SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction

10.1186/1471-2164-11-S4-S21BMC Genomics11SUPPL. 4S2

Early clearance of Chikungunya virus in children is associated with a strong innate immune response

Chikungunya fever (CHIKF) is a global infectious disease which can affect a wide range of age groups. The pathological and immunological response upon Chikungunya virus (CHIKV) infection have been reported over the last few years. However, the clinical profile and immune response upon CHIKV infection in children remain largely unknown. In this study, we analyzed the clinical and immunological response, focusing on the cytokine/chemokine profile in a CHIKV-infected pediatric cohort from Sarawak, Malaysia. Unique immune mediators triggered upon CHIKV infection were identified through meta-analysis of the immune signatures between this pediatric group and cohorts from previous outbreaks. The data generated from this study revealed that a broad spectrum of cytokines/chemokines is up-regulated in a sub-group of virus-infected children stratified according to their viremic status during hospitalization. Furthermore, different immune mediator profiles (the levels of pro-inflammatory cytokines, chemokines and growth and other factors) were observed between children and adults. This study gives an important insight to understand the immune response of CHIKV infection in children and would aid in the development of better prognostics and clinical management for children

Early clearance of Chikungunya virus in children is associated with a strong innate immune response

Chikungunya fever (CHIKF) is a global infectious disease which can affect a wide range of age groups. The pathological and immunological response upon Chikungunya virus (CHIKV) infection have been reported over the last few years. However, the clinical profile and immune response upon CHIKV infection in children remain largely unknown. In this study, we analyzed the clinical and immunological response, focusing on the cytokine/chemokine profile in a CHIKV-infected pediatric cohort from Sarawak, Malaysia. Unique immune mediators triggered upon CHIKV infection were identified through meta-analysis of the immune signatures between this pediatric group and cohorts from previous outbreaks. The data generated from this study revealed that a broad spectrum of cytokines/chemokines is up-regulated in a sub-group of virus-infected children stratified according to their viremic status during hospitalization. Furthermore, different immune mediator profiles (the levels of pro-inflammatory cytokines, chemokines and growth and other factors) were observed between children and adults. This study gives an important insight to understand the immune response of CHIKV infection in children and would aid in the development of better prognostics and clinical management for children

HLA Class I Restriction as a Possible Driving Force for Chikungunya Evolution

After two decades of quiescence, epidemic resurgence of Chikungunya fever (CHIKF) was reported in Africa, several islands in the Indian Ocean, South-East Asia and the Pacific causing unprecedented morbidity with some cases of fatality. Early phylogenetic analyses based on partial sequences of Chikungunya virus (CHIKV) have led to speculation that the virus behind recent epidemics may result in greater pathogenicity. To understand the reasons for these new epidemics, we first performed extensive analyses of existing CHIKV sequences from its introduction in 1952 to 2009. Our results revealed the existence of a continuous genotypic lineage, suggesting selective pressure is active in CHIKV evolution. We further showed that CHIKV is undergoing mild positive selection, and that site-specific mutations may be driven by cell-mediated immune pressure, with occasional changes that resulted in the loss of human leukocyte antigen (HLA) class I-restricting elements. These findings provide a basis to understand Chikungunya virus evolution and reveal the power of post-genomic analyses to understand CHIKV and other viral epidemiology. Such an approach is useful for studying the impact of host immunity on pathogen evolution, and may help identify appropriate antigens suitable for subunit vaccine formulations

Unique Epitopes Recognized by Antibodies Induced in Chikungunya Virus-Infected Non-Human Primates: Implications for the Study of Immunopathology and Vaccine Development

<div><p>Chikungunya virus (CHIKV) is an <i>Alphavirus</i> that causes chronic and incapacitating arthralgia in humans. Although patient cohort studies have shown the production of CHIKV specific antibodies, the fine specificity of the antibody response against CHIKV is not completely defined. The macaque model of CHIKV infection was established due to limitations of clinical specimens. More importantly, its close relation to humans will allow the study of chronic infection and further identify important CHIKV targets. In this study, serum samples from CHIKV-infected macaques collected at different time-points post infection were used to characterize the antibody production pattern and kinetics. Results revealed that anti-CHIKV antibodies were neutralizing and the E2 glycoprotein, Capsid, nsP1, nsP3 and nsP4 proteins were targets of the anti-CHIKV antibody response in macaques. Furthermore, linear B-cell epitopes recognized by these anti-CHIKV antibodies were identified, and mapped to their structural localization. This characterizes the specificity of anti-CHIKV antibody response in macaques and further demonstrates the importance of the different regions in CHIKV-encoded proteins in the adaptive immune response. Information from this study provides critical knowledge that will aid in the understanding of CHIKV infection and immunity, vaccine design, and pre-clinical efficacy studies.</p></div

Mapping of CHIKV B-cell epitopes within CHIKV proteome.

<p>Sera from CHIKV-infected macaques (16 and 180 dpi) were diluted 1∶2,000 and subjected to peptide-based ELISA with a peptide library covering the CHIKV proteome, using pooled peptides (named P1, P2, etc) from the structural (<i>A,</i> Capsid, <i>B,</i> E2) and non-structural (<i>C,</i> nsP1, <i>D,</i> nsP3 and <i>E,</i> nsP4) proteins. Sera from non-infected macaques were used as negative controls. *Pooled peptides were considered to contain positive linear B-cell epitopes when OD values obtained with sera from CHIKV-infected macaques were above mean +3 SD of the OD values obtained with sera from non-infected macaques. Data are presented as OD values obtained using sera from infected macaques, minus the OD values obtained using sera from non-infected macaques, for the corresponding pooled peptides. Data represent an average of two independent experiments (mean ± SD).</p

Analysis of anti-CHIKV antibodies recognizing linear B-cell epitopes.

<p><i>A,</i> Serum samples from CHIKV-infected macaques (n = 1–3) were collected at 9, 16, 100 and 180 dpi. Peptide-based ELISA covering the CHIKV proteome, encompassing the non-structural and structural proteins, was performed with sera diluted at 1∶2,000. Regions of amino acid sequence corresponding to the identified linear B-cell epitopes are indicated on the genome organization schematic diagram. <i>B,</i> The percentage of antibody recognition for various CHIKV epitopes is indicated on the pie-charts. The percentage was calculated according to the equation: % antibody recognition = 100 x (OD values from pooled peptide group/sum of OD values from all pooled peptide groups).</p

Localization of linear CHIKV B-cell epitopes within the CHIKV proteome.

<p><i>A,</i> Schematic representation of identified B-cell epitopes in nsP1, nsP3, nsP4 and Capsid protein. <i>B,</i> Schematic representation of identified B-cell epitopes in E2 glycoprotein. Epitopes in the E2 glycoprotein were located based on structural data retrieved from PDB number: 3N44. Epitopes in the Capsid, nsP1, nsP3 and nsP4 proteins were located based on structures predicted by I-TASSER server.</p

Antibody profiles of sera from CHIKV-infected macaques.

<p><i>A,</i> Virus-specific IgG and IgM antibody titers in serum samples, at a dilution of 1∶2,000 were determined by ELISA using purified CHIK virions. Serum samples from CHIKV-infected macaques (n = 1–3) were collected at 16 and 180 dpi and subjected to virion-based ELISA, using 96-well plates pre-coated with purified CHIKV (IMT) virions. Sera from non-infected macaques were used as negative controls. Data are presented as mean ± SD and representative of 2 independent experiments with similar results. <i>B,</i> Visualization of CHIKV by immunofluorescence in CHIKV-infected cultures after seroneutralization. Virus samples were pre-incubated with heat-inactivated sera from CHIKV-infected macaques collected at 16 and 180 dpi, before being added to HEK 293T cells. Infection without pre-incubation with sera (No sera) was used as a control. Analysis was performed at 6 hours post-infection (hpi). Scale bar in white: 50 µm. Representative microscopic images for each treatment condition (macaque sera dilution at 1∶800) are shown. <i>C, In vitro</i> neutralizing activity of sera from CHIKV-infected macaques. Samples (Healthy macaque sera, 16 and 180 dpi) were tested against IMT or SGP11 viruses, in triplicates at a dilution 1∶800 for healthy macaque sera; between 1∶100 and 1∶800 for CHIKV-infected macaque sera. Results are representative of 3 independent experiments, presented as mean ± SD, and expressed as percentage of control infection. *<i>p</i><0.05, Mann-Whitney <i>U</i> test.</p