Copy number variation of chikungunya ECSA virus with disease symptoms among Indian patients

Viremia and clinical manifestations in acute febrile patients of Chikungunya infection during the 2016 CHIKV outbreak in Delhi, India

Background

Chikungunya virus (CHIKV) is an infectious agent that caused several outbreaks among different countries and affected approximately 1.3 million Indian populations. It is transmitted by Aedes mosquito-either A. albopictus or A. aegypti. Generally, the clinical manifestations of CHIKV infection involve high-grade fever, joint pain, skin rashes, headache, and myalgia. The present study aims to investigate the relationship between the CHIKV virus load and clinical symptoms of the CHIKV infection so that better patient management can be done in the background of the CHIKV outbreak as there is no licensed anti-viral drug and approved vaccines available against CHIKV.

Methods

CHIKV RTPCR positive samples (n = 18) (Acute febrile patients having D.O.F ≤ 7 days) were taken for the quantification of CHIKV viremia by Real-Time PCR. Clinical features of the febrile patients were recorded during the collection of blood samples.

Results

The log mean virus load of 18 RT-PCR-positive samples was 1.3 × 106 copies/mL (1.21 × 103-2.33 × 108 copies/mL). Among the observed clinical features, the log mean virus load (CHIKV) of the patients without skin rash is higher than in the patients with skin rash (6.61 vs 5.5, P = 0.0435).

Conclusion

The conclusion of the study was that the patients with skin rashes had lower viral load and those without skin rashes had higher viral load.

Monolithic affinity columns in 3D printed microfluidics for chikungunya RNA detection

Mosquito-borne pathogens plague much of the world, yet rapid and simple diagnosis is not available for many affected patients. Using a custom stereolithography 3D printer, we created microfluidic devices with affinity monoliths that could retain, noncovalently attach a fluorescent tag, and detect oligonucleotide and viral RNA. We optimized the fluorescent binding and sample load times using an oligonucleotide sequence from chikungunya virus (CHIKV). We also tested the specificity of CHIKV capture relative to genetically similar Sindbis virus. Moreover, viral RNA from both viruses was flowed through capture columns to study the efficiency and specificity of the column for viral CHIKV. We detected ~107 loaded viral genome copies, which was similar to levels in clinical samples during acute infection. These results show considerable promise for development of this platform into a rapid mosquito-borne viral pathogen detection system.

An Overview of Indian Biomedical Research on the Chikungunya Virus with Particular Reference to Its Vaccine, an Unmet Medical Need

Chikungunya virus (CHIKV) is an infectious agent spread by mosquitos, that has engendered endemic or epidemic outbreaks of Chikungunya fever (CHIKF) in Africa, South-East Asia, America, and a few European countries. Like most tropical infections, CHIKV is frequently misdiagnosed, underreported, and underestimated; it primarily affects areas with limited resources, like developing nations. Due to its high transmission rate and lack of a preventive vaccine or effective treatments, this virus poses a serious threat to humanity. After a 32-year hiatus, CHIKV reemerged as the most significant epidemic ever reported, in India in 2006. Since then, CHIKV-related research was begun in India, and up to now, more than 800 peer-reviewed research papers have been published by Indian researchers and medical practitioners. This review gives an overview of the outbreak history and CHIKV-related research in India, to favor novel high-quality research works intending to promote effective treatment and preventive strategies, including vaccine development, against CHIKV infection.

Chikungunya fever

Chikungunya virus is widespread throughout the tropics, where it causes recurrent outbreaks of chikungunya fever. In recent years, outbreaks have afflicted populations in East and Central Africa, South America and Southeast Asia. The virus is transmitted by Aedes aegypti and Aedes albopictus mosquitoes. Chikungunya fever is characterized by severe arthralgia and myalgia that can persist for years and have considerable detrimental effects on health, quality of life and economic productivity. The effects of climate change as well as increased globalization of commerce and travel have led to growth of the habitat of Aedes mosquitoes. As a result, increasing numbers of people will be at risk of chikungunya fever in the coming years. In the absence of specific antiviral treatments and with vaccines still in development, surveillance and vector control are essential to suppress re-emergence and epidemics.

Vector competence of lambda-cyhalothrin resistant Aedes aegypti strains for dengue-2, Zika and chikungunya viruses in Colombia

Aedes aegypti is the primary vector of dengue, Zika, and chikungunya viruses. Studies have shown that insecticide resistance affects vector competence (VC) of some mosquito species. This study evaluates the effect of resistance to lambda-cyhalothrin and kdr V1016I mutation genotypes on the VC of Ae. aegypti strains for DENV-2, ZIKV, and CHIKV. Three Ae. aegypti strains with gradual lambda-cyhalothrin resistance (susceptible, resistant, and highly resistant) were infected with DENV-2, ZIKV, and CHIKV. Individual mosquitoes were tested to detect virus infection in the abdomen and head-salivary glands, using RT-PCR, and genotypes for V1016I mutations using allele-specific PCR. Recorded VC variables were midgut infection rate (MIR), dissemination rate (DIR), and dissemination efficiency (DIE). Lambda-cyhalothrin resistance affects differentially VC variables for ZIKV, DENV-2, and CHIKV. For ZIKV, an apparent gradual increase in DIR and DIE with the increase in insecticide resistance was observed. For DENV-2 the MIR and DIE were higher in insecticide resistant strains. For CHIKV, only MIR could be evaluated, this variable was higher in insecticide resistance strains. The presence of kdr V1016I mutation on mosquito resistant strains did not affect VC variables for three study viruses.

Molecular aspects of Chikungunya virus infections in cancer patients

BACKGROUND

Chikungunya virus (CHIKV) is an arbovirus that can cause chronic and debilitating manifestations. The first autochthonous case in Rio de Janeiro state was diagnosed in 2015, and an outbreak was declared in 2016.

OBJECTIVE

The aim of this work was to evaluate CHIKV viral load in serum, plasma and urine in cancer patients to determine the best sample for diagnosis, as well as perform molecular characterisation and phylogenetic analysis of circulating strains.

METHODS

Paired serum, plasma and urine collected from 31 cancer patients were tested by real-time quantitative polymerase chain reaction (qPCR) and a segment of the CHIKV E1 gene was sequenced.

FINDINGS

We detected 11 CHIKV+ oncological patients. Paired samples analyses of nine patients showed a different pattern of detection. Also, a higher viral load in plasma (6.84 log₁₀) and serum (6.07 log₁₀) vs urine (3.76 log₁₀) was found. Phylogenetic analysis and molecular characterisation revealed East/Central/Southern Africa (ECSA) genotype circulation and three amino acids substitutions (E1-K211T, E1-M269V, E1-T288I) in positive patients.

MAIN CONCLUSION

The results indicate the bioequivalence of serum and plasma for CHIKV diagnosis, with urine being an important complement. ECSA genotype was circulating among patients in the period of the 2016 outbreak with K211T, M269V and T288I substitution.

Epidemiology and molecular characterization of chikungunya virus from human cases in North India, 2016

Chikungunya virus (CHIKV), an arthropod-borne Alphavirus is responsible for chikungunya disease. Arthralgia and arthritis are the major symptom. Some patients recover early while others for a very long time. This study provides, epidemiology and molecular characterization of three whole-genome sequences of CHIKV and assessed phylogenetic analysis, physiological properties, antigenicity, and B-cell epitope prediction by in silico. We report the clinical epidemiology of 325 suspected patients. Of these, 118 (36.30%) were confirmed CHIKV positive by either PCR or ELISA. Clinical analysis showed joint pain, joint swelling and headache were frequent and significant features. Phylogenie analysis showed the currently circulating strain is in close clustring to Africa, Uganda, and Singapore CHIKV strains. Molecular characterization by WGS was done. Thirty eight amino acid changes in the nonstructural proteins were found with respect to the S27 (ECSA) strain. Of these five located in nsP2. Similarly, 34 amino acid changes in structural proteins were observed. The major change was notice; in E3 protein hydropathicity -0.281 to -0.362, in E2 isoelectric point (pI) 8.24 to 8.37, instability index 66.08 to 71.062, aliphatic index varied from 74.69 to 68.59 and E3 75.79 to 70.05. In nsP1 protein pI varies from 6.62 to 8.04, while no other change was observed in structural and nonstructural protein. The linear B-cell epitopes, position, and number varied with the mutation. The molecular characterizations of WGS demonstrate the observation of protein, antigenicity with respect to the mutation.

Chikungunya Outbreaks in India: A Prospective Study Comparing Neutralization and Sequelae during Two Outbreaks in 2010 and 2016

Chikungunya fever (CHIKF) is a major public health concern and is caused by chikungunya virus (CHIKV). In 2005, the virus was reintroduced into India, resulting in massive outbreaks in several parts of the country. During 2010 and 2016 outbreaks, we recruited 588 patients from a tertiary care hospital in New Delhi, India, during the acute phase of CHIKF; collected their blood and clinical data; and determined their arthralgic status 12 weeks post-onset of fever. We evaluated IgM/IgG CHIKV-binding antibodies and their neutralizing capacity, sequenced complete genomes of 21 CHIKV strains, and correlated mutations with patient sequelae status. We also performed infections in murine models using representative strains from each outbreak to evaluate differences in pathogenesis. Our screening and analysis revealed that patients of the 2016 outbreak developed earlier IgM and neutralizing antibody responses that were negatively correlated with sequelae, compared with 2010 patients. Mutations that correlated with human disease progression were also correlated with enhanced murine virulence and pathogenesis. Overall, our study suggests that the development of early neutralizing antibodies and sequence variation in clinical isolates are predictors of human sequelae.

Re-emergence of Chikungunya virus infection in Eastern India

Chikungunya fever is a major public health issue in India. Re-emergence of chikungunya virus (CHIKV) in West Bengal was detected after 32 years in 2006. After 2010, this infection was in apparent decline, but in 2016 a massive outbreak affected the country. Present study was carried out to understand CHIKV infection dynamics during recent outbreaks in West Bengal, Eastern India and its implication on disease manifestations. Blood was collected from 641 symptomatic patients. Patients' sera were serologically diagnosed to detect presence of anti-chikungunya-IgM antibodies. Viral RNA was extracted; presence of CHIKV genome and its respective viral load was determined by real time quantitative reverse transcription-PCR (real-time qRT-PCR). Statistical analysis was performed using EPI INFO software. CHIKV infection was detected in 24.64% of symptomatic patients. Middle-aged patients (31-40 years) were predominantly affected; clinically, both arthralgia and joint-swelling were significantly prevalent among CHIKV-infected patients. Myalgia, joint-swelling, and arthralgic manifestation were found in significantly higher frequency among patients with high chikungunya viral load (> 10,000 copies/ml). Thus, this study clearly indicated the re-emergence of CHIKV in Eastern India. Significant presence of myalgia, joint swelling, and arthralgia among chikungunya patients with high viral load implied association of disease severity with viral load; requiring vigilance for proper management of infected patients as this disease is highly morbid in nature. However, in addition to chikungunya virus, other viral, bacterial, and protozoal infections also occur during post-monsoon season in India, having overlapping symptoms. Hence, continuous monitoring of these infections is required for better clinical management of patients.

Beyond Fever and Pain: Diagnostic Methods for Chikungunya Virus

Chikungunya virus (CHIKV) is an alphavirus that is primarily transmitted by Aedes species mosquitoes. Though reports of an illness consistent with chikungunya date back over 200 years, CHIKV only gained worldwide attention during a massive pandemic that began in East Africa in 2004. Chikungunya, the clinical illness caused by CHIKV, is characterized by a rapid onset of high fever and debilitating joint pain, though in practice, etiologic confirmation of CHIKV requires the availability and use of specific laboratory diagnostics. Similar to infections caused by other arboviruses, CHIKV infections are most commonly detected with a combination of molecular and serological methods, though cell culture and antigen detection are reported. This review provides an overview of available CHIKV diagnostics and highlights aspects of basic virology and epidemiology that pertain to viral detection. Although the number of chikungunya cases has decreased since 2014, CHIKV has become endemic in countries across the tropics and will continue to cause sporadic outbreaks in naive individuals. Consistent access to accurate diagnostics is needed to detect individual cases and initiate timely responses to new outbreaks.

Chikungunya virus: genomic microevolution in Eastern India and its in-silico epitope prediction

This is the first study reporting whole genome sequences of two CHIKV strains (KJ679577 and KJ679578) isolated from Eastern Indian patients sera during 2010-2011 outbreak, both of which were of ECSA genotype, but from different subgroups: Indian Ocean outbreak and ECSA subtypes. Furthermore, viral sequences were analyzed using different in-silico approaches to identify potential genetic variations that might have functional implications on various aspects of virus replication, viral protein functionality, immunogenicity and transmission. Epitope prediction analysis revealed 70.9% increase in number of MHC Class-II interacting epitopes of KJ679578 and 25-28% increase in Class-I interacting epitopes of KJ679577 and KJ679578 compared to that of EF027141 (CHIKV of Asian genotype circulating in India during 1973, after which CHIKV infection disappeared from India for three decades). CHIKV peptides DLAKLAFKRSSKYDLECAQIPVHMKSDA and KVVLCGDPKQCGFFNMMQMKYNYNHNI were predicted to interact with maximum number of HLA Class-I (68 and 76.5%, respectively) and Class-II (47 and 100%, respectively) alleles present within Indian population with allele frequency of > 0.1 and were also recognized as predicted B-cell epitopes with BCPred score between 0.766 and 0.961 and with antigenicity ranging from 0.52 to 1.69; thus these peptides might be used to induce T- and B-cell-mediated immunity against CHIKV. Thus, the present study might help to bridge the gap between virus microevolution and its implication in host immunity by taking into account viral genetic and conformational changes. Predicted epitopes might be used as promising targets for peptide-based vaccine development and rapid diagnostics against CHIKV infection.

Molecular and Clinical Characterization of Chikungunya Virus Infections in Southeast Mexico

Chikungunya fever is an arthropod-borne infection caused by Chikungunya virus (CHIKV). Even though clinical features of Chikungunya fever in the Mexican population have been described before, there is no detailed information. The aim of this study was to perform a full description of the clinical features in confirmed Chikungunya-infected patients and describe the molecular epidemiology of CHIKV. We evaluated febrile patients who sought medical assistance in Tapachula, Chiapas, Mexico, from June through July 2015. Infection was confirmed with molecular and serological methods. Viruses were isolated and the E1 gene was sequenced. Phylogeny reconstruction was inferred using maximum-likelihood and maximum clade credibility approaches. We studied 52 patients with confirmed CHIKV infection. They were more likely to have wrist, metacarpophalangeal, and knee arthralgia. Two combinations of clinical features were obtained to differentiate between Chikungunya fever and acute undifferentiated febrile illness. We obtained 10 CHIKV E1 sequences that grouped with the Asian lineage. Seven strains diverged from the formerly reported. Patients infected with the divergent CHIKV strains showed a broader spectrum of clinical manifestations. We defined the complete clinical features of Chikungunya fever in patients from Southeastern Mexico. Our results demonstrate co-circulation of different CHIKV strains in the state of Chiapas.

Evidence of dengue and chikungunya virus co-infection and circulation of multiple dengue serotypes in a recent Indian outbreak

In India, dengue endemic areas overlap with chikungunya-affected areas and both the viruses are transmitted by same vector, Aedes aegypti - thereby increasing opportunity of co-infection by both viruses. Present study was carried out to understand the DENV-CHIKV infection dynamics during recent outbreaks in eastern India (West Bengal state) and its implication on disease manifestations. Blood was collected from 326 symptomatic febrile patients. Patients' serum was subjected to serological diagnosis for presence of anti-dengue-IgM, anti-chikungunya-IgM antibodies and dengue-NS1 antigen by ELISA. Viral RNA was extracted, and presence of dengue virus (DENV) and chikungunya virus (CHIKV) genome, their viral load (VL), and serotype among infected patients' plasma was determined by real-time qRT-PCR. Statistical analysis was performed by using EPI INFO software. DENV and CHIKV were detected in 54% and 33% of symptomatic patients respectively, among whom 23% were harboring both viruses. WHO classified warning signs were detected among 64% DENV patients and 61% DENV-CHIKV double-infected patients. Patients with warning signs always had much higher DEN VL than those without warning signs. Hemorrhagic manifestation and abdominal pain was found in significantly higher frequency among patients with high dengue VL (>10,000 copies/ml). DENV2 was the most predominant serotype among monotypic dengue patients, whereas DENV2-DENV4 combination was most prevalent among patients infected with dual dengue serotypes. This study indicated that DENV-CHIKV double infection and high dengue VL contributed towards severe disease manifestations among infected patients. DENV2 and DENV2-DENV4 combination were the most prevalent serotype(s) found in current outbreak.

Chikungunya virus pathogenesis: From bedside to bench

Chikungunya virus (CHIKV) is an arbovirus transmitted to humans by mosquito bite. A decade ago, the virus caused a major outbreak in the islands of the Indian Ocean, then reached India and Southeast Asia. More recently, CHIKV has emerged in the Americas, first reaching the Caribbean and now extending to Central, South and North America. It is therefore considered a major public health and economic threat. CHIKV causes febrile illness typically associated with debilitating joint pains. In rare cases, it may also cause central nervous system disease, notably in neonates. Joint symptoms may persist for months to years, and lead to arthritis. This review focuses on the spectrum of signs and symptoms associated with CHIKV infection in humans. It also illustrates how the analysis of clinical and biological data from human cohorts and the development of animal and cellular models of infection has helped to identify the tissue and cell tropisms of the virus and to decipher host responses in benign, severe or persistent disease. This article forms part of a symposium in Antiviral Research on "Chikungunya discovers the New World".

Single-Stranded RNA Viruses

In this chapter, we describe 73 zoonotic viruses that were isolated in Northern Eurasia and that belong to the different families of viruses with a single-stranded RNA (ssRNA) genome. The family includes viruses with a segmented negative-sense ssRNA genome (families Bunyaviridae and Orthomyxoviridae) and viruses with a positive-sense ssRNA genome (families Togaviridae and Flaviviridae). Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Other viruses described in the chapter can cause epizootics in wild or domestic animals: Geta virus (GETV, Alphavirus), Influenza A virus (Influenzavirus A), Bhanja virus (BHAV, Phlebovirus) and more. The chapter also discusses both ecological peculiarities that promote the circulation of these viruses in natural foci and factors influencing the occurrence of epidemic and epizootic outbreaks

Global protein profiling studies of chikungunya virus infection identify different proteins but common biological processes

Chikungunya fever (CHIKF) caused by the mosquito-transmitted chikungunya virus (CHIKV) swept into international prominence from late 2005 as an epidemic of CHIKF spread around countries surrounding the Indian Ocean. Although significant advances have been made in understanding the pathobiology of CHIKF, numerous questions still remain. In the absence of commercially available specific drugs to treat the disease, or a vaccine to prevent the diseases, the questions have particular significance. A number of studies have used global proteome analysis to increase our understanding of the process of CHIKV infection using a number of different experimental techniques and experimental systems. In all, over 700 proteins have been identified in nine different analyses by five different groups as being differentially regulated. Remarkably, only a single protein, eukaryotic elongation factor 2, has been identified by more than two different groups as being differentially regulated during CHIKV infection. This review provides a critical overview of the studies that have used global protein profiling to understand CHIKV infection and shows that while a broad consensus is emerging on which biological processes are altered during CHIKV infection, this consensus is poorly supported in terms of consistent identification of any key proteins mediating those biological processes.