New insights into chikungunya virus emergence and spread from Southeast Asia

Infectomics of Chikungunya Virus: Roles Played by Host Factors

Chikungunya virus (CHIKV), prevalent in tropical regions, is known for causing frequent outbreaks, particularly in Central Africa, South America, and Southeast Asia. It is an arbovirus transmitted by the Aedes (Ae.) aegypti and Ae. albopictus mosquitoes. Infections lead to severe joint and muscle pain, which can linger and significantly impair an individual's health, quality of life, and economic stability. Recent climatic changes and the globalization of travel have facilitated the worldwide spread of these mosquitoes. Currently, no U.S. Food and Drug Administration (FDA) approved drug is available for treating CHIKV infection. Recently, the FDA approved a live, attenuated vaccine called Ixchiq. However, this vaccine has been linked to side effects, leading the FDA to mandate additional post-marketing studies to assess the risk of severe adverse reactions similar to the virus. An emerging strategy in drug development focuses on targeting host factors that the virus exploits rather than the viral proteins themselves. This review explores the interactions between CHIKV and host factors that could be potential therapeutic targets. Despite progress in understanding the life cycle of CHIKV, the immune system's role in combating the virus still needs to be fully understood. Investigating treatments that enhance the host's immune response may offer new paths to combating CHIKV.

Dengue Virus and Zika Virus Seroprevalence in the South Pacific Populations of the Cook Islands and Vanuatu

Arboviral diseases are serious threats to global health with increasing prevalence and potentially severe complications. Significant arthropod-borne viruses are the dengue viruses (DENV 1-4), the Zika virus (ZIKV), and the chikungunya virus (CHIKV). Among the areas most affected is the South Pacific Region (SPR). Here, arboviruses not only cause a high local burden of disease, but the region has also proven to contribute to their global spread. Outpatient serum samples collected between 08/2016 and 04/2017 on three islands of the island states of Vanuatu and the Cook Islands were tested for anti-DENV- and anti-ZIKV-specific antibodies (IgG) using enzyme-linked immunosorbent assays (ELISA). ELISA test results showed 89% of all test sera from the Cook Islands and 85% of the Vanuatu samples to be positive for anti-DENV-specific antibodies. Anti-ZIKV antibodies were identified in 66% and 52%, respectively, of the test populations. Statistically significant differences in standardized immunity levels were found only at the intranational level. Our results show that in both the Cook Islands and Vanuatu, residents were exposed to significant Flavivirus transmission. Compared to other seroprevalence studies, the marked difference between ZIKV immunity levels and previously published CHIKV seroprevalence rates in our study populations is surprising. We propose the timing of ZIKV and CHIKV emergence in relation to recurrent DENV outbreaks and the impact of seasonality as explanatory external factors for this observation. Our data add to the knowledge of arboviral epidemics in the SPR and contribute to a better understanding of virus spread, including external conditions with potential influence on outbreak dynamics. These data may support preventive and rapid response measures in the affected areas, travel-related risk assessment, and infection identification in locals and returning travelers.

Drugs targeting structural and nonstructural proteins of the chikungunya virus: A review

Chikungunya virus (CHIKV) is a single positive-stranded RNA virus of the Togaviridae family and Alphavirus genus, with a typical lipid bilayer envelope structure, and is the causative agent of human chikungunya fever (CHIKF). The U.S. Food and Drug Administration has recently approved the first chikungunya vaccine, Ixchiq; however, vaccination rates are low, and CHIKF is prevalent owing to its periodic outbreaks. Thus, developing effective anti-CHIKV drugs in clinical settings is imperative. Viral proteins encoded by the CHIKV genome play vital roles in all stages of infection, and developing therapeutic agents that target these CHIKV proteins is an effective strategy to improve CHIKF treatment efficacy and reduce mortality rates. Therefore, in the present review article, we aimed to investigate the basic structure, function, and replication cycle of CHIKV and comprehensively outline the current status and future advancements in anti-CHIKV drug development, specifically targeting nonstructural (ns) proteins, including nsP1, nsP2, nsP3, and nsP4 and structural proteins such as capsid (C), E3, E2, 6K, and E1.

The impact of arthritogenic viruses in oral tissues

Arthritis and periodontitis are inflammatory diseases that share several immunopathogenic features. The expansion in the study of virus-induced arthritis has shed light on how this condition could impact other parts of the human body, including the mouth. Viral arthritis is an inflammatory joint disease caused by several viruses, most notably the alphaviruses Chikungunya virus (CHIKV), Sindbis virus (SINV), Ross River virus (RRV), Mayaro virus (MAYV), and O'nyong'nyong virus (ONNV). These viruses can induce an upsurge of matrix metalloproteinases and immune-inflammatory mediators such as Interleukin-6 (IL6), IL-1β, tumor necrosis factor, chemokine ligand 2, and receptor activator of nuclear factor kappa-B ligand in the joint and serum of infected individuals. This can lead to the influx of inflammatory cells to the joints and associated muscles as well as osteoclast activation and differentiation, culminating in clinical signs of swelling, pain, and bone resorption. Moreover, several data indicate that these viral infections can affect other sites of the body, including the mouth. The human oral cavity is a rich and diverse microbial ecosystem, and viral infection can disrupt the balance of microbial species, causing local dysbiosis. Such events can result in oral mucosal damage and gingival bleeding, which are indicative of periodontitis. Additionally, infection by RRV, CHIKV, SINV, MAYV, or ONNV can trigger the formation of osteoclasts and upregulate pro-osteoclastogenic inflammatory mediators, interfering with osteoclast activation. As a result, these viruses may be linked to systemic conditions, including oral manifestations. Therefore, this review focuses on the involvement of alphavirus infections in joint and oral health, acting as potential agents associated with oral mucosal inflammation and alveolar bone loss. The findings of this review demonstrate how alphavirus infections could be linked to the comorbidity between arthritis and periodontitis and may provide a better understanding of potential therapeutic management for both conditions.

Chikungunya virus (CHIKV) seroprevalence in the South Pacific populations of the Cook Islands and Vanuatu with associated environmental and social factors

BACKGROUND

Arthropod-borne diseases pose a significant and increasing risk to global health. Given its rapid dissemination, causing large-scale outbreaks with severe human infections and economic loss, the Chikungunya virus (CHIKV) is one of the most important arboviruses worldwide. Despite its significance, the real global impact of CHIKV remains underestimated as outbreak data are often incomplete and based solely on syndromic surveillance. During 2011-2016, the South Pacific Region was severely affected by several CHIKV-epidemics, yet the area is still underrepresented in arboviral research.

METHODS

465 outpatient serum samples collected between 08/2016 and 04/2017 on three islands of the island states Vanuatu (Espiritu Santo) and the Cook Islands (Rarotonga, Aitutaki) were tested for anti-CHIKV specific antibodies using Enzyme-linked immunosorbent Assays.

RESULTS

A total of 30% (Cook Islands) and 8% (Vanuatu) of specimens were found positive for anti-CHIKV specific antibodies with major variations in national and intranational immunity levels. Seroprevalence throughout all age groups was relatively constant. Four potential outbreak-protective factors were identified by comparing the different study settings: presence of Ae. albopictus (in absence of ECSA E1-A226V-mutation CHIKV), as well as low levels of human population densities, residents' travel activity and tourism.

CONCLUSION

This is the first seroprevalence study focussing on an arboviral disease in the Cook Islands and Vanuatu. It highlights the impact of the 2014/2015 CHIKV epidemic on the Cook Islands population and shows that a notable part of the Vanuatu test population was exposed to CHIKV although no outbreaks were reported. Our findings supplement the knowledge concerning CHIKV epidemics in the South Pacific Region and contribute to a better understanding of virus dissemination, including outbreak modifying factors. This study may support preventive and rapid response measures in affected areas, travel-related risk assessment and infection identification in returning travellers.

TRIAL REGISTRATION

ClinicalTrials.gov Aachen: 051/16_09/05/2016 Cook Islands Ref.: #16-16 Vanuatu Ref.: MOH/DG 10/1/1-GKT/lr.

Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants

The simultaneous transmission of two lineages of the chikungunya virus (CHIKV) was discovered after the pathogen's initial arrival in Brazil. In Oiapoque (Amapá state, north Brazil), the Asian lineage (CHIKV-Asian) was discovered, while in Bahia state, the East-Central-South-African lineage (CHIKV-ECSA) was discovered (northeast Brazil). Since then, the CHIKV-Asian lineage has been restricted to the Amazon region (mostly in the state of Amapá), whereas the ECSA lineage has expanded across the country. Despite the fact that the Asian lineage was already present in the Amazon region, the ECSA lineage brought from the northeast caused a large outbreak in the Amazonian state of Roraima (north Brazil) in 2017. Here, CHIKV spread in the Amazon region was studied by a Zika-Dengue-Chikungunya PCR assay in 824 serum samples collected between 2013 and 2016 from individuals with symptoms of viral infection in the Amapá state. We found 11 samples positive for CHIKV-Asian, and, from these samples, we were able to retrieve 10 full-length viral genomes. A comprehensive phylogenetic study revealed that nine CHIKV sequences came from a local transmission cluster related to Caribbean strains, whereas one sequence was related to sequences from the Philippines. These findings imply that CHIKV spread in different ways in Roraima and Amapá, despite the fact that both states had similar climatic circumstances and mosquito vector frequencies.

Molecular characterization of chikungunya virus isolates from two localized outbreaks during 2014-2019 in Kerala, India

After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission routes can be traced by complete genome sequencing studies. We investigated two outbreaks in 2014 and 2019 in Kerala, India. Chikungunya virus (CHIKV) was isolated from the samples, and whole genomes were sequenced for a 2014 isolate and a 2019 isolate. Phylogenetic analysis revealed that the isolates formed a separate group with a 2019 isolate from Pune, Maharashtra, and belonged to the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of the E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have been caused by a virus that had been circulating in India since 2014. A detailed study is needed to investigate the evolution of CHIKV in India.

Targeting Chikungunya Virus Entry: alternatives for new inhibitors in drug discovery

Chikungunya virus (CHIKV) is an Alphavirus (Togaviridae) responsible for Chikungunya fever (CHIKF) that is mainly characterized by a severe polyarthralgia, in which it is transmitted by the bite of infected Aedes aegypti and Ae. albopictus mosquitoes. Nowadays, there no licensed vaccines or approved drugs to specifically treat this viral disease. Structural viral proteins participate in key steps of its replication cycle, such as viral entry, membrane fusion, nucleocapsid assembly, and virus budding. In this context, envelope E3-E2-E1 glycoproteins complex could be targeted for designing new drug candidates. In this review, aspects of the CHIKV entry process are discussed to provide insights to assist the drug discovery process. Moreover, several natural, nature-based and synthetic compounds, as well as repurposed drugs and virtual screening, are also explored as alternatives for developing CHIKV entry inhibitors. Finally, we provided a complimentary analysis of studies involving inhibitors that were not explored by in silico methods. Based on this, Phe118, Val179, and Lys181 were found to be the most frequent residues, being present in 89.6, 82.7, and 93.1% of complexes, respectively. Lastly, some chemical aspects associated with interactions of these inhibitors and mature envelope E3-E2-E1 glycoproteins' complex were discussed to provide data for scientists worldwide, supporting their search for new inhibitors against this emerging arbovirus.

Molecular Epidemiology, Evolution and Reemergence of Chikungunya Virus in South Asia

Chikungunya virus (CHIKV) is a vector (mosquito)-transmitted alphavirus (family Togaviridae). CHIKV can cause fever and febrile illness associated with severe arthralgia and rash. Genotypic and phylogenetic analysis are important to understand the spread of CHIKV during epidemics and the diversity of circulating strains for the prediction of effective control measures. Molecular epidemiologic analysis of CHIKV is necessary to understand the complex interaction of vectors, hosts and environment that influences the genotypic evolution of epidemic strains. In this study, different works published during 1950s to 2020 concerning CHIKV evolution, epidemiology, vectors, phylogeny, and clinical outcomes were analyzed. Outbreaks of CHIKV have been reported from Bangladesh, Bhutan, India, Pakistan, Sri Lanka, Nepal, and Maldives in South Asia during 2007–2020. Three lineages- Asian, East/Central/South African (ECSA), and Indian Ocean Lineage (IOL) are circulating in South Asia. Lineage, ECSA and IOL became predominant over Asian lineage in South Asian countries during 2011–2020 epidemics. Further, the mutant E1-A226V is circulating in abundance with Aedes albopictus in India, Bangladesh, Nepal, and Bhutan. CHIKV is underestimated as clinical symptoms of CHIKV infection merges with the symptoms of dengue fever in South Asia. Failure to inhibit vector mediated transmission and predict epidemics of CHIKV increase the risk of larger global epidemics in future. To understand geographical spread of CHIKV, most of the studies focused on CHIKV outbreak, biology, pathogenesis, infection, transmission, and treatment. This updated study will reveal the collective epidemiology, evolution and phylogenies of CHIKV, supporting the necessity to investigate the circulating strains and vectors in South Asia.

Interepidemic Detection of Chikungunya Virus Infection and Transmission in Northeastern Thailand

Chikungunya fever is a viral mosquito-borne, acute febrile illness associated with rash, joint pain, and occasionally prolonged polyarthritis. Chikungunya outbreaks have been reported worldwide including many provinces of Thailand. Although chikungunya virus (CHIKV) occurs in Thailand, details on its epidemiology are lacking compared with dengue, a common mosquito-borne disease in the country. Therefore, study on CHIKV and its epidemiology in both humans and mosquitoes is required to better understand its importance clinically and dynamics in community settings. So a prospective examination of virus circulation in human and mosquito populations in northeastern Thailand using serological and molecular methods, including the genetic characterization of the virus, was undertaken. The study was conducted among febrile patients in eight district hospitals in northeastern Thailand from June 2016 to October 2017. Using real-time PCR on the conserved region of nonstructural protein 1 gene, CHIKV was detected in eight (4.9%) of 161 plasma samples. Only one strain yielded a sequence of sufficient size allowing for phylogenetic analysis. In addition, anti-CHIKV IgM and IgG were detected in six (3.7%) and 17 (10.6%) patient plasma samples. The single sequenced sample belonged to the East/Central/South Africa (ECSA) genotype and was phylogenetically similar to the Indian Ocean sub-lineage. Adult Aedes mosquitoes were collected indoors and within a 100-m radius from the index case house and four neighboring houses. CHIKV was detected in two of 70 (2.9%) female Aedes aegypti mosquito pools. This study clearly demonstrated the presence and local transmission of the ECSA genotype of CHIKV in the northeastern region of Thailand.

Chikungunya virus infections in Finnish travellers 2009-2019

The mosquito-borne chikungunya virus (CHIKV) causes an acute febrile illness with rash, joint and muscle pain.A realtime RT-PCR assay for CHIKV detecting non-structural protein (nsP2; CHIKV nsP2-RT-qPCR) was set up. All the serodiagnosed CHIKV cases detected during 2009-2019 in Finland were screened with the assay, followed by isolations attempts and sequencing using Sanger and next generation sequencing (NGS). To validate the assay external and in-house quality control samples were used and all were correctly identified. Specificity of the assay was 100%. Assay was sensitive to detect CHIKV RNA in dilution of 10^-8.During years 2009-2019 34 patients were diagnosed for acute CHIKV infection. Twelve out of 34 cases were positive by CHIKV nsP2-RT-qPCR.Two CHIKV isolations succeeded from two individuals infected originally in Thailand, 2019. From 12 CHIKV nsP2-RT-qPCR positive samples, five (42%) CHIKVs were successfully sequenced. In this study, CHIKVs from year 2019 clustered with CHIKV ECSA-lineage forming sub-cluster with strains from ones detected in Bangladesh 2017, and the ones from Jamaica (2014) within Asian lineage showing highest similarity to strains detected in Caribbean outbreak 2013-15.  Majority of the CHIKV infections detected in Finland originates from Asia and virus lineages reflect the global circulation of the pathogen.

Cas13b-dependent and Cas13b-independent RNA knockdown of viral sequences in mosquito cells following guide RNA expression

Aedes aegypti and Aedes albopictus mosquitoes are vectors of the RNA viruses chikungunya (CHIKV) and dengue that currently have no specific therapeutic treatments. The development of new methods to generate virus-refractory mosquitoes would be beneficial. Cas13b is an enzyme that uses RNA guides to target and cleave RNA molecules and has been reported to suppress RNA viruses in mammalian and plant cells. We investigated the potential use of the Prevotella sp. P5-125 Cas13b system to provide viral refractoriness in mosquito cells, using a virus-derived reporter and a CHIKV split replication system. Cas13b in combination with suitable guide RNAs could induce strong suppression of virus-derived reporter RNAs in insect cells. Surprisingly, the RNA guides alone (without Cas13b) also gave substantial suppression. Our study provides support for the potential use of Cas13b in mosquitoes, but also caution in interpreting CRISPR/Cas data as we show that guide RNAs can have Cas-independent effects.

Genome Sequences of Chikungunya Virus Strains from Bangladesh and Thailand

We sequenced the genomes of two chikungunya virus isolates obtained from viremic patients who had traveled to Australia. The first patient acquired the infection in Bangladesh in 2017, and the second was infected in Thailand in 2019. Phylogenetic sequence analysis demonstrated that both isolates belonged to the East/Central/South African genotype.

We sequenced the genomes of two chikungunya virus isolates obtained from viremic patients who had traveled to Australia. The first patient acquired the infection in Bangladesh in 2017, and the second was infected in Thailand in 2019. Phylogenetic sequence analysis demonstrated that both isolates belonged to the East/Central/South African genotype.

Chikungunya virus in Asia - Pacific: a systematic review

Chikungunya virus (CHIKV) is a mosquito-borne pathogen that causes an acute febrile syndrome and severe, debilitating rheumatic disorders in humans that may persist for months. CHIKV’s presence in Asia dates from at least 1954, but its epidemiological profile in the region remains poorly understood. We systematically reviewed CHIKV emergence, epidemiology, clinical features, atypical manifestations and distribution of virus genotypes, in 47 countries from South East Asia (SEA) and the Western Pacific Region (WPR) during the period 1954–2017. Following the Cochrane Collaboration guidelines, Pubmed and Scopus databases, surveillance reports available in the World Health Organisation (WHO) and government websites were systematically reviewed. Of the 3504 records identified, 461 were retained for data extraction. Although CHIKV has been circulating in Asia almost continuously since the 1950s, it has significantly expanded its geographic reach in the region from 2005 onwards. Most reports identified in the review originated from India. Although all ages and both sexes can be affected, younger children and the elderly are more prone to severe and occasionally fatal forms of the disease, with child fatalities recorded since 1963 from India. The most frequent clinical features identified were arthralgia, rash, fever and headache. Both the Asian and East-Central-South African (ECSA) genotypes circulate in SEA and WPR, with ECSA genotype now predominant. Our findings indicate a substantial but poorly documented burden of CHIKV infection in the Asia-Pacific region. An evidence-based consensus on typical clinical features of chikungunya could aid in enhanced diagnosis and improved surveillance of the disease.

Molecular and phylogenetic analysis of Chikungunya virus in Central India during 2016 and 2017 outbreaks reveal high similarity with recent New Delhi and Bangladesh strains

Central India witnessed Chikungunya virus (CHIKV) outbreaks in 2016 and 2017. The present report is a hospital based cross-sectional study on the serological and molecular epidemiology of the outbreak. Mutational and phylogenetic analysis was conducted to ascertain the genetic relatedness of the central Indian strains with other Indian and global strains. Chikungunya infection was confirmed in the clinically suspected patients by the detection of anti-CHIKV IgM antibody by ELISA and viral RNA by RT-PCR. A representative set of the RT-PCR positive samples were sequenced for E1 gene and analyzed to identify the emerging mutations and establish their phylogenetic relationship, particularly with other contemporary strains. Phylogenetic analysis revealed the present strains to be of East Central South African (ECSA) genotype. Emergence of a variant strain was observed in the year 2016, which became the predominant strain in this region in 2017. The strains showed significant identity with recent New Delhi strains of 2015 and 2016 and Bangladesh strains of 2017. The epidemic mutation A226V which emerged in 2006 outbreaks of India and Indian Ocean Islands was found to be absent in the current strains. Among the important mutations viz. K211E, M269 V, D284E, I317V & V322A observed in the recent strains. I317V is a novel mutation which has emerged very recently as it was found only in central Indian (2016, 2017), New Delhi strains (2015, 2016) and Bangladesh strains (2017). This study has identified a unique mutation E1:I317V in the Central Indian strains, which is present only in recent New Delhi and Bangladesh strains till date. This study highlights the need for continuous molecular surveillance of circulating CHIKV strains in order to facilitate the prompt identification of novel strains of this virus and enable the elucidation of their clinical correlates.

A potent prolyl tRNA synthetase inhibitor antagonizes Chikungunya and Dengue viruses

Arboviruses represent a group of pathogens that can spread efficiently throughout human populations by hematophagous arthropod vectors. The mosquito-borne (re)emerging Chikungunya and Dengue viruses belong to the alphavirus and flavivirus genus, respectively, with no approved therapeutics or safe vaccines for humans. Transmitted by the same vector Aedes spp., these viruses cause significant morbidity and mortality in endemic areas. Due to the increasing likelihood of co-circulation and co-infection with viruses, we aimed to identify a pharmacologically targetable host factor that can inhibit multiple viruses and show that a potent antagonist of prolyl tRNA synthetase (halofuginone) suppresses both Chikungunya and Dengue viruses. Host tRNA synthetase inhibition may signify an additional approach to combat present and future epidemic pathogens.

On the Home Front: Specialised Reference Testing for Dengue in the Australasian Region

Reference laboratories are vital for disease control and interpreting the complexities and impact of emerging pathogens. The role of these centralized facilities extends beyond routine screening capabilities to provide rapid, specific, and accurate diagnoses, advanced data analysis, consultation services, and sophisticated disease surveillance and monitoring. Within the Australasian region, the Public Health Virology Laboratory (PHV), Forensic and Scientific Services, Department of Health, Queensland Government, Australia, and the Institute of Environmental Science and Research Limited (ESR), New Zealand (NZ) perform specialised reference testing and surveillance for dengue viruses (DENVs) and other emerging arthropod-borne viruses (arboviruses), including chikungunya virus (CHIKV) and Zika virus (ZIKV). With a focus on DENV, we review the reference testing performed by PHV (2005 to 2017) and ESR (2008 to 2017). We also describe how the evolution and expansion of reference-based methodologies and the adoption of new technologies have provided the critical elements of preparedness and early detection that complement frontline public health control efforts and limit the spread of arboviruses within Australasia.