and adapt to changing questions, interventions and data availability.

Mutations in chikungunya virus nsP4 decrease viral fitness and sensitivity to the broad-spectrum antiviral 4'-Fluorouridine

Chikungunya virus (CHIKV) is an arthritogenic alphavirus that has re-emerged to cause large outbreaks of human infections worldwide. There are currently no approved antivirals for treatment of CHIKV infection. Recently, we reported that the ribonucleoside analog 4'-fluorouridine (4'-FlU) is a highly potent inhibitor of CHIKV replication, and targets the viral nsP4 RNA dependent RNA polymerase. In mouse models, oral therapy with 4'-FlU diminished viral tissue burdens and virus-induced disease signs. To provide critical evidence for the potential of 4'-FlU as a CHIKV antiviral, here we selected for CHIKV variants with decreased 4'-FlU sensitivity, identifying two pairs of mutations in nsP2 and nsP4. The nsP4 mutations Q192L and C483Y were predominantly responsible for reduced sensitivity. These variants were still inhibited by higher concentrations of 4'-FlU, and the mutations did not change nsP4 fidelity or provide a virus fitness advantage in vitro or in vivo. Pathogenesis studies in mice showed that the nsP4-C483Y variant caused similar disease and viral tissue burden as WT CHIKV, while the nsP4-Q192L variant was strongly attenuated. Together these results support the potential of 4'-FlU to be an important antiviral against CHIKV.

Deep mutationally scanned (DMS) CHIKV E3/E2 virus library maps viral amino acid preferences and predicts viral escape mutants of neutralizing CHIKV antibodies

As outbreaks of chikungunya virus (CHIKV), a mosquito-borne alphavirus, continue to present public health challenges, additional research is needed to generate protective and safe vaccines and effective therapeutics. Prior research has established a role for antibodies in mediating protection against CHIKV infection, and the early appearance of CHIKV-specific IgG or IgG neutralizing antibodies protects against progression to chronic CHIKV disease in humans. However, the importance of epitope specificity for these protective antibodies and how skewed responses contribute to development of acute and chronic CHIKV-associated joint disease remains poorly understood. Here, we describe the deep mutational scanning of one of the dominant targets of neutralizing antibodies during CHIKV infection, the E3/E2 (also known as p62) glycoprotein complex, to simultaneously test thousands of p62 mutants against selective pressures of interest in a high throughput manner. Characterization of the virus library revealed achievement of high diversity while also selecting out non-functional virus variants. Furthermore, this study provides evidence that this virus library system can comprehensively map sites critical for the neutralization function of antibodies of both known and unknown p62 domain specificities.

The global health and economic burden of chikungunya from 2011 to 2020: a model-driven analysis on the impact of an emerging vector-borne disease

INTRODUCTION

Chikungunya is a mosquito-borne arboviral disease posing an emerging global public health threat. Understanding the global burden of chikungunya is critical for designing effective prevention and control strategies. However, current estimates of the economic and health impact of chikungunya remain limited and are potentially underestimated. This study aims to provide a comprehensive overview of the chikungunya burden worldwide.

METHODS

We analysed the global burden of chikungunya between 2011 and 2020 and calculated disability-adjusted life years (DALYs) and direct and indirect costs using a data-driven simulation model. The main outcomes were the number of cases, the total DALY burden, and the direct and indirect costs of acute and chronic chikungunya between 2011 and 2020.

RESULTS

Our study revealed a total of 18.7 million chikungunya cases in 110 countries between 2011 and 2020, causing 1.95 million DALYs. Most of this burden was found in the Latin American and Caribbean region. The total economic burden caused by chikungunya over these 10 years was estimated at $2.8 billion in direct costs and $47.1 billion in indirect costs worldwide. Long-term chronic illness was the source of most costs and DALYs.

CONCLUSION

Chikungunya has a higher disease burden than was previously estimated and costs related to the disease are substantial. Especially in combination with its unpredictable nature, chikungunya could significantly impact local health systems. Insights from this study could inform decision makers on the impact of chikungunya on population health and help them to appropriately allocate resources to protect vulnerable populations from this debilitating disease.

Chikungunya vaccine development, challenges, and pathway toward public health impact

Chikungunya is a neglected tropical disease of growing public health concern with outbreaks in more than 114 countries in Asia, Africa, Americas, Europe, and Oceania since 2004. There are no specific antiviral treatment options for chikungunya virus infection. This article describes the chikungunya vaccine pipeline and assesses the challenges in the path to licensure, access, and uptake of chikungunya vaccines in populations at risk. Ixchiq (VLA1533/Ixchiq - Valneva) was the first licensed chikungunya vaccine by the US Food and Drug Administration in November 2023, European Medicines Agency in May 2024, and Health Canada in June 2024. Five chikungunya vaccine candidates (BBV87 - BBIL/IVI, MV-CHIK - Themis Bioscience, ChAdOx1 Chik - University of Oxford, PXVX0317 / VRC-CHKVLP059-00-VP - Bavarian Nordic, and mRNA-1388 - Moderna) are in development. Evidence on chikungunya disease burden alongside the public health and economic impact of vaccination are critical for decision-making on chikungunya vaccine introduction in endemic and epidemic settings. Further, global and regional stakeholders need to agree on a sustainable financing mechanism for manufacturing at scale to facilitate fair access and equitable vaccine distribution to at-risk populations in different geographic settings. This could partly be facilitated through obtaining consensus on scientific and regulatory principles for initial vaccine introduction and generating evidence on chikungunya burden and disease awareness among populations at risk. Specifically, this article advocates for the formation of a global chikungunya vaccine consortium that includes regulators, policymakers, sponsors, and manufacturers to assist in overcoming the global and local challenges for chikungunya vaccine licensure, policy, financing, demand generation, and access to at-risk populations.

How mathematical modelling can inform outbreak response vaccination

Mathematical models are established tools to assist in outbreak response. They help characterise complex patterns in disease spread, simulate control options to assist public health authorities in decision-making, and longer-term operational and financial planning. In the context of vaccine-preventable diseases (VPDs), vaccines are one of the most-cost effective outbreak response interventions, with the potential to avert significant morbidity and mortality through timely delivery. Models can contribute to the design of vaccine response by investigating the importance of timeliness, identifying high-risk areas, prioritising the use of limited vaccine supply, highlighting surveillance gaps and reporting, and determining the short- and long-term benefits. In this review, we examine how models have been used to inform vaccine response for 10 VPDs, and provide additional insights into the challenges of outbreak response modelling, such as data gaps, key vaccine-specific considerations, and communication between modellers and stakeholders. We illustrate that while models are key to policy-oriented outbreak vaccine response, they can only be as good as the surveillance data that inform them.

From bench to clinic: the development of VLA1553/IXCHIQ, a live-attenuated chikungunya vaccine

BACKGROUND

Over the past 20 years, over 5 million cases of chikungunya, a mosquito-transmitted viral disease, have been reported in over 110 countries. Until recently, preventative strategies for chikungunya were largely ineffective, relying on vector control and individual avoidance of mosquito bites.

METHODS

This review outlines the preclinical and clinical efficacy and safety data that led to the approval of VLA1553 (IXCHIQ®), a live-attenuated vaccine against chikungunya disease. It also describes the innovative development pathway of VLA1553, based on an immunological surrogate of protection, and discusses ongoing and future post-licensure studies.

RESULTS

In mice and non-human primate models, VLA1553 elicited high titres of neutralizing antibodies, conferred protection against wild-type chikungunya virus challenge and raised no safety concerns. A Phase 1 clinical trial of VLA1553 demonstrated 100% seroconversion among 120 healthy participants, with sustained neutralizing antibody titres after 12 months. These results and determination of a surrogate marker of protection led to advancement of VLA1553 directly into Phase 3 clinical development, as agreed with the US Food and Drug Administration (FDA) and the European Medicines Agency. The pivotal Phase 3 trial met its primary immunogenicity endpoint, achieving seroprotective levels based on immuno-bridging in baseline seronegative participants 28 days post-vaccination. These findings enabled submission of a Biologics Licence Application to the FDA for accelerated approval of VLA1553 in the US for adults aged ≥18 years. Ongoing and planned studies will confirm the clinical efficacy/effectiveness and safety of VLA1553 in adults and younger individuals, and will generate data in chikungunya endemic countries that have the highest unmet need.

CONCLUSION

VLA1553 is the first vaccine approved for the prevention of chikungunya disease in adults, following accelerated development based on a serological surrogate marker of protection. VLA1553 adds to strategies to reduce the spread and burden of chikungunya in endemic populations and travellers.

Understanding the Transmission Dynamics of the Chikungunya Virus in Africa

The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underreporting and underdiagnosis. Here, we review the literature and analyse publicly available cases, outbreaks, and genomic data, providing insights into the epidemiology, genetic diversity, and transmission dynamics of CHIKV in Africa. Our analyses reveal the circulation of geographically distinct CHIKV genotypes, with certain regions experiencing a disproportionate burden of disease. Phylogenetic analysis of sporadic outbreaks in West Africa suggests repeated emergence of the virus through enzootic spillover, which is markedly different from inferred transmission dynamics in East Africa, where the virus is often introduced from Asian outbreaks, including the recent reintroduction of the Indian Ocean lineage from the Indian subcontinent to East Africa. Furthermore, there is limited evidence of viral movement between these two regions. Understanding the history and transmission dynamics of outbreaks is crucial for effective public health planning. Despite advances in surveillance and research, diagnostic and surveillance challenges persist. This review and secondary analysis highlight the importance of ongoing surveillance, research, and collaboration to mitigate the burden of CHIKV in Africa and improve public health outcomes.