75 results on '"Aruna D de Silva"'
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2. Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka.
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Himali S Jayasinghearachchi, Enoka M Corea, Kumari I Jayaratne, Regina A Fonseka, Thilini A Muthugama, Jayanthi Masakorala, Ravija Yc Ramasinghe, and Aruna D De Silva
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundMelioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in Southeast Asia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania.MethodsThe distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis.ResultsThe Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia.ConclusionThis study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania.
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- 2021
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3. Outcomes among children and adults at risk of severe dengue in Sri Lanka: Opportunity for outpatient case management in countries with high disease burden.
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Champica K Bodinayake, Ajith DeS Nagahawatte, Vasantha Devasiri, Niroshana J Dahanayake, Gaya B Wijayaratne, Nayani P Weerasinghe, Madureka Premamali, Tianchen Sheng, Bradly P Nicholson, Harshanie A Ubeysekera, Ruvini Mp Kurukulasooriya, Aruna D de Silva, Truls Østbye, Christopher W Woods, and L Gayani Tillekeratne
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundHealthcare systems in dengue-endemic countries are often overburdened due to the high number of patients hospitalized according to dengue management guidelines. We systematically evaluated clinical outcomes in a large cohort of patients hospitalized with acute dengue to support triaging of patients to ambulatory versus inpatient management in the future.Methods/principal findingsFrom June 2017- December 2018, we conducted surveillance among children and adults with fever within the prior 7 days who were hospitalized at the largest tertiary-care (1,800 bed) hospital in the Southern Province, Sri Lanka. Patients who developed platelet count ≤100,000/μL (threshold for hospital admission in Sri Lanka) and who met at least two clinical criteria consistent with dengue were eligible for enrollment. We confirmed acute dengue by testing sera collected at enrollment for dengue NS1 antigen or IgM antibodies. We defined primary outcomes as per the 1997 and 2009 World Health Organization (WHO) classification criteria: dengue hemorrhagic fever (DHF; WHO 1997), dengue shock syndrome (DSS; WHO 1997), and severe dengue (WHO 2009). Overall, 1064 patients were confirmed as having acute dengue: 318 (17.4%) by NS1 rapid antigen testing and 746 (40.7%) by IgM antibody testing. Of these 1064 patients, 994 (93.4%) were adults ≥18 years and 704 (66.2%) were male. The majority (56, 80%) of children and more than half of adults (544, 54.7%) developed DHF during hospitalization, while 6 (8.6%) children and 22 (2.2%) adults developed DSS. Overall, 10 (14.3%) children and 113 (11.4%) adults developed severe dengue. A total of 2 (0.2%) patients died during hospitalization.ConclusionsOne-half of patients hospitalized with acute dengue progressed to develop DHF and a very small number developed DSS or severe dengue. Developing an algorithm for triaging patients to ambulatory versus inpatient management should be the future goal to optimize utilization of healthcare resources in dengue-endemic countries.
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- 2021
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4. Evaluation of the WHO 2009 classification for diagnosis of acute dengue in a large cohort of adults and children in Sri Lanka during a dengue-1 epidemic.
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Champica K Bodinayake, L Gayani Tillekeratne, Ajith Nagahawatte, Vasantha Devasiri, Wasantha Kodikara Arachchi, John J Strouse, October M Sessions, Ruvini Kurukulasooriya, Anna Uehara, Shiqin Howe, Xin Mei Ong, Sharon Tan, Angelia Chow, Praveen Tummalapalli, Aruna D De Silva, Truls Østbye, Christopher W Woods, Duane J Gubler, and Megan E Reller
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BACKGROUND:Dengue is a leading cause of fever and mimics other acute febrile illnesses (AFI). In 2009, the World Health Organization (WHO) revised criteria for clinical diagnosis of dengue. METHODOLOGY/PRINCIPAL FINDINGS:The new WHO 2009 classification of dengue divides suspected cases into three categories: dengue without warning signs, dengue with warning signs and severe dengue. We evaluated the WHO 2009 classification vs physicians' subjective clinical diagnosis (gestalt clinical impression) in a large cohort of patients presenting to a tertiary care center in southern Sri Lanka hospitalized with acute febrile illness. We confirmed acute dengue in 388 patients (305 adults ≥ 18 years and 83 children), including 103 primary and 245 secondary cases, of 976 patients prospectively enrolled with AFI. At presentation, both adults and children with acute dengue were more likely than those with other AFI to have leukopenia and thrombocytopenia. Additionally, adults were more likely than those with other AFI to have joint pain, higher temperatures, and absence of crackles on examination whereas children with dengue were more likely than others to have sore throat, fatigue, oliguria, and elevated hematocrit and transaminases. Similarly, presence of joint pain, thrombocytopenia, and absence of cough were independently associated with secondary vs primary dengue in adults whereas no variables were different in children. The 2009 WHO dengue classification was more sensitive than physicians' clinical diagnosis for identification of acute dengue (71.5% vs 67.1%), but was less specific. However, despite the absence of on-site diagnostic confirmation of dengue, clinical diagnosis was more sensitive on discharge (75.2%). The 2009 WHO criteria classified almost 75% as having warning signs, even though only 9 (2.3%) patients had evidence of plasma leakage and 16 (4.1%) had evidence of bleeding. CONCLUSIONS/SIGNIFICANCE:In a large cohort with AFI, we identified features predictive of dengue vs other AFI and secondary vs primary dengue in adults versus children. The 2009 WHO dengue classification criteria had high sensitivity but low specificity compared to physicians' gestaldt diagnosis. Large cohort studies will be needed to validate the diagnostic yield of clinical impression and specific features for dengue relative to the 2009 WHO classification criteria.
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- 2018
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5. Emergence of Epidemic Dengue-1 Virus in the Southern Province of Sri Lanka.
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Champica K Bodinayake, L Gayani Tillekeratne, Ajith Nagahawatte, Vasantha Devasiri, Wasantha Kodikara Arachichi, John J Strouse, October M Sessions, Ruvini Kurukulasooriya, Anna Uehara, Shiqin Howe, Xin Mei Ong, Sharon Tan, Angelia Chow, Praveen Tummalapalli, Aruna D De Silva, Truls Østbye, Christopher W Woods, Duane J Gubler, and Megan E Reller
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Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
BACKGROUND:Dengue is a frequent cause of acute febrile illness with an expanding global distribution. Since the 1960s, dengue in Sri Lanka has been documented primarily along the heavily urbanized western coast with periodic shifting of serotypes. Outbreaks from 2005-2008 were attributed to a new clade of DENV-3 and more recently to a newly introduced genotype of DENV-1. In 2007, we conducted etiologic surveillance of acute febrile illness in the Southern Province and confirmed dengue in only 6.3% of febrile patients, with no cases of DENV-1 identified. To re-evaluate the importance of dengue as an etiology of acute febrile illness in this region, we renewed fever surveillance in the Southern Province to newly identify and characterize dengue. METHODOLOGY/PRINCIPAL FINDINGS:A cross-sectional surveillance study was conducted at the largest tertiary care hospital in the Southern Province from 2012-2013. A total of 976 patients hospitalized with acute undifferentiated fever were enrolled, with 64.3% male and 31.4% children. Convalescent blood samples were collected from 877 (89.6%). Dengue virus isolation, dengue RT-PCR, and paired IgG ELISA were performed. Acute dengue was confirmed as the etiology for 388 (39.8%) of 976 hospitalizations, with most cases (291, 75.0%) confirmed virologically and by multiple methods. Among 351 cases of virologically confirmed dengue, 320 (91.2%) were due to DENV-1. Acute dengue was associated with self-reported rural residence, travel, and months having greatest rainfall. Sequencing of selected dengue viruses revealed that sequences were most closely related to those described from China and Southeast Asia, not nearby India. CONCLUSIONS/SIGNIFICANCE:We describe the first epidemic of DENV-1 in the Southern Province of Sri Lanka in a population known to be susceptible to this serotype because of prior study. Dengue accounted for 40% of acute febrile illnesses in the current study. The emergence of DENV-1 as the foremost serotype in this densely populated but agrarian population highlights the changing epidemiology of dengue and the need for continued surveillance and prevention.
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- 2016
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6. Properties of MHC class I presented peptides that enhance immunogenicity.
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Jorg J A Calis, Matt Maybeno, Jason A Greenbaum, Daniela Weiskopf, Aruna D De Silva, Alessandro Sette, Can Keşmir, and Bjoern Peters
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Biology (General) ,QH301-705.5 - Abstract
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4-6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses.
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- 2013
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7. Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance
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Emily R. Ko, Megan E. Reller, L. Gayani Tillekeratne, Champica K. Bodinayake, Cameron Miller, Thomas W. Burke, Ricardo Henao, Micah T. McClain, Sunil Suchindran, Bradly Nicholson, Adam Blatt, Elizabeth Petzold, Ephraim L. Tsalik, Ajith Nagahawatte, Vasantha Devasiri, Matthew P. Rubach, Venance P. Maro, Bingileki F. Lwezaula, Wasantha Kodikara-Arachichi, Ruvini Kurukulasooriya, Aruna D. De Silva, Danielle V. Clark, Kevin L. Schully, Deng Madut, J. Stephen Dumler, Cecilia Kato, Renee Galloway, John A. Crump, Geoffrey S. Ginsburg, Timothy D. Minogue, and Christopher W. Woods
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Medicine ,Science - Abstract
Abstract Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant (USA, Sri Lanka) discovery cohort with adjudicated viral or bacterial infections of diverse etiology or non-infectious disease mimics. We then derived and cross-validated gene expression classifiers including: 1) a single model to distinguish bacterial vs. viral (Global Fever-Bacterial/Viral [GF-B/V]) and 2) a two-model system to discriminate bacterial and viral in the context of noninfection (Global Fever-Bacterial/Viral/Non-infectious [GF-B/V/N]). We then translated to a multiplex RT-PCR assay and independent validation involved 101 participants (USA, Sri Lanka, Australia, Cambodia, Tanzania). The GF-B/V model discriminated bacterial from viral infection in the discovery cohort an area under the receiver operator curve (AUROC) of 0.93. Validation in an independent cohort demonstrated the GF-B/V model had an AUROC of 0.84 (95% CI 0.76–0.90) with overall accuracy of 81.6% (95% CI 72.7–88.5). Performance did not vary with age, demographics, or site. Host transcriptional response diagnostics distinguish bacterial and viral illness across global sites with diverse endemic pathogens.
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- 2023
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8. Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health
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Himali S. Jayasinghearachchi, Thilini A. Muthugama, Jayanthi Masakorala, Upeksha S. Kulasekara, Kumari Jayaratne, D. A. Dasun N. Jayatunga, Aruna D. De Silva, and Enoka M. Corea
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General Veterinary - Abstract
Burkholderia pseudomallei is the causative agent of the potentially fatal infection, melioidosis. This study provides the first evidence for the presence of B. pseudomallei in soil and water in Sri Lanka. Targeted sampling of soil and natural water sources was done between November 2019 and October 2020 over eight field visits encompassing the neighborhood of 28 culture and/or antibody-positive melioidosis patients in northwestern, western and southern Sri Lanka. A total of eight environmental isolates of B. pseudomallei (BPs-env1 to BPs-env8) were cultured from 116 soil and 117 natural water samples collected from 72 locations. The presence of B. pseudomallei in soil and natural water in these areas poses a risk of melioidosis for populations cultivating crops in such soils and using untreated water from these sources for drinking, bathing, and other domestic purposes. Identifying sites positive for B. pseudomallei may help to mitigate risk by raising public awareness of contaminated environmental sources and allowing soil and water remediation.
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- 2023
9. Transcriptomics of Acute DENV-Specific CD8+ T Cells Does Not Support Qualitative Differences as Drivers of Disease Severity
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Alba Grifoni, Hannah Voic, Esther Dawen Yu, Jose Mateus, Kai Mei Yan Fung, Alice Wang, Grégory Seumois, Aruna D. De Silva, Rashika Tennekon, Sunil Premawansa, Gayani Premawansa, Rashmi Tippalagama, Ananda Wijewickrama, Ashu Chawla, Jason Greenbaum, Bjoern Peters, Vijayanand Pandurangan, Daniela Weiskopf, and Alessandro Sette
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Pharmacology ,Infectious Diseases ,viruses ,Drug Discovery ,Immunology ,virus diseases ,Pharmacology (medical) ,biochemical phenomena, metabolism, and nutrition ,CD8+ T cells ,DENV ,hemorrhagic disease ,transcriptome ,phenotypes - Abstract
While several lines of evidence suggest a protective role of T cells against disease associated with Dengue virus (DENV) infection, their potential contribution to immunopathology in the acute phase of DENV infection remains controversial, and it has been hypothesized that the more severe form of the disease (dengue hemorrhagic fever, DHF) is associated with altered T cell responses. To address this question, we determined the transcriptomic profiles of DENV-specific CD8+ T cells in a cohort of 40 hospitalized dengue patients with either a milder form of the disease (dengue fever, DF) or a more severe disease form (dengue hemorrhagic fever, DHF). We found multiple transcriptomic signatures, one associated with DENV-specific interferon-gamma responding cells and two other gene signatures, one specifically associated with the acute phase and the other with the early convalescent phase. Additionally, we found no differences in quantity and quality of DENV-specific CD8+ T cells based on disease severity. Taken together with previous findings that did not detect altered DENV-specific CD4 T cell responses, the current analysis argues against alteration in DENV-specific T cell responses as being a correlate of immunopathology.
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- 2022
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10. An increase in p62/NBR1 levels in melioidosis patients of Sri Lanka exhibit a characteristic of potential host biomarker
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Robert G. Ulrich, Cyra M Ranji, Mohan Natesan, Aruna D. De Silva, Enoka Corea, and Kamal U Saikh
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Adult ,Male ,0301 basic medicine ,Microbiology (medical) ,autophagy ,Burkholderia pseudomallei ,Melioidosis ,030231 tropical medicine ,Biology ,Microbiology ,Peripheral blood mononuclear cell ,Disease, Diagnosis and Diagnostics ,Proinflammatory cytokine ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Pathogen ,Sri Lanka ,Intracellular parasite ,p62 ,Autophagy ,Intracellular Signaling Peptides and Proteins ,RNA-Binding Proteins ,NBR1 ,General Medicine ,biology.organism_classification ,medicine.disease ,cytokines ,030104 developmental biology ,Immunology ,Leukocytes, Mononuclear ,Biomarker (medicine) ,Female ,Biomarkers ,Research Article - Abstract
Introduction. Melioidosis, caused by Burkholderia pseudomallei , in endemic areas, poses a challenge for treating the diseased populations without accurate diagnosis, and the disease-specific biomarkers linked with the infection have yet to be reported. Due to the invasive nature of the causative agent, Burkholderia pseudomallei , host innate effector mechanisms, including autophagy are known to be activated, resulting in differential expression of cellular proteins and immune markers. Identification of a disease-specific biomarker associated with B. pseudomallei infection will be helpful to facilitate rapid confirmation of melioidosis, which would enable early treatment and therapeutic success. Aim. We aimed to assess the levels of a host autophagy component, p62/NBR1, which function as a cargo-receptor in the process of autophagy activation leading to the degradation of ubiquitin-coated intracellular bacteria in which p62/NBR1 itself is degraded in the clearance of the pathogen. We further probed the extent of intracellular p62/NBR1 degradation and assessed its potential as a melioidosis biomarker. Methodology. We analysed peripheral blood mononuclear cell (PBMC) lysates using an ELISA-based assay for detecting cytosolic autophagy-related proteins p62/NBR1. We measured p62/NBR1 levels in diseased (confirmed B. pseudomallei infection) and non -diseased populations and utilized receiver operating characteristic (ROC) curve and max Youden index analysis for evaluating potential disease biomarker characteristics. Results. Our results revealed a three to fivefold increase in p62/NBR1 levels confirmed melioidosis cases compared to uninfected healthy donors. Comparable to p62/NBR1, levels of cytosolic LC3-I levels also increased, whereas the levels of degraded membrane bound form LC3-II was low, suggesting autophagy deficiency. Proinflammatory serum cytokine response, particularly IL-6, was consistently higher alongside B. pseudomallei infection in comparison to healthy controls. Conclusions. ROC curve and max Youden index analysis suggest that increased p62/NBR1 levels in diseased populations display characteristics of a potential disease biomarker in melioidosis and illustrates that an elevated p62/NBR1 level, in conjunction with B. pseudomallei infection associated with autophagy deficiency.
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- 2020
11. Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka
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Enoka Corea, Aruna D. De Silva, Shivankari Krishnananthasivam, Vaithehi R. Francis, Thilini A. Muthugama, H.S. Jayasinghearachchi, J Masakorala, and Harindra D. Sathkumara
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Microbiology (medical) ,sequence type ,Burkholderia pseudomallei ,Melioidosis ,Epidemiology ,Population ,Infectious and parasitic diseases ,RC109-216 ,Disease cluster ,Microbiology ,Research Letter ,nonclonal ,medicine ,Humans ,case cluster ,bacteria ,education ,Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka ,Sri Lanka ,education.field_of_study ,biology ,medicine.disease ,biology.organism_classification ,Infectious Diseases ,Medicine ,melioidosis ,Sri lanka ,geographic locations - Abstract
A melioidosis case cluster of 10 blood culture-positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.
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- 2021
12. Evaluation of ELISA-Based Multiplex Peptides for the Detection of Human Serum Antibodies Induced by Zika Virus Infection across Various Countries
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Laise de Moraes, Aruna D. De Silva, Tamara García-Salum, Kennedy T. L. Gifford, Kimberly García, Daniel G. Olson, Viviane Boaventura, Lillian Nunes Gomes, Daniela Weiskopf, Gene S. Tan, Guillermo M. Ruiz-Palacios, Stephen Panossian, Kevan Akrami, Antônio Augusto Moura da Silva, Maria del Pilar Martinez Viedma, Ivette Lorenzana, Rafael A. Medina, Brett E. Pickett, Isis Figueroa, Cecilia Perret, Ricardo Khouri, Alessandro Sette, and Leda Parham
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0301 basic medicine ,Adult ,Male ,Adolescent ,030231 tropical medicine ,Enzyme-Linked Immunosorbent Assay ,Cross Reactions ,Antibodies, Viral ,Sensitivity and Specificity ,Microbiology ,Neutralization ,Article ,Zika virus ,Serology ,Cohort Studies ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,antibody diagnostic ,Humans ,Multiplex ,zika virus ,Child ,Aged ,Aedes ,biology ,Zika Virus Infection ,seropositivity ,Outbreak ,Infant ,bioinformatics ,Middle Aged ,biology.organism_classification ,Virology ,QR1-502 ,High-Throughput Screening Assays ,virology ,Flavivirus ,030104 developmental biology ,Infectious Diseases ,Immunoglobulin M ,Child, Preschool ,Immunoglobulin G ,biology.protein ,Female ,ELISA ,Antibody ,Peptides - Abstract
Zika virus (ZIKV) is a mosquito-borne Flavivirus with a positive-sense RNA genome, which are generally transmitted through the bite of an infected Aedes mosquito. ZIKV infections could be associated with neurological sequelae that, and otherwise produces similar clinical symptoms as other co-circulating pathogens. Past infection with one member of the Flavivirus genus often induces cross-reactive antibodies against other flaviruses. These attributes complicate the ability to differentially diagnose ZIKV infection from other endemic mosquito-borne viruses, making it both a public health issue as well as a diagnostic challenge. We report the results from serological analyses using arbovirus-specific peptides on 339 samples that were previously collected from 6 countries. Overall, we found that our multiplexed peptide-based ELISA was highly efficient for identifying ZIKV antibodies as early as 2 weeks post infection, and that it correlates with microneutralization, plaque reduction neutralization tests (PRNTs) and commercial tests for ZIKV in previously characterized samples. We observed that seropositivity varied by patient cohort, reflecting the sampling period in relation to the 2015–2016 ZIKV outbreak. This work evaluates the accuracy, specificity, and sensitivity of our peptide-based ELISA method for detecting ZIKV antibodies from geographically diverse regions. These findings can contribute to ongoing serological methods development and can be adapted for use in future studies.
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- 2021
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13. Pre-existing T Cell Memory against Zika Virus
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John Pham, Blake Schouest, John Sydney, Jose Mateus, Alba Grifoni, James D. Brien, Eva Harris, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, and Angel Balmaseda
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Adult ,CD4-Positive T-Lymphocytes ,Cellular immunity ,cross-reactivity ,T-Lymphocytes ,viruses ,Immunology ,T cells ,Cellular Response to Infection ,Epitopes, T-Lymphocyte ,Immunodominance ,Cross Reactions ,Dengue virus ,medicine.disease_cause ,Microbiology ,Epitope ,Dengue fever ,Zika virus ,Dengue ,Viral Proteins ,03 medical and health sciences ,0302 clinical medicine ,HLA Antigens ,Virology ,medicine ,Humans ,Antigens, Viral ,030304 developmental biology ,preexisting memory ,0303 health sciences ,dengue virus ,biology ,Zika Virus Infection ,virus diseases ,Zika Virus ,biochemical phenomena, metabolism, and nutrition ,medicine.disease ,biology.organism_classification ,Flavivirus ,medicine.anatomical_structure ,Insect Science ,Peptides ,Immunologic Memory ,Memory T cell ,030215 immunology - Abstract
The mosquito-borne Zika virus (ZIKV) has spread rapidly into regions where dengue virus (DENV) is endemic, and flavivirus cross-reactive T cell responses have been observed repeatedly in animal models and in humans. Preexisting cellular immunity to DENV is thought to contribute to protection in subsequent ZIKV infection, but the epitope targets of cross-reactive T cell responses have not been comprehensively identified. Using human blood samples from the regions of Nicaragua and Sri Lanka where DENV is endemic that were collected before the global spread of ZIKV in 2016, we employed an in vitro expansion strategy to map ZIKV T cell epitopes in ZIKV-unexposed, DENV-seropositive donors. We identified 93 epitopes across the ZIKV proteome, and we observed patterns of immunodominance that were dependent on antigen size and sequence identity to DENV. We confirmed the immunogenicity of these epitopes through a computational HLA binding analysis, and we showed that cross-reactive T cells specifically recognize ZIKV peptides homologous to DENV sequences. We also found that these CD4 responses were derived from the memory T cell compartment. These data have implications for understanding the dynamics of flavivirus-specific T cell immunity in areas of endemicity. IMPORTANCE Multiple flaviviruses, including Zika virus (ZIKV) and the four serotypes of dengue virus (DENV), are prevalent in the same large tropical and equatorial areas, which are inhabited by hundreds of millions of people. The interplay of DENV and ZIKV infection is especially relevant, as these two viruses are endemic in largely overlapping regions, have significant sequence similarity, and share the same arthropod vector. Here, we define the targets of preexisting immunity to ZIKV in unexposed subjects in areas where dengue is endemic. We demonstrate that preexisting immunity to DENV could shape ZIKV-specific responses, and DENV-ZIKV cross-reactive T cell populations can be expanded by stimulation with ZIKV peptides. The issue of potential ZIKV and DENV cross-reactivity is of relevance for understanding patterns of natural immunity, as well as for the development of diagnostic tests and vaccines.
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- 2021
14. Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles
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Simon Mallal, Shu Liang, Elizabeth J. Phillips, Yuan Tian, Alessandro Sette, Pandurangan Vijayanand, N.D. Suraj Goonawardhana, Mariana Babor, Daniela Weiskopf, Ricardo da Silva Antunes, Grégory Seumois, Alba Grifoni, Bjoern Peters, Jerome Lane, and Aruna D. De Silva
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Adult ,Male ,0301 basic medicine ,Receptors, CCR7 ,Adolescent ,viruses ,T cell ,Receptors, Antigen, T-Cell ,CD8-Positive T-Lymphocytes ,Biology ,Epitope ,Dengue ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,T-Lymphocyte Subsets ,medicine ,Humans ,Cytotoxic T cell ,Aged ,Effector ,T-cell receptor ,virus diseases ,General Medicine ,Dengue Virus ,Middle Aged ,biochemical phenomena, metabolism, and nutrition ,Acquired immune system ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Leukocyte Common Antigens ,Female ,Transcriptome ,Immunologic Memory ,CD8 ,Research Article - Abstract
Accumulating evidence demonstrates that CD8(+) T cells contribute to protection from severe dengue virus (DENV) disease and vaccine efficacy. Nevertheless, molecular programs associated with DENV-specific CD8(+) T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific CD8(+) T cells isolated after stimulation with DENV epitopes from donors who had been infected with DENV multiple times and would therefore be expected to have significant levels of adaptive immunity. We found that DENV-specific CD8(+) T cells mainly consisted of effector memory subsets, namely CD45RA(−)CCR7(−) effector memory (Tem) and CD45RA(+)CCR7(−) effector memory re-expressing CD45RA (Temra) cells, which enacted specific gene expression profiles upon stimulation with cognate antigens. DENV-specific CD8(+) T cell subsets in general, and Temra cells in particular, were fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses. Furthermore, we found that DENV-specific CD8(+) Tem and Temra cells showed some unique T cell receptor features in terms of overlap and variable (V) gene usage. This study provides a transcriptomic definition of DENV-specific activated human CD8(+) T cell subsets and defines a benchmark profile that vaccine-specific responses could aim to reproduce.
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- 2019
15. Respiratory Viral Infection: An Underappreciated Cause of Acute Febrile Illness Admissions in Southern Sri Lanka
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Vasantha Devasiri, Wasantha Kodikara Arachchi, Aruna D. De Silva, Champica K Bodinayake, Sky Vanderburg, Christopher W. Woods, Bradly P. Nicholson, Megan E. Reller, Ryan A. Simmons, L. Gayani Tillekeratne, Truls Østybe, Lawrence P. Park, Ajith Nagahawatte, and Ruvini Kurukulasooriya
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Adult ,Male ,medicine.medical_specialty ,Adolescent ,Fever ,viruses ,030231 tropical medicine ,medicine.disease_cause ,Virus ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Human metapneumovirus ,Interquartile range ,Risk Factors ,Internal medicine ,Virology ,Odds Ratio ,Medicine ,Humans ,Respiratory system ,Child ,Respiratory Tract Infections ,Disease burden ,Aged ,Sri Lanka ,biology ,business.industry ,Articles ,Middle Aged ,biology.organism_classification ,Vaccination ,Hospitalization ,Infectious Diseases ,Virus Diseases ,Child, Preschool ,Respiratory virus ,Female ,Parasitology ,Seasons ,Rhinovirus ,business - Abstract
The contribution of respiratory viruses to acute febrile illness (AFI) burden is poorly characterized. We describe the prevalence, seasonality, and clinical features of respiratory viral infection among AFI admissions in Sri Lanka. We enrolled AFI patients ≥ 1 year of age admitted to a tertiary care hospital in southern Sri Lanka, June 2012-October 2014. We collected epidemiologic/clinical data and a nasal or nasopharyngeal sample that was tested using polymerase chain reaction (Luminex NxTAG, Austin, TX). We determined associations between weather data and respiratory viral activity using the Spearman correlation and assessed respiratory virus seasonality using a Program for Appropriate Technology definition. Bivariable and multivariable regression analyses were conducted to identify features associated with respiratory virus detection. Among 964 patients, median age was 26.2 years (interquartile range 14.6-39.9) and 646 (67.0%) were male. One-fifth (203, 21.1%) had respiratory virus detected: 13.9% influenza, 1.4% human enterovirus/rhinovirus, 1.4% parainfluenza virus, 1.1% respiratory syncytial virus, and 1.1% human metapneumovirus. Patients with respiratory virus identified were younger (median 9.8 versus 27.7 years, P < 0.001) and more likely to have respiratory signs and symptoms. Influenza A and respiratory viral activity peaked in February-June each year. Maximum daily temperature was associated with influenza and respiratory viral activity (P = 0.03 each). Patients with respiratory virus were as likely as others to be prescribed antibiotics (55.2% versus 52.6%, P = 0.51), and none reported prior influenza vaccination. Respiratory viral infection was a common cause of AFI. Improved access to vaccines and respiratory diagnostics may help reduce disease burden and inappropriate antibiotic use.
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- 2019
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16. T cell responses induced by attenuated flavivirus vaccination are specific and show limited cross-reactivity with other flavivirus species
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Aruna D. De Silva, Alba Grifoni, Angel Balmaseda, Conner K. Kidd, James D. Brien, Stephen S. Whitehead, Hannah Voic, Anna P. Durbin, Alessandro Sette, Eva Harris, Daniela Weiskopf, Sandeep Kumar Dhanda, Anette Stryhn, Søren Buus, and Sean A. Diehl
- Subjects
CD4-Positive T-Lymphocytes ,Male ,viruses ,Epitopes, T-Lymphocyte ,Sequence Homology ,CD8-Positive T-Lymphocytes ,Dengue virus ,Antibodies, Viral ,medicine.disease_cause ,Cross-reactivity ,Epitope ,Dengue fever ,Dengue ,0302 clinical medicine ,Cytotoxic T cell ,0303 health sciences ,Attenuated vaccine ,biology ,Zika Virus Infection ,Vaccination ,Yellow Fever Vaccine ,virus diseases ,Middle Aged ,Flavivirus ,medicine.anatomical_structure ,Female ,Yellow fever virus ,Adult ,Adolescent ,T cell ,Immunology ,Dengue Vaccines ,Cross Reactions ,Vaccines, Attenuated ,Microbiology ,Flavivirus Infections ,Young Adult ,03 medical and health sciences ,Antigen ,Virology ,Yellow Fever ,Vaccines and Antiviral Agents ,medicine ,Humans ,Encephalitis, Japanese ,030304 developmental biology ,Viral Vaccines ,Zika Virus ,Dengue Virus ,biochemical phenomena, metabolism, and nutrition ,medicine.disease ,biology.organism_classification ,Antibodies, Neutralizing ,Insect Science ,Leukocytes, Mononuclear ,West Nile Fever ,030215 immunology - Abstract
Members of the flavivirus genus share a high level of sequence similarity and often circulate in the same geographical regions. However, whether T cells induced by one viral species cross-react with other related flaviviruses has not been globally addressed. Here, we tested pools of epitopes derived from dengue (DENV), zika (ZIKV), Japanese Encephalitis (JEV), West Nile (WNV), and yellow fever (YFV) viruses by Intracellular Cytokine Staining (ICS) using PBMCs of individuals naturally exposed to DENV or immunized with DENV (TV005) or YF17D vaccines. CD8 T cell responses recognized epitopes from multiple flaviviruses, however, the magnitude of cross-reactive responses was consistently several-fold lower than those to the autologous epitope pools, and associated with lower expression of activation markers such as CD40L, CD69, and CD137. Next, we characterized the antigen sensitivity of short-term T cell lines (TCL) representing twenty-nine different individual epitope/donor combinations. TCL derived from DENV monovalent vaccinees induced CD8 and CD4 T cells that cross-reacted within the DENV serocomplex but were consistently associated with more than 100-fold lower antigen sensitivity for most other flaviviruses, with no cross-recognition of YFV derived peptides. CD8 and CD4 TCL from YF17D vaccinees were associated with very limited cross-reactivity with any other flaviviruses, and in five out of eight cases more than 1000-fold lower antigen sensitivity. Overall, our data suggest limited cross-reactivity for both CD4 and CD8 T cell responses between flaviviruses and has implications for understanding immunity elicited by natural infection, and strategies to develop live attenuated vaccines against flaviviral species.ImportanceThe envelope (E) protein is the dominant target of neutralizing antibodies for dengue virus (DENV) and yellow fever virus (YFV). Accordingly, several DENV vaccine constructs use the E protein in a live attenuated vaccine format, utilizing a backbone derived from a heterologous flavivirus (such as YF) as a delivery vector. This backbone comprises the non-structural (NS) and capsid (C) antigens which are dominant targets of T cell responses. Here, we demonstrate that cross-reactivity at the level of T cell responses amongst different flaviviruses is very limited, despite high levels of sequence homology. Thus, the use of heterologous flavivirus species as a live attenuated vaccine vector is not likely to generate optimal T cell responses, and might thus impair vaccine performance.
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- 2020
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17. Genetic risk for dengue hemorrhagic fever and dengue fever in multiple ancestries
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Win Lai May, Jorge E. Osorio, Leda Parham, Min Thein, Mark Loeb, Dang Duc Anh, Binod Neupane, Khin Saw Aye, Eva Harris, Aruna D. De Silva, Pardeep Singh, Kenji Hirayama, Elsa Marina Rojas, Esteban E. Díaz-González, Cynthia Rodriguez, Rosa M. Sanchez-Casas, Luis Angel Villar, Ildefonso Fernández-Salas, Ananda Wijewickrama, Filemon Bucardo, Guillaume Paré, Guillermina Kuan, Yaoska Reyes, Lan Weiss, Scott B. Halstead, Jennifer Margaret Newton, Lionel Gresh, Ivette Lorenzana, Patricia Blandon, Sunil Premawansa, Gayani Premawansa, Angel Balmaseda, and Sasha Eskandarian
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0301 basic medicine ,Adult ,Male ,Risk ,medicine.medical_specialty ,Multifactorial Inheritance ,Research paper ,Dengue hemorrhagic fever ,lcsh:Medicine ,Single-nucleotide polymorphism ,Genome-wide association study ,General Biochemistry, Genetics and Molecular Biology ,Dengue fever ,Cohort Studies ,Dengue ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Risk Factors ,Internal medicine ,Genetics ,Medicine ,Humans ,GWAS ,Genetic Predisposition to Disease ,Severe Dengue ,Genetic risk ,South east asian ,Child ,Phylogeny ,Ancestry ,lcsh:R5-920 ,business.industry ,lcsh:R ,virus diseases ,General Medicine ,Odds ratio ,medicine.disease ,030104 developmental biology ,Quartile ,030220 oncology & carcinogenesis ,Female ,business ,lcsh:Medicine (General) ,Genome-Wide Association Study - Abstract
Background: Genetic risk factors for dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) and dengue fever (DF) are limited, in particular there are sparse data on genetic risk across diverse populations. Methods: We conducted a genome-wide association study (GWAS) in a derivation and validation sample of 7, 460 participants of Latin American, South Asian, and South East Asian ancestries. We then developed a weighted polygenic risk score (PRS) for each participant in each of the validation cohorts of the three ancestries to predict the risk of DHF/DSS compared to DF, DHF/DSS compared to controls, and, DF compared to controls. Findings: The risk of DHF/DSS was significantly increased, odds ratio [OR] 1.84 (95%CI 1.47 to 2.31) (195 SNPs), compared to DF, fourth PRS quartile versus first quartile, in the validation cohort. The risk of DHF/DSS compared to controls was increased (OR=3.94; 95% CI 2.84 to 5.45) (278 SNPs), as was the risk of DF compared to controls (OR=1.97; 95%CI 1.63 to 2.39) (251 SNPs). Risk increased in a dose-dependent manner with increase in quartiles of PRS across comparisons. Significant associations persisted for PRS built within ancestries and applied to the same or different ancestries as well as for PRS built for one outcome (DHF/DSS or DF) and applied to the other. Interpretation: There is a strong genetic effect that predisposes to risk of DHF/DSS and DF. The genetic risk for DHF/DSS is higher than that for DF when compared to controls, and this effect persists across multiple ancestries. Keywords: Dengue, Genetics, Risk, GWAS, Ancestry
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- 2020
18. Clinical, Bacteriologic, and Geographic Stratification of Melioidosis Emerges from the Sri Lankan National Surveillance Program
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Mohan Natesan, Adam J. Merritt, Enoka Corea, Aruna D. De Silva, Timothy J. J. Inglis, Harindra D. Sathkumara, and Shivankari Krishnananthasivam
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0301 basic medicine ,medicine.medical_specialty ,Melioidosis ,Burkholderia pseudomallei ,030231 tropical medicine ,Geographic Mapping ,Bacteremia ,03 medical and health sciences ,0302 clinical medicine ,Virology ,Internal medicine ,Water Quality ,Epidemiology ,medicine ,Odds Ratio ,Cluster Analysis ,Humans ,Soil Microbiology ,Sri Lanka ,biology ,Mortality rate ,Outbreak ,Odds ratio ,Articles ,medicine.disease ,biology.organism_classification ,Bacterial Typing Techniques ,030104 developmental biology ,Infectious Diseases ,Population Surveillance ,Multilocus sequence typing ,Parasitology - Abstract
Melioidosis, a potentially fatal tropical infection, is said to be underdiagnosed in low-income countries. An increase in melioidosis cases in Sri Lanka allowed us to analyze the relationship among clinical outcome, bacteriology, epidemiology, and geography in the first 108 laboratory-confirmed cases of melioidosis from a nationwide surveillance program. The additional 76 cases of laboratory-confirmed melioidosis confirmed further associations between Burkholderia pseudomallei multilocus sequence typing (MLST) and infection phenotype; ST1137/unifocal bacteremic infection (χ2 = 3.86, P < 0.05), ST1136/multifocal infection without bacteremia (χ2 = 15.8, P < 0.001), and ST1132/unifocal nonbacteremic infection (χ2 = 6.34, P = 0.02). ST1137 infections were predominantly seen in the Western Province, whereas ST1132, 1135, and 1136 infections predominated in the Northwestern Province. Early participating centers in the surveillance program had a lower melioidosis-associated mortality than later participants (χ2 = 3.99, P < 0.05). The based upon related sequence types (eBURST) algorithm, a MLST clustering method that infers founding genotypes and patterns of descent for related isolates and clonal complexes in an unrooted tree, showed uneven distribution of sequence types (STs). There was spatial clustering of the commonest STs (ST1132, 1136, and 1137) in the Western, Northwestern, and Central provinces. The recent increase in melioidosis in Sri Lanka uncovered by laboratory-enhanced surveillance is likely to be the result of a combination of improved laboratory detection, increased clinician awareness, recruitment of clinical centers, and small outbreaks. Further development of the surveillance program into a national genotyping-supported melioidosis registry will improve melioidosis diagnosis, treatment, and prevention where underdiagnosis and mortality rates remain high.
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- 2018
19. Burden and Seasonality of Viral Acute Respiratory Tract Infections among Outpatients in Southern Sri Lanka
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Megan E. Reller, Truls Østbye, Jeremy Hsiang, David Shapiro, Champica K Bodinayake, Ajith Nagahawatte, L. Gayani Tillekeratne, Ruvini Kurukulasooriya, Vasantha Devasiri, Aruna D. De Silva, Bradley Nicholson, and Christopher W. Woods
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Adult ,Male ,medicine.medical_specialty ,Adolescent ,viruses ,030231 tropical medicine ,medicine.disease_cause ,Virus ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Human metapneumovirus ,Virology ,Epidemiology ,Outpatients ,medicine ,Prevalence ,Infection control ,Humans ,030212 general & internal medicine ,Child ,Respiratory Tract Infections ,Aged ,Sri Lanka ,Aged, 80 and over ,Respiratory tract infections ,biology ,business.industry ,virus diseases ,Infant ,Articles ,Middle Aged ,biology.organism_classification ,Vaccination ,Infectious Diseases ,Virus Diseases ,Child, Preschool ,Acute Disease ,Viruses ,Respiratory virus ,Parasitology ,Female ,Seasons ,Rhinovirus ,business - Abstract
In tropical and subtropical settings, the epidemiology of viral acute respiratory tract infections varies widely between countries. We determined the etiology, seasonality, and clinical presentation of viral acute respiratory tract infections among outpatients in southern Sri Lanka. From March 2013 to January 2015, we enrolled outpatients presenting with influenza-like illness (ILI). Nasal/nasopharyngeal samples were tested in duplicate using antigen-based rapid influenza testing and multiplex polymerase chain reaction (PCR) for respiratory viruses. Monthly proportion positive was calculated for each virus. Bivariable and multivariable logistic regression were used to identify associations between sociodemographic/clinical information and viral detection. Of 571 subjects, most (470, 82.3%) were ≥ 5 years of age and 53.1% were male. A respiratory virus was detected by PCR in 63.6% (N = 363). Common viral etiologies included influenza (223, 39%), human enterovirus/rhinovirus (HEV/HRV, 14.5%), respiratory syncytial virus (RSV, 4.2%), and human metapneumovirus (hMPV, 3.9%). Both ILI and influenza showed clear seasonal variation, with peaks from March to June each year. RSV and hMPV activity peaked from May to July, whereas HEV/HRV was seen year-round. Patients with respiratory viruses detected were more likely to report pain with breathing (odds ratio [OR] = 2.60, P = 0.003), anorexia (OR = 2.29, P < 0.001), and fatigue (OR = 2.00, P = 0.002) compared with patients with no respiratory viruses detected. ILI showed clear seasonal variation in southern Sri Lanka, with most activity during March to June; peak activity was largely due to influenza. Targeted infection prevention activities such as influenza vaccination in January-February may have a large public health impact in this region.
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- 2017
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20. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry
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Mayuko Saito, Robert H. Gilman, Daniela Weiskopf, Julie G. Burel, Cecilia S. Lindestam Arlehamn, Jose Zapardiel-Gonzalo, Pandurangan Vijayanand, Alessandro Sette, Yu Qian, Bjoern Peters, Richard H. Scheuermann, Aruna D. De Silva, and Randy Taplitz
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Adult ,CD4-Positive T-Lymphocytes ,Male ,0301 basic medicine ,T cell ,Immunology ,Population ,Cell Count ,Context (language use) ,Biology ,Article ,Immunophenotyping ,Workflow ,Flow cytometry ,03 medical and health sciences ,Sex Factors ,0302 clinical medicine ,Immune system ,Latent Tuberculosis ,T-Lymphocyte Subsets ,medicine ,Humans ,Immunology and Allergy ,education ,Systems immunology ,education.field_of_study ,Latent tuberculosis ,medicine.diagnostic_test ,Age Factors ,Replicate ,Flow Cytometry ,medicine.disease ,CD56 Antigen ,030104 developmental biology ,medicine.anatomical_structure ,Leukocytes, Mononuclear ,Female ,030215 immunology - Abstract
In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies.
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- 2017
21. Development of Envelope Protein Antigens To Serologically Differentiate Zika Virus Infection from Dengue Virus Infection
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Erwin Camacho, Tulika Singh, Stephen D Graham, Holly Heimsath, Jorge E. Osorio, Eva Harris, Aruna D. De Silva, Helen M. Lazear, James A. Brackbill, Daniela Weiskopf, Alessandro Sette, Angel Balmaseda, Helena Lucia Barroso dos Reis, Cesar A. Lopez, Reynaldo Dietze, Sallie R. Permar, Aravinda M. de Silva, Camila Giuberti, Guei-Jiun Alice Liou, Michel J. Miley, Matthew H. Collins, Ramesh Jadi, and Lakshmanane Premkumar
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0301 basic medicine ,Microbiology (medical) ,Time Factors ,viruses ,Enzyme-Linked Immunosorbent Assay ,Biology ,Dengue virus ,Cross Reactions ,medicine.disease_cause ,Antibodies, Viral ,Virus ,Epitope ,Serology ,Zika virus ,Dengue ,03 medical and health sciences ,Epitopes ,Antigen ,Viral Envelope Proteins ,Virology ,medicine ,Humans ,Flavivirus Infections ,Serologic Tests ,Longitudinal Studies ,Antigens, Viral ,Comparative epitope mapping ,Surveillance ,Zika Virus Infection ,Flavivirus ,Cross-reactivity ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Antibodies, Neutralizing ,Recombinant Proteins ,3. Good health ,030104 developmental biology ,Antibody-binding region ,Immunoglobulin G ,Population Surveillance ,ELISA ,Computational prediction ,Serological diagnosis - Abstract
Artículo digital, Zika virus (ZIKV) is an emerging flavivirus that can cause birth defects and neurologic complications. Molecular tests are effective for diagnosing acute ZIKV infection, although the majority of infections produce no symptoms at all or present after the narrow window in which molecular diagnostics are dependable. Serology is a reliable method for detecting infections after the viremic period; however, most serological assays have limited specificity due to cross-reactive antibodies elicited by flavivirus infections. Since ZIKV and dengue virus (DENV) widely cocirculate, distinguishing ZIKV infection from DENV infection is particularly important for diagnosing individual cases or for surveillance to coordinate public health responses.
- Published
- 2019
22. Whole-Genome Sequences of Eight Clinical Isolates of Burkholderia pseudomallei from Melioidosis Patients in Eastern Sri Lanka
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Thimirangi R. Abeysekere, Enoka Corea, Harindra D. Sathkumara, H.S. Jayasinghearachchi, Vaithehi R. Francis, Aruna D. De Silva, and Shivankari Krishnananthasivam
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0303 health sciences ,Melioidosis ,biology ,030306 microbiology ,Burkholderia pseudomallei ,Genome Sequences ,social sciences ,bacterial infections and mycoses ,medicine.disease ,biology.organism_classification ,Genome ,Microbiology ,03 medical and health sciences ,Immunology and Microbiology (miscellaneous) ,parasitic diseases ,Genetics ,medicine ,bacteria ,Sri lanka ,Molecular Biology ,geographic locations ,030304 developmental biology - Abstract
Here, we report whole-genome sequences (WGS) of eight clinical isolates of Burkholderia pseudomallei obtained from melioidosis patients with sepsis in eastern Sri Lanka.
- Published
- 2019
23. Characterization of Magnitude and Antigen Specificity of HLA-DP, DQ, and DRB3/4/5 Restricted DENV-Specific CD4+ T Cell Responses
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Eugene Moore, Alessandro Sette, Aruna D. De Silva, Hannah Voic, John Sidney, Simon Mallal, Bjoern Peters, Daniela Weiskopf, Elizabeth J. Phillips, Aravinda M. de Silva, Ramesh Jadi, and Alba Grifoni
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lcsh:Immunologic diseases. Allergy ,CD4-Positive T-Lymphocytes ,0301 basic medicine ,HLA-DP Antigens ,Immunology ,Epitopes, T-Lymphocyte ,HLA-DP ,Immunodominance ,Biology ,HLA-DRB3/4/5 ,Epitope ,Dengue ,Interferon-gamma ,CD4+T cells ,03 medical and health sciences ,Negative selection ,0302 clinical medicine ,Antigen ,Antibody Specificity ,HLA-DQ ,Humans ,Immunology and Allergy ,Allele ,Alleles ,Original Research ,DENV ,ELISPOT ,adaptive immunity ,Dengue Virus ,Molecular biology ,030104 developmental biology ,lcsh:RC581-607 ,HLA-DRB1 Chains ,030215 immunology - Abstract
Background: Dengue Virus (DENV) associated disease is a major public health problem. Assessment of HLA class II restricted DENV-specific responses is relevant for immunopathology and definition of correlates of protection. While previous studies characterized responses restricted by the HLA-DRB1 locus, the responses associated with other class II loci have not been characterized to date. Accordingly, we mapped HLA-DP, DQ, and DRB3/4/5 restricted DENV-specific CD4 T cell epitopes in PBMCs derived from the DENV endemic region Sri Lanka. Methods: We studied 12 DP, DQ, and DRB3/4/5 alleles that are commonly expressed and provide worldwide coverage >82% for each of the loci analyzed and >99% when combined. CD4+ T cells purified by negative selection were stimulated with pools of HLA-predicted binders for 2 weeks with autologous APC. Epitope reactive T cells were enumerated using IFNγ ELISPOT assay. This strategy was previously applied to identify DRB1 restricted epitopes. In parallel, membrane expression levels of HLA-DR, DP, and DQ proteins was assessed using flow cytometry. Results: Epitopes were identified for all DP, DQ, and DRB3/4/5 allelic variants albeit with magnitudes significantly lower than the ones previously observed for the DRB1 locus. This was in line with lower membrane expression of HLA-DP and DQ molecules on the PBMCs tested, as compared to HLA-DR. Significant differences between loci were observed in antigen immunodominance. Capsid responses were dominant for DRB1/3/4/5 and DP alleles but negligible for the DQ alleles. NS3 responses were dominant in the case of DRB1/3/4/5 and DQ but absent in the case of DP. NS1 responses were prominent in the case of the DP alleles, but negligible in the case of DR and DQ. In terms of epitope specificity, repertoire was largely overlapping between DRB1 and DRB3/4/5, while DP and DQ loci recognized largely distinct epitope sets. Conclusion: The HLA-DP, DQ, and DRB3/4/5 loci mediate DENV-CD4 specific immune responses of lower magnitude as compared to HLA-DRB1, consistent with their lower levels of expression. The responses are associated with distinct and characteristic patterns of immunodominance, and variable epitope overlap across loci.
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- 2019
24. High Levels of Serum Angiopoietin 2 and Angiopoietin 2/1 Ratio at the Critical Stage of Dengue Hemorrhagic Fever in Patients and Association with Clinical and Biochemical Parameters
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Gayani Premawansa, Aruna D. De Silva, Shiroma M. Handunnetti, Karunayokiny Kanapathippillai, Maheshi Mapalagamage, Tharanga Fernando, Ananda R. Wickremasinghe, Sharmila Thillainathan, and Sunil Premawansa
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0301 basic medicine ,Microbiology (medical) ,Serum ,medicine.medical_specialty ,Dengue hemorrhagic fever ,Gastroenterology ,Dengue fever ,Angiopoietin ,Angiopoietin-2 ,Dengue ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,medicine ,Angiopoietin-1 ,Humans ,In patient ,Severe Dengue ,Endothelial dysfunction ,Stage (cooking) ,Immunoassays ,business.industry ,Angiopoietin 2 ,medicine.disease ,030104 developmental biology ,030220 oncology & carcinogenesis ,cardiovascular system ,Biomarker (medicine) ,business ,hormones, hormone substitutes, and hormone antagonists - Abstract
Longitudinal changes of serum angiopoietin 1 (Ang-1) and angiopoietin 2 (Ang-2) associated with endothelial stability in dengue patients with different disease stages were studied. Serum Ang-1 and Ang-2 levels were measured in confirmed dengue fever (DF) patients on admission (DFA, n = 40) and discharge (DFD, n = 20); in dengue hemorrhagic fever (DHF) patients on admission (DHFA, n = 40), at critical stage (DHFC, n = 36), and on discharge (DHFD, n = 20); and in healthy controls (HC, n = 25). DHFC had the highest serum Ang-2 and lowest Ang-1 levels compared to DFA, DHFA, and HC (P < 0.050). The ratio of serum Ang-2/Ang-1 in DHFC was the highest among all study categories tested (P < 0.001). Significant positive correlations were observed between serum Ang-1 and platelet count in DHFA (Pearson r = 0.653, P < 0.001) and between Ang-1 and pulse pressure in DHFC (r = 0.636, P = 0.001). Using a cutoff value of 1.01 for the Ang-2/Ang-1 ratio for DHFC, a sensitivity of 83.2% and a specificity of 81.2% discerning DF from DHF were obtained. Therefore, serum Ang-2/Ang-1 could be used as a biomarker for endothelial dysfunction in severe dengue at the critical stage.
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- 2019
25. Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-Producing CD4 T Cells and Their Association with Severe Dengue Disease
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Ananda Wijewickrama, Pandurangan Vijayanand, Alessandro Sette, Bjoern Peters, Sara Herrera-de la Mata, Luzia Maria de-Oliveira-Pinto, Aruna D. De Silva, Eva Harris, N.D. Suraj Goonawardhana, Daniela Weiskopf, Sunil Premawansa, Angel Balmaseda, Gayani Premawansa, Alba Grifoni, Grégory Seumois, Denise Hinz, Yuan Tian, and Cheryl Kim
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Cell ,virus diseases ,Biology ,Dengue virus ,medicine.disease_cause ,medicine.disease ,Dengue fever ,Transcriptome ,Interleukin 22 ,Pathogenesis ,Interleukin 10 ,medicine.anatomical_structure ,Immunology ,medicine ,Cytotoxic T cell - Abstract
Dengue virus (DENV) can cause diseases ranging from self-limiting dengue fever (DF) to more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Whether DENV-specific T cells contribute to the protection against or pathogenesis of severe dengue disease is not well defined. In this study, we identified a novel IL-10+IFN-Υ+ double positive (DP) CD4 T cell subset that predominated the antigen-specific CD4 T cell response during acute DENV infection. While some of the transcriptomic and proteomic signatures of DP cells marginally overlapped with previously identified markers of cytotoxic CD4 T cells and type 1 regulatory T (Tr1)-like cell, the vast majority of the genes differentially expressed in DP cells were novel and included genes such as IL21, IL22, CD109, and CCR1. Although we observed higher frequencies of DENV-specific DP cells in DHF patients than in DF patients, their transcriptomic profile was similar in these two groups of patients, suggesting that dengue disease severity is not associated with altered phenotypic or functional attributes of this novel CD4 T cell subset. Overall, our in-depth transcriptomic, phenotypic, and functional analyses revealed a novel DENV-specific DP cell subset in patients with acute dengue disease and argue against altered CD4 T cell response as a determinant of disease severity.
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- 2019
26. Immunodominant Dengue Virus-Specific CD8 + T Cell Responses Are Associated with a Memory PD-1 + Phenotype
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Cristhiam Cerpas, John Sidney, Ruklanthi de Alwis, Derek J. Bangs, Aruna D. De Silva, Alessandro Sette, Bjoern Peters, Daniela Weiskopf, Michael A. Angelo, Anira N. Fernando, Lionel Gresh, Eva Harris, and Angel Balmaseda
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Cytotoxicity, Immunologic ,0301 basic medicine ,T cell ,Programmed Cell Death 1 Receptor ,Immunology ,Population ,Epitopes, T-Lymphocyte ,Gene Expression ,HLA-A24 Antigen ,Cellular Response to Infection ,Nicaragua ,T-Cell Antigen Receptor Specificity ,Human leukocyte antigen ,Immunodominance ,CD8-Positive T-Lymphocytes ,Biology ,Dengue virus ,Lymphocyte Activation ,medicine.disease_cause ,Microbiology ,Immunophenotyping ,Dengue ,Interferon-gamma ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,HLA Antigens ,T-Lymphocyte Subsets ,Virology ,medicine ,Humans ,Cytotoxic T cell ,education ,Alleles ,education.field_of_study ,Dengue Virus ,Phenotype ,030104 developmental biology ,medicine.anatomical_structure ,Insect Science ,HLA-B35 Antigen ,Immunologic Memory ,CD8 ,030215 immunology - Abstract
Dengue disease is a large public health problem that mainly afflicts tropical and subtropical regions. Understanding of the correlates of protection against dengue virus (DENV) is poor and hinders the development of a successful human vaccine. The present study aims to define DENV-specific CD8 + T cell responses in general and those of HLA alleles associated with dominant responses in particular. In human blood donors in Nicaragua, we observed a striking dominance of HLA B-restricted responses in general and of the allele B*35:01 in particular. Comparing these patterns to those in the general population of Sri Lanka, we found a strong correlation between restriction of the HLA allele and the breadth and magnitude of CD8 + T cell responses, suggesting that HLA genes profoundly influence the nature of responses. The majority of gamma interferon (IFN-γ) responses were associated with effector memory phenotypes, which were also detected in non-B*35:01-expressing T cells. However, only the B*35:01 DENV-specific T cells were associated with marked expression of the programmed death 1 protein (PD-1). These cells did not coexpress other inhibitory receptors and were able to proliferate in response to DENV-specific stimulation. Thus, the expression of particular HLA class I alleles is a defining characteristic influencing the magnitude and breadth of CD8 responses, and a distinct, highly differentiated phenotype is specifically associated with dominant CD8 + T cells. These results are of relevance for both vaccine design and the identification of robust correlates of protection in natural immunity. IMPORTANCE Dengue is an increasingly significant public health problem as its mosquito vectors spread over greater areas; no vaccines against the virus have yet been approved. An important step toward vaccine development is defining protective immune responses; toward that end, we here characterize the phenotype of the immunodominant T cell responses. These DENV-reactive T cells express high levels of the receptor programmed death 1 protein (PD-1), while those from disease-susceptible alleles do not. Not only does this represent a possible correlate of immunodominance, but it raises the hypothesis that PD-1 might be a regulator that prevents excessive damage while preserving antiviral function. Further, as this study employs distinct populations (Nicaraguan and Sri Lankan donors), we also confirmed that this pattern holds despite geographic and ethnic differences. This finding indicates that HLA type is the major determinant in shaping T cell responses.
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- 2016
27. Preliminary study on chronic granulomatous disease in Sri Lanka
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W. M. D. K. Dasanayake, Aruna D. De Silva, Noorul Mifra Faiz, Shalinda Jude Arjuna Fernando, Rathnayake Mudiyanselage Chandima Hasanthi Karunatilake, Geethani Devika Wickramasinghe, Nilhan Rajiva de Silva, and Shiroma Mangaika Handunnetti
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lcsh:Immunologic diseases. Allergy ,Tuberculosis ,Disease ,CYBB ,03 medical and health sciences ,0302 clinical medicine ,Chronic granulomatous disease ,Germline mutation ,medicine ,NCF1 ,X-linked ,Splice site mutation ,NADPH oxidase ,business.industry ,Mortality rate ,General Medicine ,medicine.disease ,030220 oncology & carcinogenesis ,Mycobacterial infections ,Immunology ,Primary immunodeficiency ,lcsh:RC581-607 ,business ,030215 immunology - Abstract
Background Chronic granulomatous disease (CGD) is a rare primary immunodeficiency of the phagocytic cells, which results in absent or diminished levels of microbicidal reactive oxygen species. The disease occurs due to germline mutations in the genes encoding the five subunits of NADPH oxidase complex. The present study is a pilot study to understand the clinical and genetic aspects of CGD in Sri Lanka. Methods Clinical records of thirteen CGD patients were analysed and compared with similar studies performed in different countries and regions to identify patterns in demographics, clinical manifestations and infectious agents. Genomic DNA and cDNA were analysed in eight patients to identify mutations in CYBB and NCF1 genes, thereby to ascertain the potential X-linked and autosomal recessive (AR) CGD patients. Results The onset of symptoms in the patient cohort was very early (mean 4.6 months) compared to 20 months in India and 23.9 months in Latin America. Similarly, the age at diagnosis was lower (mean 1.6 years after birth) compared to other studies; 4.5 years in India and 6.1 years in Europe. Pulmonary manifestations were the most common (85%), followed by skin/subcutaneous infections (77%) and lymphadenopathy (62%). The death rate of local patients (38%) was higher than other countries (India 35%, Europe 20%). Majority (77%) were treated for tuberculosis at some point in life. Genetic analysis confirmed six out of eight patients as X-linked CGD cases with mutations in CYBB gene. A novel splice site mutation was identified in P-07 at position c.141+6 which resulted in the deletion of entire exon 2. Two siblings (P-05 and P-06) from consanguineous parents, were identified with AR-CGD based on the homozygous GT deletion mutation in NCF1 gene. Conclusions The clinical presentation, manifestations and genetic subtypes in the local cohort, appear to be comparable with global trends. Mycobacterial infections should be investigated and treated with more prominence. Effective treatment options are required to control the high mortality rate.
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- 2018
28. Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-producing CD4 T Cells and Their Association with Dengue Disease
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Aruna D. De Silva, Sara Herrera-de la Mata, Alba Grifoni, Ananda Wijewickrama, Sunil Premawansa, Cheryl Kim, Gayani Premawansa, Alessandro Sette, Grégory Seumois, Denise Hinz, Daniela Weiskopf, Yuan Tian, Bjoern Peters, Luzia Maria de-Oliveira-Pinto, N.D. Suraj Goonawardhana, Angel Balmaseda, Eva Harris, Pandurangan Vijayanand, and Jose Mateus
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Adult ,Male ,0301 basic medicine ,CCR1 ,Adolescent ,Receptors, CCR1 ,Biology ,Dengue virus ,GPI-Linked Proteins ,medicine.disease_cause ,Severity of Illness Index ,T-Lymphocytes, Regulatory ,Article ,General Biochemistry, Genetics and Molecular Biology ,Dengue fever ,Transcriptome ,Pathogenesis ,Interleukin 22 ,Interferon-gamma ,03 medical and health sciences ,0302 clinical medicine ,Antigens, CD ,medicine ,Humans ,Cytotoxic T cell ,Severe Dengue ,lcsh:QH301-705.5 ,Interleukins ,virus diseases ,Dengue Virus ,Middle Aged ,medicine.disease ,Virology ,Interleukin-10 ,Neoplasm Proteins ,3. Good health ,Interleukin 10 ,030104 developmental biology ,lcsh:Biology (General) ,Gene Expression Regulation ,Case-Control Studies ,Female ,030217 neurology & neurosurgery ,Signal Transduction ,T-Lymphocytes, Cytotoxic - Abstract
SUMMARY Dengue virus (DENV) can cause diseases ranging from dengue fever (DF) to more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Whether antiviral T cells contribute to the protection against or pathogenesis of severe disease is not well defined. Here, we identified antigen-specific IL-10+IFN-γ+ double-positive (DP) CD4 T cells during acute DENV infection. While the transcriptomic signatures of DP cells partially overlapped with those of cytotoxic and type 1 regulatory CD4 T cells, the majority of them were non-cytotoxic/Tr1 and included IL21, IL22, CD109, and CCR1. Although we observed a higher frequency of DP cells in DHF, the transcriptomic profile of DP cells was similar in DF and DHF, suggesting that DHF is not associated with the altered phenotypic or functional attributes of DP cells. Overall, this study revealed a DENV-specific DP cell subset in patients with acute dengue disease and argues against altered DP cells as a determinant of DHF., In Brief Tian et al. identify and characterize antigen-specific IL-10+IFN-γ+ double-positive (DP) CD4 T cells in acute dengue patients. DP cells display similar transcriptomic profiles in mild DF and severe DHF, despite their increased frequency in DHF, suggesting that DHF is not associated with the altered phenotype or functionality of DP cells., Graphical Abstract
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- 2019
29. Emergence of a Dengue virus serotype 2 causing the largest ever dengue epidemic in Sri Lanka
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Anishgoby Rajendran, Chandima Jeewandara, Samitha Fernando, Shawn A Abeynaike, Ranmalie Abeyesekere, Pathum Asela Perera, Desha Dilani, Geethal S. Bandara Jayerathne, Aruna D. De Silva, Laksiri Gomes, Suraj Goonawardhana, Rashmi Tippalagama, Ananda Wijewickrama, and Gathsaurie Neelika Malavige
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Serotype ,medicine.medical_specialty ,business.industry ,Secondary infection ,Odds ratio ,Dengue virus ,medicine.disease ,medicine.disease_cause ,Virology ,Virus ,Dengue fever ,Epidemiology ,medicine ,Sri lanka ,business - Abstract
BackgroundSri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. As it was felt that more patients appeared to develop complications and severe dengue, we compared clinical features of patients with acute dengue, with the previous circulating serotype (DENV1) and also sequenced the new virus, to determine the lineage of the virus.Methodology/Principal findingsWe studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. 65 (82.3%) of those with DENV1 and 86 (92.4%) of those with DENV2 were experiencing a secondary infection. The risk of developing dengue haemorrhagic fever (DHF) was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (pWhole genome sequencing showed that these DENV-2 isolates belonged to a cosmopolitan strain and was genetically more distant than the DENV-2 strains that circulated from 1981 to 2004 in Sri Lanka.Conclusions/significanceSince this DENV2 strain appears to cause more severe forms of clinical disease, it would be important to determine variations in the virus genome or other factors that could have contributed to severe disease.Author summarySri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. We studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. The risk of developing dengue haemorrhagic fever was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (p
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- 2018
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30. Longitudinal analysis of antibody cross-neutralization following Zika and dengue virus infection in Asia and the Americas
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Magelda Montoya, Ramesh Jadi, Samuel Schildhauer, Juthathip Mongkolsapaya, Gavin R. Screaton, Eva Harris, Wanwisa Dejnirattisai, Henry Puerta-Guardo, Hasitha Tissera, Sirijitt Vasanawathana, Angel Balmaseda, Leah C. Katzelnick, Aruna D. De Silva, Matthew H. Collins, Piyada Supasa, Prida Malasit, Aravinda M. de Silva, Medical Research Council (MRC), and Wellcome Trust
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Male ,0301 basic medicine ,Serotype ,cross-reactivity ,viruses ,VACCINE ,Nicaragua ,Dengue virus ,Antibodies, Viral ,medicine.disease_cause ,DISEASE ,Neutralization ,Zika virus ,Serology ,Dengue ,flavivirus ,Immunology and Allergy ,Longitudinal Studies ,Child ,Neutralizing antibody ,biology ,Zika Virus Infection ,virus diseases ,11 Medical And Health Sciences ,Flavivirus ,Infectious Diseases ,Child, Preschool ,Female ,Antibody ,BURDEN ,Life Sciences & Biomedicine ,Asia ,longitudinal ,Adolescent ,Immunology ,Cross Reactions ,Microbiology ,03 medical and health sciences ,PEDIATRIC COHORT ,Neutralization Tests ,medicine ,Humans ,Immunologic Factors ,neutralizing antibodies ,Science & Technology ,Infant ,Zika Virus ,06 Biological Sciences ,Dengue Virus ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Antibodies, Neutralizing ,Virology ,REACTIVITY ,Latin America ,030104 developmental biology ,biology.protein ,Americas ,DEPENDENT ENHANCEMENT ,RESPONSES - Abstract
Background The four dengue virus serotypes (DENV1-4) and Zika virus (ZIKV) are related mosquito-borne flaviviruses of major importance globally. While monoclonal antibodies and plasma from DENV-immune donors can neutralize or enhance ZIKV in vitro and in small animal models, and vice versa, the extent, duration, and significance of cross-reactivity remains unknown, particularly in flavivirus-endemic regions. Methods We studied neutralizing antibodies to ZIKV and DENV1-4 in longitudinal serologic specimens through 3 years post-infection from people in Latin America and Asia with laboratory-confirmed DENV infections. We also evaluated neutralizing antibodies to ZIKV and DENV1-4 in Zika patients through 6 months post-infection. Results In Zika patients, the highest neutralizing antibody titers were to ZIKV, with low-level cross-reactivity to DENV1-4 that was greater in DENV-immune individuals. We found in primary and secondary DENV infections, neutralizing antibody titers to ZIKV were markedly lower than to the infecting DENV and heterologous DENV serotypes. Cross-neutralization was greatest in early convalescence, then ZIKV neutralization decreased, remaining at low levels over time. Conclusions Patterns of antibody cross-neutralization suggest ZIKV lies outside the DENV serocomplex. Neutralizing antibody titers can distinguish ZIKV from DENV infections when all viruses are analyzed simultaneously. These findings have implications for understanding natural immunity and vaccines.
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- 2018
31. Is Total Serum Nitrite and Nitrate (NOx) Level in Dengue Patients a Potential Prognostic Marker of Dengue Hemorrhagic Fever?
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Aruna D. De Silva, Gayani Premawansa, Sunil Premawansa, Tharanga Fernando, Karunayokiny Kanapathippillai, Maheshi Mapalagamage, Sharmila Thillainathan, Rajitha Wickremasinghe, and Shiroma M. Handunnetti
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0301 basic medicine ,Adult ,Male ,inorganic chemicals ,medicine.medical_specialty ,Dengue hemorrhagic fever ,Adolescent ,Article Subject ,030231 tropical medicine ,Clinical Biochemistry ,Gastroenterology ,Sensitivity and Specificity ,Dengue fever ,Nitric oxide ,Dengue ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Nitrate ,Internal medicine ,Genetics ,Medicine ,Humans ,In patient ,Nitrite ,Molecular Biology ,NOx ,Nitrites ,lcsh:R5-920 ,Nitrates ,business.industry ,Biochemistry (medical) ,Case-control study ,General Medicine ,Middle Aged ,respiratory system ,medicine.disease ,030104 developmental biology ,chemistry ,Case-Control Studies ,Female ,business ,lcsh:Medicine (General) ,Biomarkers ,Research Article - Abstract
Potential use of total nitrite plus nitrate (NOx) and nitrite (NO2−) separately as surrogate markers for serum nitric oxide in severe dengue and their longitudinal changes along with the progression of infection was studied. Deproteinized sera from confirmed dengue fever (DF,n=145) and dengue hemorrhagic fever (DHF,n=74) patients on admission—A, critical—C, discharge—D, and convalescence—CON stages and from age-gender matched healthy individuals (HC,n=77) were taken to assess NO2−and NOx levels using Griess and modified Griess assays. Serum NOx in DHFA was significantly lower compared to DFA (p<0.001). HC had the lowest NOx and NO2−compared to all patient categories (p<0.001) except NO2−in DF-CON and DHF-CON and NOx in DHF-CON. Serum NOx and NO2−in DHF patients admitted on fever day 3 (DHFA-3) was significantly lower compared to DFA-3 (p<0.05). Cut-off values of 4.46 μM for NOx (91.3% sensitivity and 80.1% specificity) and 1.25 μM for NO2−(75.0% sensitivity and 73.3% specificity) were obtained for day 3 of fever. Serum NOx may be used as potential prognostic marker of DHF in patients presenting with DF in the early stage (on day 3 of fever) of the disease.
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- 2018
32. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka
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Michael A. Angelo, Cecilia S. Lindestam Arlehamn, Aruna D. De Silva, Simon Mallal, John Sidney, Sunil Premawansa, Gayani Premawansa, Alessandro Sette, Rashmi Tippalagama, Elizabeth J. Phillips, Ananda Wijewickrama, Steven J. Mack, April Frazier, Suraj Goonewardana, Daniela Weiskopf, Shay Leary, and Alba Grifoni
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0301 basic medicine ,Male ,HLA-DP Antigens ,T-Lymphocytes ,Mice ,0302 clinical medicine ,Gene Frequency ,Genotype ,Ethnicity ,Immunology and Allergy ,Moors ,skin and connective tissue diseases ,Genetics ,Histocompatibility Testing ,General Medicine ,Hardy–Weinberg principle ,Healthy Volunteers ,HLA-A ,HLA typing ,Female ,Sequence Analysis ,Sinhalese ,musculoskeletal diseases ,Adult ,Colombo ,Tamil ,Immunology ,Locus (genetics) ,Human leukocyte antigen ,HLA-C Antigens ,Biology ,Article ,03 medical and health sciences ,Clinical Research ,HLA-DQ Antigens ,HLA-B Antigens ,Animals ,Humans ,Allele ,Allele frequency ,Sri Lanka ,HLA-A Antigens ,DNA ,HLA-DR Antigens ,Sequence Analysis, DNA ,HLA alleles ,Good Health and Well Being ,030104 developmental biology ,030215 immunology - Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies on T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were not detected at any locus. Several alleles were found in >30% of individuals, including the class II alleles DPB1 * 04:01, DPB1 * 02:01, DQB1 * 06:01 and DRB1 * 07:01, and the class I alleles A * 33:03 and A * 24:02. Genotype data will be available in the Allele Frequencies Net Database.
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- 2017
33. Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
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Zheng Fu, Veronique Schulten, Sunil Premawansa, Sandy L. Rosales, Alessandro Sette, Pandurangan Vijayanand, Yuan Tian, Rashika N. Tennekoon, Aruna D. De Silva, Bjoern Peters, Gaelle Picarda, Mariana Babor, Jerome Lane, Gayani Premawansa, Jose Zapardiel-Gonzalo, Ananda Wijewickrama, Grégory Seumois, Veena S. Patil, Julie G. Burel, Jason A. Greenbaum, and Daniela Weiskopf
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CD4-Positive T-Lymphocytes ,Male ,0301 basic medicine ,Herpesvirus 4, Human ,Cytomegalovirus ,General Physics and Astronomy ,CD8-Positive T-Lymphocytes ,Dengue virus ,medicine.disease_cause ,Granzymes ,Heterogeneous-Nuclear Ribonucleoproteins ,Receptors, G-Protein-Coupled ,0302 clinical medicine ,Immunology and Allergy ,Cytotoxic T cell ,lcsh:Science ,Cells, Cultured ,Genetics ,Multidisciplinary ,biology ,Effector ,Middle Aged ,Phenotype ,3. Good health ,Cell biology ,Adult ,Receptors, CCR7 ,Adolescent ,Science ,Immunology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Young Adult ,03 medical and health sciences ,Signaling Lymphocytic Activation Molecule Family ,medicine ,Humans ,Aged ,Perforin ,Gene Expression Profiling ,General Chemistry ,Dengue Virus ,Gene expression profiling ,Core Binding Factor Alpha 3 Subunit ,030104 developmental biology ,GPR56 ,Granzyme ,biology.protein ,Leukocyte Common Antigens ,lcsh:Q ,T-Box Domain Proteins ,Immunologic Memory ,030215 immunology - Abstract
The expression of CD45RA is generally associated with naive T cells. However, a subset of effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation with unknown molecular characteristics and functions. CD4 TEMRA cells have been implicated in protective immunity against pathogens such as dengue virus (DENV). Here we show that not only the frequency but also the phenotype of CD4 TEMRA cells are heterogeneous between individuals. These cells can be subdivided into two major subsets based on the expression of the adhesion G protein-coupled receptor GPR56, and GPR56+ TEMRA cells display a transcriptional and proteomic program with cytotoxic features that is distinct from effector memory T cells. Moreover, GPR56+ TEMRA cells have higher levels of clonal expansion and contain the majority of virus-specific TEMRA cells. Overall, this study reveals the heterogeneity of CD4 TEMRA cells and provides insights into T-cell responses against DENV and other viral pathogens., Memory T cells are essential for combating recurring infection by promoting prompt and effective immune responses. Here the authors show, via system biology approaches, that human CD4 memory T cells contains a CD45RA-rexpressing pool that can be further subsetted by the expression of GPR56 for distinct functionalities.
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- 2017
34. An Under-Recognized Influenza Epidemic Identified by Rapid Influenza Testing, Southern Sri Lanka, 2013
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Champica K Bodinayake, Ajith Nagahawatte, Christopher W. Woods, L. Gayani Tillekeratne, Dhammika Vidanagama, Aruna D. De Silva, Ruvini Kurukulasooriya, Megan E. Reller, Wasantha Kodikara Arachchi, Truls Østybe, and Vasantha Devasiri
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Adult ,Male ,Pediatrics ,medicine.medical_specialty ,Adolescent ,Fever ,Vomiting ,Cross-sectional study ,medicine.drug_class ,Antibiotics ,medicine.disease_cause ,Cohort Studies ,Young Adult ,Nasopharynx ,Surveys and Questionnaires ,Virology ,Influenza, Human ,Outpatients ,Prevalence ,Influenza A virus ,Humans ,Medicine ,Young adult ,Child ,Epidemics ,Sri Lanka ,Respiratory tract infections ,business.industry ,Infant ,virus diseases ,Articles ,Middle Aged ,Models, Theoretical ,Cross-Sectional Studies ,Infectious Diseases ,Cough ,Child, Preschool ,Female ,Parasitology ,Sri lanka ,medicine.symptom ,business ,Cohort study - Abstract
Influenza accounts for a large burden of acute respiratory tract infections in high-income countries; data from lower-income settings are limited due to lack of confirmatory testing. Consecutive outpatients presenting to the largest tertiary care hospital in southern Sri Lanka were surveyed for influenza-like illness (ILI), defined as acute onset of fever ≥ 38.0°C and cough. Patients were administered a questionnaire and nasal/nasopharyngeal sampling for rapid influenza A/B testing. We enrolled 311 patients with ILI from March to November 2013: 170 (54.7%) children and 172 (55.3%) males. Approximately half (147, 47.3%) tested positive for influenza, but 253 (81.4%) were prescribed antibiotics. On bivariable analysis, symptoms associated with influenza included pain with breathing (P < 0.001), headache (P = 0.005), fatigue (P = 0.003), arthralgias (P = 0.003), and myalgias (P = 0.006) in children and pain with breathing (P = 0.01), vomiting (P = 0.03), and arthralgias (P = 0.03) in adults. Our final clinical predictive models had low sensitivity and fair specificity—50.0% (95% CI: 38.6–61.4%) and 83.2% (95% CI: 73.4–90.0%), respectively, in children and 52.2% (95% CI: 39.9–64.2%) and 81.4% (95% CI: 70.0–89.4%), respectively, in adults. Our study confirms the ability of rapid influenza testing to identify an influenza epidemic in a setting in which testing is not routinely available.
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- 2015
35. Global Assessment of Dengue Virus-Specific CD4
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Alba, Grifoni, Michael A, Angelo, Benjamin, Lopez, Patrick H, O'Rourke, John, Sidney, Cristhiam, Cerpas, Angel, Balmaseda, Cassia G T, Silveira, Alvino, Maestri, Priscilla R, Costa, Anna P, Durbin, Sean A, Diehl, Elizabeth, Phillips, Simon, Mallal, Aruna D, De Silva, Godwin, Nchinda, Celine, Nkenfou, Matthew H, Collins, Aravinda M, de Silva, Mei Qiu, Lim, Paul A, Macary, Filippo, Tatullo, Tom, Solomon, Vijaya, Satchidanandam, Anita, Desai, Vasanthapram, Ravi, Josefina, Coloma, Lance, Turtle, Laura, Rivino, Esper G, Kallas, Bjoern, Peters, Eva, Harris, Alessandro, Sette, and Daniela, Weiskopf
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HLA ,epitope ,dengue virus ,viruses ,Immunology ,virus diseases ,adaptive immunity ,biochemical phenomena, metabolism, and nutrition ,CD4+ T cells ,Original Research - Abstract
Background Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4+ T cell responses, we mapped HLA-DRB1-restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua. Methods HLA class II epitopes in the population of Managua were identified by an in vitro IFNγ ELISPOT assay. CD4+ T cells purified by magnetic bead negative selection were stimulated with HLA-matched epitope pools in the presence of autologous antigen-presenting cells, followed by pool deconvolution to identify specific epitopes. The epitopes identified in this study were combined with those previously identified in the DENV endemic region of Sri Lanka, to generate a “megapool” (MP) consisting of 180 peptides specifically designed to achieve balanced HLA and DENV serotype coverage. The DENV CD4MP180 was validated by intracellular cytokine staining assays. Results We detected responses directed against a total of 431 epitopes, representing all 4 DENV serotypes, restricted by 15 different HLA-DRB1 alleles. The responses were associated with a similar pattern of protein immunodominance, overall higher magnitude of responses, as compared to what was observed previously in the Sri Lanka region. Based on these epitope mapping studies, we designed a DENV CD4 MP180 with higher and more consistent coverage, which allowed the detection of CD4+ T cell DENV responses ex vivo in various cohorts of DENV exposed donors worldwide, including donors from Nicaragua, Brazil, Singapore, Sri Lanka, and U.S. domestic flavivirus-naïve subjects immunized with Tetravalent Dengue Live-Attenuated Vaccine (TV005). This broad reactivity reflects that the 21 HLA-DRB1 alleles analyzed in this and previous studies account for more than 80% of alleles present with a phenotypic frequency ≥5% worldwide, corresponding to 92% phenotypic coverage of the general population (i.e., 92% of individuals express at least one of these alleles). Conclusion The DENV CD4 MP180 can be utilized to measure ex vivo responses to DENV irrespective of geographical location.
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- 2017
36. Prior Dengue Virus Exposure Shapes T Cell Immunity to Zika Virus in Humans
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Paulo Vieira Damasco, Guillermina Kuan, Bjoern Peters, Luzia Maria de-Oliveira-Pinto, Anna P. Durbin, Aravinda M. de Silva, James E. Crowe, Esper G. Kallas, Cristhiam Cerpas, John Pham, Simon Mallal, Sheridan Martini, Eva Harris, Julie E. Ledgerwood, Priscilla R. Costa, Josefina Coloma, Barney S. Graham, Diogo M. Magnani, Josephine Cox, Elizabeth J. Phillips, Sean A. Diehl, Alvino Maestri, Daniela Weiskopf, John Sidney, Patrick H. O'Rourke, Phillip J. Norris, Matthew H. Collins, Alessandro Sette, Aruna D. De Silva, Sinu Paul, Tom Solomon, Lance Turtle, Michael J. Ricciardi, Michael P. Busch, Héctor Vivanco-Cid, Angel Balmaseda, Alba Grifoni, Mars Stone, Elzinandes Leal de Azeredo, Cassia G. T. Silveira, David I. Watkins, and Dermody, Terence S
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0301 basic medicine ,Male ,cross-reactivity ,viruses ,T-Lymphocytes ,Epitopes, T-Lymphocyte ,Cellular Response to Infection ,Dengue virus ,medicine.disease_cause ,Medical and Health Sciences ,Epitope ,Dengue fever ,Zika virus ,Cohort Studies ,Epitopes ,Cytotoxic T cell ,2.1 Biological and endogenous factors ,Aetiology ,Child ,Vaccines ,biology ,Zika Virus Infection ,virus diseases ,Biological Sciences ,Middle Aged ,3. Good health ,medicine.anatomical_structure ,Infectious Diseases ,Child, Preschool ,Female ,Infection ,Biotechnology ,Adult ,Adolescent ,T cell ,Immunology ,T cells ,Dengue Vaccines ,Immunodominance ,Cross Reactions ,Vaccines, Attenuated ,Microbiology ,Vaccine Related ,03 medical and health sciences ,Young Adult ,heterologous immunity ,Biodefense ,Virology ,medicine ,Humans ,Preschool ,ZIKV ,Aged ,immunodominance ,DENV ,Agricultural and Veterinary Sciences ,Prevention ,Inflammatory and immune system ,Zika Virus ,biochemical phenomena, metabolism, and nutrition ,Dengue Virus ,medicine.disease ,biology.organism_classification ,Vector-Borne Diseases ,030104 developmental biology ,Attenuated ,Emerging Infectious Diseases ,Good Health and Well Being ,T-Lymphocyte ,Insect Science ,Immunization ,Memory T cell - Abstract
While progress has been made in characterizing humoral immunity to Zika virus (ZIKV) in humans, little is known regarding the corresponding T cell responses to ZIKV. Here, we investigate the kinetics and viral epitopes targeted by T cells responding to ZIKV and address the critical question of whether preexisting dengue virus (DENV) T cell immunity modulates these responses. We find that memory T cell responses elicited by prior infection with DENV or vaccination with tetravalent dengue attenuated vaccines (TDLAV) recognize ZIKV-derived peptides. This cross-reactivity is explained by the sequence similarity of the two viruses, as the ZIKV peptides recognized by DENV-elicited memory T cells are identical or highly conserved in DENV and ZIKV. DENV exposure prior to ZIKV infection also influences the timing and magnitude of the T cell response. ZIKV-reactive T cells in the acute phase of infection are detected earlier and in greater magnitude in DENV-immune patients. Conversely, the frequency of ZIKV-reactive T cells continues to rise in the convalescent phase in DENV-naive donors but declines in DENV-preexposed donors, compatible with more efficient control of ZIKV replication and/or clearance of ZIKV antigen. The quality of responses is also influenced by previous DENV exposure, and ZIKV-specific CD8 T cells from DENV-preexposed donors selectively upregulated granzyme B and PD1, unlike DENV-naive donors. Finally, we discovered that ZIKV structural proteins (E, prM, and C) are major targets of both the CD4 and CD8 T cell responses, whereas DENV T cell epitopes are found primarily in nonstructural proteins. IMPORTANCE The issue of potential ZIKV and DENV cross-reactivity and how preexisting DENV T cell immunity modulates Zika T cell responses is of great relevance, as the two viruses often cocirculate and Zika virus has been spreading in geographical regions where DENV is endemic or hyperendemic. Our data show that memory T cell responses elicited by prior infection with DENV recognize ZIKV-derived peptides and that DENV exposure prior to ZIKV infection influences the timing, magnitude, and quality of the T cell response. Additionally, we show that ZIKV-specific responses target different proteins than DENV-specific responses, pointing toward important implications for vaccine design against this global threat.
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- 2017
37. Host gene expression analysis in Sri Lankan melioidosis patients
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Aruna D. De Silva, Enoka Corea, Shivankari Krishnananthasivam, Mohan Natesan, Harindra D. Sathkumara, and Nimanthi Jayathilaka
- Subjects
0301 basic medicine ,Bacterial Diseases ,Melioidosis ,Gene Expression ,Disease ,Pathology and Laboratory Medicine ,Immune Receptors ,Biochemistry ,Antibiotics ,Genes, Regulator ,Medicine and Health Sciences ,Toll-like Receptors ,Immune Response ,Regulation of gene expression ,Immune System Proteins ,Antimicrobials ,lcsh:Public aspects of medicine ,Drugs ,Infectious Diseases ,Epigenetics ,Research Article ,Signal Transduction ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,030106 microbiology ,Immunology ,Biology ,Real-Time Polymerase Chain Reaction ,Microbiology ,Sepsis ,Diagnosis, Differential ,03 medical and health sciences ,Immune system ,Signs and Symptoms ,Diagnostic Medicine ,Microbial Control ,medicine ,Genetics ,Humans ,Immunologic Factors ,Gene Regulation ,Sri Lanka ,Pharmacology ,Burkholderia pseudomallei ,Gene Expression Profiling ,Public Health, Environmental and Occupational Health ,Biology and Life Sciences ,Proteins ,lcsh:RA1-1270 ,Cell Biology ,medicine.disease ,biology.organism_classification ,Gene expression profiling ,030104 developmental biology ,Infectious disease (medical specialty) ,Biomarkers - Abstract
Background Melioidosis is a life threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei predominantly found in southeast Asia and northern Australia. Studying the host transcription profiles in response to infection is crucial for understanding disease pathogenesis and correlates of disease severity, which may help improve therapeutic intervention and survival. The aim of this study was to analyze gene expression levels of human host factors in melioidosis patients and establish useful correlation with disease biomarkers, compared to healthy individuals and patients with sepsis caused by other pathogens. Methods The study population consisted of 30 melioidosis cases, 10 healthy controls and 10 sepsis cases caused by other pathogens. Total RNA was extracted from peripheral blood mononuclear cells (PBMC’s) of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by real time quantitative polymerase chain reaction (RT-qPCR). Principal findings Inflammatory response genes; TLR4, late onset inflammatory mediator HMGB1, genes associated with antigen presentation; MICB, PSMB2, PSMB8, PSME2, epigenetic regulators; DNMT3B, HDAC1, HDAC2 were significantly down regulated, whereas the anti-inflammatory gene; IL4 was up regulated in melioidosis patients compared to sepsis cases caused by other pathogens. Septicaemic melioidosis cases showed significant down regulation of IL8 compared to sepsis cases caused by other pathogens. HMGB1, MICB, PSMB8, PSMB2, PSME2, HDAC1, HDAC2 and DNMT3B showed consistent down regulation of gene expression in melioidosis patients compared to other sepsis infection, irrespective of comorbidities such as diabetes, duration of clinical symptoms and antibiotic treatment. Significance Specific immune response genes and epigenetic regulators are differentially expressed among melioidosis patients and patients with sepsis caused by other pathogens. Therefore, these genes may serve as biomarkers for disease diagnosis to distinguish melioidosis from cases of sepsis due to other infections and therapeutic intervention for melioidosis., Author summary Melioidosis is a life threatening infectious disease caused by a soil-associated gram-negative bacterium, B. pseudomallei. Melioidosis is endemic in southeast Asia and northern Australia; however, the global distribution of B. pseudomallei and the disease burden of melioidosis is still poorly understood. Melioidosis is severely under-reported in several tropical countries in which it is probably endemic and warrants a public health response. A recent research article predicts the global melioidosis burden to be 165 million cases with a predicted 73 million cases from the high risk zone of south Asia. Melioidosis is difficult to treat as B. pseudomallei is resistant to many antibiotics and requires a long course of treatment. Mortality rate remains high in endemic areas with reoccurrence being common. Therefore, it is imperative to diagnose the disease at an early stage and provide vital clinical care to reduce the mortality rate. With limitations in treatment and lack of a vaccine, it is crucial to study the immune response mechanisms to this infection to get a better understanding of disease pathogenesis and susceptibility. Therefore, this study aimed to analyze the gene expression levels of important immune response genes and epigenetic modifiers to establish useful correlation for diagnostic and therapeutic purposes.
- Published
- 2017
38. Gene Expression Profile of Human Cytokines in Response to Burkholderia pseudomallei Infection
- Author
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Aruna D. De Silva, Harindra D. Sathkumara, Enoka Corea, Mohan Natesan, and Shivankari Krishnananthasivam
- Subjects
0301 basic medicine ,Burkholderia pseudomallei ,Melioidosis ,lcsh:QR1-502 ,Disease ,host immune responses ,Biology ,Microbiology ,lcsh:Microbiology ,Sepsis ,Pathogenesis ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,gene expression profiling ,medicine ,Molecular Biology ,030208 emergency & critical care medicine ,medicine.disease ,biology.organism_classification ,QR1-502 ,030104 developmental biology ,Infectious disease (medical specialty) ,Immunology ,human host cytokine cascade ,Tumor necrosis factor alpha ,melioidosis - Abstract
Melioidosis is an underreported infectious disease, caused by the Gram-negative bacterium Burkholderia pseudomallei. Understanding the disease susceptibility and pathogenesis is crucial for developing newer diagnostic and therapeutic strategies for this life-threatening infection. In this study, we aimed to analyze the gene expression levels of important cytokines in melioidosis patients and establish useful correlates with disease biomarkers compared to cases of sepsis infection caused by other pathogens and healthy individuals. A Qiagen common human cytokines array profiling the gene expression of 84 important cytokines by real-time quantitative PCR (RT-qPCR) was used. We analyzed 26 melioidosis cases, 5 healthy controls, and 10 cases of sepsis infection caused by other pathogens. Our results showed consistently upregulated expression of interleukins (IL) interleukin-4 (IL-4), interleukin-17 alpha (IL-17A), IL-23A, and IL-24, interferons (IFN) interferon alpha 1 (IFNA1) and interferon beta 1 (IFNB1), tumor necrosis factor (TNF) superfamily 4 (TNFSF4), transforming growth factor (TGF) superfamily, bone morphogenetic proteins 3 and 6 (BMP3 and BMP6), transforming growth factor beta 1 (TGFB1), and other growth factors, including macrophage colony-stimulating factor (M-CSF), C-fos-induced growth factor (FIGF), and platelet-derived growth factor alpha (PDGFA) polypeptide, in melioidosis patients compared to their expression in other sepsis cases, irrespective of comorbidities, duration of fever/clinical symptoms, and antibiotic treatment. Our findings indicate a dominant Th2- and Th17-type-cytokine response, suggesting that their dysregulation at initial stages of infection may play an important role in disease pathogenesis. IL-1A, interleukin-1 beta (IL-1B), and IL-8 were significantly downregulated in septicemic melioidosis patients compared to their expression in other sepsis cases. These differentially expressed genes may serve as biomarkers for melioidosis diagnosis and targets for therapeutic intervention and may help us understand immune response mechanisms. IMPORTANCE Melioidosis is a life-threatening infectious disease caused by a soil-associated Gram-negative bacterium, B. pseudomallei. Melioidosis is endemic in Southeast Asia and northern Australia; however, the global distribution of B. pseudomallei and the disease burden of melioidosisis are still poorly understood. Melioidosis is difficult to treat, as B. pseudomallei is intrinsically resistant to many antibiotics and requires a long course of antibiotic treatment. The mortality rates remain high in areas of endemicity, with reoccurrence being common. Therefore, it is imperative to diagnose the disease at an early stage and provide vital clinical care to reduce the mortality rate. With limitations in treatment and lack of a vaccine, it is crucial to study the immune response mechanisms to this infection to get a better understanding of disease susceptibility and pathogenesis. Therefore, this study aimed to analyze the gene expression levels of important cytokines to establish useful correlations for diagnostic and therapeutic purposes.
- Published
- 2017
39. Human CD4 + T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity
- Author
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Beth D. Kirkpatrick, Patrick H. O'Rourke, Alba Grifoni, Aruna D. De Silva, Simon Mallal, Sean A. Diehl, Bjoern Peters, Stephen S. Whitehead, Sinu Paul, Anna P. Durbin, Michael A. Angelo, John Sidney, Daniela Weiskopf, Elizabeth J. Phillips, and Alessandro Sette
- Subjects
0301 basic medicine ,Attenuated vaccine ,T cell ,Immunology ,Dengue virus ,Biology ,medicine.disease_cause ,medicine.disease ,Microbiology ,Virology ,Dengue fever ,Vaccination ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Antigen ,Insect Science ,medicine ,030212 general & internal medicine ,CD8 ,Dengue vaccine - Abstract
Dengue virus (DENV) is responsible for growing numbers of infections worldwide and has proven to be a significant challenge for vaccine development. We previously demonstrated that CD8 + T cell responses elicited by a dengue live attenuated virus (DLAV) vaccine resemble those observed after natural infection. In this study, we screened peripheral blood mononuclear cells (PBMCs) from donors vaccinated with a tetravalent DLAV vaccine (TV005) with pools of dengue virus-derived predicted major histocompatibility complex (MHC) class II binding peptides. The definition of CD4 + T cell responses after live vaccination is important because CD4 + T cells are known contributors to host immunity, including cytokine production, help for CD8 + T and B cells, and direct cytotoxicity against infected cells. While responses to all antigens were observed, DENV-specific CD4 + T cells were focused predominantly on the capsid and nonstructural NS3 and NS5 antigens. Importantly, CD4 + T cell responses in vaccinees were similar in magnitude and breadth to those after natural infection, recognized the same antigen hierarchy, and had similar profiles of HLA restriction. We conclude that TV005 vaccination has the capacity to elicit CD4 + cell responses closely mirroring those observed in a population associated with natural immunity. IMPORTANCE The development of effective vaccination strategies against dengue virus infection is of high global public health interest. Here we study the CD4 T cell responses elicited by a tetravalent live attenuated dengue vaccine and show that they resemble responses seen in humans naturally exposed to dengue virus. This is an important issue, since it is likely that optimal immunity induced by a vaccine requires induction of CD4 + responses against the same antigens as those recognized as dominant in natural infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection against dengue virus.
- Published
- 2017
40. Global Assessment of Dengue Virus-Specific CD4+ T Cell Responses in Dengue-Endemic Areas
- Author
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Aravinda M. de Silva, Godwin Nchinda, Mei Qiu Lim, Elizabeth J. Phillips, Patrick H. O'Rourke, Esper G. Kallas, Simon Mallal, Aruna D. De Silva, Bjoern Peters, Alessandro Sette, Priscilla R. Costa, Cristhiam Cerpas, Josefina Coloma, Paul A. MacAry, Vasanthapram Ravi, Laura Rivino, Alvino Maestri, Lance Turtle, Sean A. Diehl, Benjamin Lopez, Anna P. Durbin, Alba Grifoni, Filippo Tatullo, Anita Desai, Eva Harris, Céline Nguefeu Nkenfou, Michael A. Angelo, Angel Balmaseda, John Sidney, Cassia G. T. Silveira, Tom Solomon, Vijaya Satchidanandam, Daniela Weiskopf, and Matthew H. Collins
- Subjects
0301 basic medicine ,lcsh:Immunologic diseases. Allergy ,viruses ,Immunology ,Population ,Immunodominance ,Human leukocyte antigen ,Dengue virus ,Biology ,medicine.disease_cause ,Epitope ,Dengue fever ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Immunology and Allergy ,ESTUDOS ANALÍTICOS ,education ,Microbiology & Cell Biology ,education.field_of_study ,epitope ,dengue virus ,ELISPOT ,virus diseases ,adaptive immunity ,biochemical phenomena, metabolism, and nutrition ,medicine.disease ,Virology ,CD4+ T cells ,3. Good health ,HLA ,030104 developmental biology ,Epitope mapping ,lcsh:RC581-607 ,030215 immunology - Abstract
Background: Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4+T cell responses, we mapped HLA-DRB1 restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua. Methods: HLA class II epitopes in the population of Managua were identified by an in vitro IFNγ ELISPOT assay. CD4+ T cells purified by magnetic bead negative selection were stimulated with HLA-matched epitope pools in the presence of autologous antigen presenting cells (APCs), followed by pool deconvolution to identify specific epitopes. The epitopes identified in this study were combined with those previously identified in the DENV endemic region of Sri Lanka, to generate a “megapool” (MP) consisting of 180 peptides specifically designed to achieve balanced HLA and DENV serotype coverage. The DENV CD4MP180 was validated by Intracellular Cytokine Staining (ICS) assays. Results: We detected responses directed against a total of 431 epitopes, representing all four DENV serotypes, restricted by 15 different HLA-DRB1 alleles. The responses were associated with a similar pattern of protein immunodominance, overall higher magnitude of responses, as compared to what was observed previously in the Sri Lanka region. Based on these epitope mapping studies, we designed a DENV CD4 MP180 with higher and more consistent coverage, which allowed the detection of CD4+ T cell DENV responses ex vivo in various cohorts of DENV exposed donors worldwide, including donors from Nicaragua, Brazil, Singapore, Sri Lanka and and U.S. domestic flavivirus-naive subjects immunized with Tetravalent Dengue Live Attenuated Vaccine (TV005). This broad reactivity reflects that the 21 HLA-DRB1 alleles analyzed in this and previous studies account for more than 80% of alleles present with a phenotypic frequency ≥ 5% worldwide, corresponding to 92% phenotypic coverage of the general population (i.e., 92% of individuals express at least one of these alleles). Conclusion: The DENV CD4 MP180 can be utilized to measure ex vivo responses to DENV irrespective of geographical location.
- Published
- 2017
41. Preexisting Neutralizing Antibody Responses Distinguish Clinically Inapparent and Apparent Dengue Virus Infections in a Sri Lankan Pediatric Cohort
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Kizzmekia S. Corbett, Aruna D. De Silva, Leah C. Katzelnick, Ananda Amerasinghe, Aravinda M. de Silva, and Hasitha Tissera
- Subjects
Male ,Serotype ,viruses ,Dengue virus ,Antibodies, Viral ,medicine.disease_cause ,Dengue fever ,Dengue ,Major Articles and Brief Reports ,Immune system ,Recurrence ,Seroepidemiologic Studies ,medicine ,Humans ,Immunology and Allergy ,Prospective Studies ,Child ,Neutralizing antibody ,Sri Lanka ,biology ,Infant ,virus diseases ,Dengue Virus ,biochemical phenomena, metabolism, and nutrition ,medicine.disease ,Antibodies, Neutralizing ,Virology ,Infectious Diseases ,Child, Preschool ,Cohort ,Immunology ,biology.protein ,Female ,Antibody - Abstract
Dengue viruses (DENVs) are mosquito-borne flaviviruses that infect humans. The clinical presentation of DENV infection ranges from inapparent infection to dengue hemorrhagic fever and dengue shock syndrome. We analyzed samples from a pediatric dengue cohort study in Sri Lanka to explore whether antibody responses differentiated clinically apparent infections from clinically inapparent infections. In DENV-naive individuals exposed to primary DENV infections, we observed no difference in the quantity or quality of acquired antibodies between inapparent and apparent infections. Children who experienced primary infections had broad, serotype–cross-neutralizing antibody responses that narrowed in breadth to a single serotype over a 12-month period after infection. In DENV immune children who were experiencing a repeat infection, we observed a strong association between preexisting neutralizing antibodies and clinical outcome. Notably, children with preexisting monospecific neutralizing antibody responses were more likely to develop fever than children with cross-neutralizing responses. Preexisting DENV neutralizing antibodies are correlated with protection from dengue disease.
- Published
- 2014
42. Calprotectin as a Biomarker for Melioidosis Disease Progression and Management
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Robert G. Ulrich, Mohan Natesan, Aruna D. De Silva, Enoka Corea, Harindra D. Sathkumara, Shivankari Krishnananthasivam, Kei Amemiya, Jennifer L. Dankmeyer, and Beverly Dyas
- Subjects
0301 basic medicine ,Microbiology (medical) ,Adult ,Male ,Serum ,medicine.medical_specialty ,Melioidosis ,Adolescent ,medicine.drug_class ,030106 microbiology ,Antibiotics ,Disease ,Gastroenterology ,Sepsis ,Cohort Studies ,03 medical and health sciences ,Young Adult ,fluids and secretions ,Pregnancy ,Internal medicine ,medicine ,Humans ,Aged ,biology ,business.industry ,Burkholderia pseudomallei ,Tropical disease ,Bacteriology ,Middle Aged ,medicine.disease ,biology.organism_classification ,Anti-Bacterial Agents ,C-Reactive Protein ,Disease Progression ,Biomarker (medicine) ,Administration, Intravenous ,Female ,Calprotectin ,Drug Monitoring ,business ,Leukocyte L1 Antigen Complex ,Biomarkers - Abstract
Melioidosis is a neglected tropical disease that is caused by the bacterium Burkholderia pseudomallei and is underreported in many countries where the disease is endemic. A long and costly administration of antibiotics is needed to clear infections, and there is an unmet need for biomarkers to guide antibiotic treatment and increase the number of patients that complete therapy. We identified calprotectin as a lead biomarker of B. pseudomallei infections and examined correlations between this serum protein and the antibiotic treatment outcomes of patients with melioidosis. Serum levels of calprotectin and C-reactive protein were significantly higher in patients with melioidosis and nonmelioidosis sepsis than in healthy controls. Median calprotectin levels were higher in patients with melioidosis than in those with nonmelioidosis sepsis, whereas C-reactive protein levels were similar in both groups. Notably, intensive intravenous antibiotic treatment of patients with melioidosis resulted in lower levels of calprotectin and C-reactive protein ( P < 0.0001), coinciding with recovery. The median percent reduction of calprotectin and C-reactive protein was 71% for both biomarkers after antibacterial therapy. In contrast, we found no significant differences in calreticulin levels between the two melioidosis treatment phases. Thus, reductions in serum calprotectin levels were linked to therapeutic responses to antibiotics. Our results suggest that calprotectin may be a sensitive indicator of melioidosis disease activity and illustrate the potential utility of this biomarker in guiding the duration of antibiotic therapy.
- Published
- 2016
43. CD4 T cell transcriptomics reveal novel diagnostic and mechanistic immune signatures of tuberculosis
- Author
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Julie G Burel, Cecilia S Lindestam Arlehamn, Mikhail Pomaznoy, Gregory Seumois, Jason A Greenbaum, Dhammika Vidanagama, Bandu Gunasena, Rashmi Tippalagama, Aruna D de Silva, Randy Taplitz, Pandurangan Vijayanand, Alessandro Sette, and Bjoern Peters
- Subjects
Immunology ,Immunology and Allergy - Abstract
As part of the Human Immune Project Consortium (HIPC) program, we are aiming to decipher CD4 T cell immune signatures of tuberculosis (TB) in the context of controlled (latent TB) and uncontrolled (active TB) infection. We found commonalities and differences in TB-specific CD4 T cell immune responses of latent TB vs active TB subjects. Both cohorts had higher frequency of peptide-reactive CD4 T cells compared to TB uninfected individuals, and showed strong upregulation of type I and type II interferon genes in response to antigen-specific in vitro stimulation. Conversely, we also detected differences in the transcriptome of CD4 T cells between latent vs active TB subjects that can inform us on TB-specific T cell immune signatures of controlled infection versus disease. In particular, active TB was associated with higher expression of genes associated with inflammation (TNF, IL-1 and TLR signaling) whereas latent TB was enriched for genes associated with metabolism, oxidative phosphorylation and neutrophil-mediated immunity. Looking at inter-individual variability, we also identified that some latent TB infected subjects showed similar expression patterns for a subset of genes to those with active TB, suggesting this molecular pattern might contain mechanistic and prognostic information on the risk of developing active TB. Overall, our approach has identified a plethora of TB-associated T cell immune signatures that allowed us to gain mechanistic insights into the key CD4 T cell components contributing to TB protective immunity. Additionally, our findings have the potential to be translated into new diagnostic and prognostic tools, in particular, identifying latent TB infected individuals at risk of developing active TB.
- Published
- 2019
44. Molecular Signatures of IL-10/IFN-γ Co-Producing CD4 T Cells During Acute Dengue Virus Infection
- Author
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Yuan Tian, Gregory Seumois, Sara Herrera de la Mata, Suraj Goonawardhana, Aruna D de Silva, Sunil Premawansa, Gayani Premawansa, Ananda Wijewickrama, Alba Grifoni, Pandurangan Vijayanand, Bjoern Peters, Daniela Weiskopf, and Alessandro Sette
- Subjects
Immunology ,Immunology and Allergy - Abstract
Dengue virus (DENV) is an emerging pathogen and a serious public health issue. It is estimated that ~390 million people are infected yearly. DENV infection is associated with a range of clinical manifestations, from asymptomatic to more severe presentations including dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). There is currently no specific therapy available for the treatment of dengue diseases other than supportive care. Thus, a better understanding of the host’s immune response against DENV, especially during the acute phase of infection, is of great public health interests. Although previous studies suggest that increased IL-10 level in the serum and plasma is associated with severe dengue disease, whether dengue-specific CD4 T cells produce IL-10 remains unknown. Here we show evidence of DENV-specific IL-10-producing CD4 T cells during acute DENV infection. Surprisingly, an IL-10+IFN-γ+ double positive (DP) CD4 T cell population is prominent in acute hospitalized DENV cases but disappear at the convalescent stage. These cells are not conventional regulatory T (Treg) cells as they lack Foxp3 expression. In contrast, RNA-sequencing and high-dimensional CyTOF analyses reveal that these cells partially exhibit previously identified signatures associated with cytotoxic CD4 T cells and type 1 regulatory T (Tr1) cells. Notably, we identified several novel signatures of DP cells including IL-19, IL-21, and IL-22, suggesting that these cells may have complex cytokine activities and functions. Overall, this study reveals unique phenotypes of DENV-specific IL-10/IFN-γ co-producing CD4 cells and provides insights into antigen-specific T cell responses during acute DENV infection.
- Published
- 2019
45. Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2Δ30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain
- Author
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Simon Mallal, John Sidney, Jonathan E. Boyson, Jason Botten, Beth D. Kirkpatrick, Bjoern Peters, Stephen S. Whitehead, Sinu Paul, Anna P. Durbin, Michael A. Angelo, Alessandro Sette, Sean A. Diehl, Alba Grifoni, Aruna D. De Silva, Elizabeth J. Phillips, and Daniela Weiskopf
- Subjects
0301 basic medicine ,CD4-Positive T-Lymphocytes ,Cellular immunity ,Enzyme-Linked Immunospot Assay ,viruses ,Immunology ,Immunodominance ,Dengue virus ,Biology ,CD8-Positive T-Lymphocytes ,medicine.disease_cause ,Microbiology ,Virus ,Dengue fever ,Dengue ,03 medical and health sciences ,Epitopes ,Interferon-gamma ,0302 clinical medicine ,Immune system ,Virology ,Vaccines and Antiviral Agents ,medicine ,Humans ,030212 general & internal medicine ,Neutralizing antibody ,3' Untranslated Regions ,Antigens, Viral ,Dengue vaccine ,Sequence Deletion ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,Dengue Virus ,medicine.disease ,030104 developmental biology ,Insect Science ,biology.protein - Abstract
A deletion variant of the dengue virus (DENV) serotype 2 (DENV2) Tonga/74 strain lacking 30 nucleotides from its 3′ untranslated region (rDEN2Δ30) has previously been established for use in a controlled human DENV challenge model. To evaluate if this model is appropriate for the derivation of correlates of protection for DENV vaccines on the basis of cellular immunity, we wanted to compare the cellular immune response to this challenge strain to the response induced by natural infection. To achieve this, we predicted HLA class I- and class II-restricted peptides from rDEN2Δ30 and used them in a gamma interferon enzyme-linked immunosorbent spot assay to interrogate CD8 + and CD4 + T cell responses in healthy volunteers infected with rDEN2Δ30. At the level of CD8 responses, vigorous ex vivo responses were detected in approximately 80% of donors. These responses were similar in terms of the magnitude and the numbers of epitopes recognized to the responses previously observed in peripheral blood mononuclear cells from donors from regions where DENV is hyperendemic. The similarity extended to the immunodominance hierarchy of the DENV nonstructural proteins, with NS3, NS5, and NS1 being dominant in both donor cohorts. At the CD4 level, the responses to rDEN2Δ30 vaccination were less vigorous than those to natural DENV infection and were more focused on nonstructural proteins. The epitopes recognized following rDEN2Δ30 infection and natural infection were largely overlapping for both the CD8 (100%) and CD4 (85%) responses. Finally, rDEN2Δ30 induced stronger CD8 responses than other, more attenuated DENV isolates. IMPORTANCE The lack of a known correlate of protection and the failure of a neutralizing antibody to correlate with protection against dengue virus have highlighted the need for a human DENV challenge model to better evaluate the candidate live attenuated dengue vaccines. In this study, we sought to characterize the immune profiles of rDEN2Δ30-infected subjects and to compare the profiles with those for subjects from areas where DENV is hyperendemic. Our data demonstrate that T cell responses to rDENV2Δ30 are largely similar to those to natural infection in terms of specificity, highlighting that the response to this virus in humans is appropriate as a model for the T cell response to primary DENV2 infection.
- Published
- 2016
46. Human CD4
- Author
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Michael A, Angelo, Alba, Grifoni, Patrick H, O'Rourke, John, Sidney, Sinu, Paul, Bjoern, Peters, Aruna D, de Silva, Elizabeth, Phillips, Simon, Mallal, Sean A, Diehl, Beth D, Kirkpatrick, Stephen S, Whitehead, Anna P, Durbin, Alessandro, Sette, and Daniela, Weiskopf
- Subjects
Adult ,CD4-Positive T-Lymphocytes ,Male ,Adolescent ,viruses ,Vaccination ,Dengue Vaccines ,Dengue Virus ,Middle Aged ,Antibodies, Viral ,Vaccines, Attenuated ,Dengue ,Viral Proteins ,Young Adult ,Antibody Specificity ,HLA Antigens ,Vaccines and Antiviral Agents ,Humans ,Female ,Cells, Cultured - Abstract
Dengue virus (DENV) is responsible for growing numbers of infections worldwide and has proven to be a significant challenge for vaccine development. We previously demonstrated that CD8+ T cell responses elicited by a dengue live attenuated virus (DLAV) vaccine resemble those observed after natural infection. In this study, we screened peripheral blood mononuclear cells (PBMCs) from donors vaccinated with a tetravalent DLAV vaccine (TV005) with pools of dengue virus-derived predicted major histocompatibility complex (MHC) class II binding peptides. The definition of CD4+ T cell responses after live vaccination is important because CD4+ T cells are known contributors to host immunity, including cytokine production, help for CD8+ T and B cells, and direct cytotoxicity against infected cells. While responses to all antigens were observed, DENV-specific CD4+ T cells were focused predominantly on the capsid and nonstructural NS3 and NS5 antigens. Importantly, CD4+ T cell responses in vaccinees were similar in magnitude and breadth to those after natural infection, recognized the same antigen hierarchy, and had similar profiles of HLA restriction. We conclude that TV005 vaccination has the capacity to elicit CD4+ cell responses closely mirroring those observed in a population associated with natural immunity.
- Published
- 2016
47. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus–Specific CD4+ T-Cell Responses
- Author
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John Sidney, Simon Mallal, Patrick H. O'Rourke, Aruna D. De Silva, Bjoern Peters, Alessandro Sette, Gayani Premawansa, Daniela Weiskopf, Elizabeth J. Phillips, Sinu Paul, Sunil Premawansa, Michael A. Angelo, Ananda Wijewickrama, and Alba Grifoni
- Subjects
0301 basic medicine ,Adult ,CD4-Positive T-Lymphocytes ,viruses ,Epitopes, T-Lymphocyte ,Human leukocyte antigen ,Disease ,Dengue virus ,Biology ,medicine.disease_cause ,Epitope ,Dengue fever ,Dengue ,03 medical and health sciences ,Major Articles and Brief Reports ,0302 clinical medicine ,medicine ,Immunology and Allergy ,Humans ,Allele ,HLA-DRB1 ,NS3 ,Dengue Virus ,medicine.disease ,Virology ,030104 developmental biology ,Infectious Diseases ,Immunology ,030215 immunology ,HLA-DRB1 Chains - Abstract
Background. Each year dengue virus (DENV) infects 400 million human but causes symptomatic disease in only a subset of patients, suggesting that host genetic factors may play a role. HLA molecules that restrict T-cell responses are one of the most polymorphic host factors in humans. Methods. Here we map HLA DRB1–restricted DENV-specific epitopes in individuals previously exposed to DENV, to identify the breadth and specificity of CD4+ T-cell responses. To investigate whether HLA-specific variations in the magnitude of response might predict associations between dengue outcomes and HLA-DRB1 alleles, we assembled samples from hospitalized patients with known severity of disease. Results. The capsid protein followed by nonstructural protein 3 (NS3), NS2A, and NS5 were the most targeted proteins. We further noticed a wide variation in magnitude of T-cell responses as a function of the restricting DRB1 allele and found several HLA alleles that showed trends toward a lower risk of hospitalized disease were associated with a higher magnitude of T-cell responses. Conclusions. Comprehensive identification of unique CD4+ T-cell epitopes across the 4 DENV serotypes allows the testing of T-cell responses by use of a simple, approachable technique and points to important implications for vaccine design.
- Published
- 2016
48. Extended-spectrum ß-Lactamase-producing Enterobacteriaceae as a Common Cause of Urinary Tract Infections in Sri Lanka
- Author
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Champica K Bodinayake, L. Gayani Tillekeratne, Ajith Nagahawatte, Bradly P. Nicholson, Maria Joyce, Christopher W. Woods, Aruna D. De Silva, Rashmi Tippalagama, Dhammika Vidanagama, and Rashmi Lewkebandara
- Subjects
0301 basic medicine ,Klebsiella pneumoniae ,030106 microbiology ,Urine ,medicine.disease_cause ,Microbiology ,law.invention ,Extended-spectrum ß-lactamases ,03 medical and health sciences ,Enterobacteriaceae ,law ,medicine ,polycyclic compounds ,Pharmacology (medical) ,Escherichia coli ,Polymerase chain reaction ,Sri Lanka ,Molecular epidemiology ,biology ,business.industry ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,bacterial infections and mycoses ,3. Good health ,Infectious Diseases ,Amikacin ,bacteria ,Original Article ,business ,Enterobacter cloacae ,medicine.drug ,Community-acquired urinary tract infections - Abstract
BACKGROUND Extended-spectrum s-lactamase-producing Enterobacteriaceae (ESBL-PE) are increasingly reported as pathogens in urinary tract infections (UTIs). However, in Sri Lanka, the clinical and molecular epidemiology of ESBL-PE implicated in UTIs has not been well described. MATERIALS AND METHODS We conducted prospective, laboratory-based surveillance from October to December 2013 at a tertiary care hospital in southern Sri Lanka and enrolled patients ≥1 year of age with clinically relevant UTIs due to ESBL-PE. Isolate identity, antimicrobial drug susceptibility, and ESBL production were determined. Presence of s-lactamase genes, bla(SHV), bla(TEM), and bla(CTX-M), was identified by polymerase chain reaction. RESULTS During the study period, Enterobacteriaceae were detected in 184 urine samples, with 74 (40.2%) being ESBL producers. Among 47 patients with ESBL-PE who had medical records available, 38 (80.9%) had clinically significant UTIs. Most UTIs (63.2%) were community acquired and 34.2% were in patients with diabetes. Among 36 cultured ESBL-PE isolates, significant susceptibility (>80%) was only retained to amikacin and the carbapenems. The group 1 bla(CTX-M) gene was present in 90.0% of Escherichia coli isolates and all Klebsiella pneumoniae and Enterobacter cloacae isolates. The bla(SHV) and bla(TEM) genes were more common in K. pneumoniae (75% and 50%) and E. cloacae (50% and 50%) isolates than in E. coli (10% and 20%) isolates, respectively. CONCLUSION The majority of UTIs caused by ESBL-PE were acquired in the community and due to organisms carrying the group 1 CTX-M s-lactamase. Further epidemiologic studies of infections due to ESBL-PE are urgently needed to better prevent and treat these infections in South Asia.
- Published
- 2016
49. Use of Rapid Influenza Testing to Reduce Antibiotic Prescriptions among Outpatients with Influenza-Like Illness in Southern Sri Lanka
- Author
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L. Gayani Tillekeratne, Champica K Bodinayake, Aruna D. De Silva, Ajith Nagahawatte, Christopher W. Woods, Wasantha Kodikara Arachchi, Ruvini Kurukulasooriya, Truls Østbye, Megan E. Reller, Dhammika Vidanagama, and Vasantha Devasiri
- Subjects
Adult ,Male ,Pediatrics ,medicine.medical_specialty ,Time Factors ,Adolescent ,Fever ,medicine.drug_class ,Antibiotics ,Physical examination ,Inappropriate Prescribing ,Cohort Studies ,Young Adult ,Virology ,Internal medicine ,Influenza, Human ,Outpatients ,medicine ,Humans ,Prospective Studies ,Medical prescription ,Practice Patterns, Physicians' ,Prospective cohort study ,Child ,Respiratory Tract Infections ,Sri Lanka ,Influenza-like illness ,Respiratory tract infections ,medicine.diagnostic_test ,business.industry ,Influenza a ,Articles ,Anti-Bacterial Agents ,Infectious Diseases ,Cough ,Child, Preschool ,Parasitology ,Female ,Sri lanka ,business - Abstract
Acute respiratory tract infections (ARTIs) are a common reason for unnecessary antibiotic prescriptions worldwide. Our objective was to determine if providing access to rapid influenza test results could reduce antibiotic prescriptions for ARTIs in a resource-limited setting. We conducted a prospective, pre-post study from March 2013 to October 2014. Outpatients presenting to a hospital in Sri Lanka were surveyed for influenza-like illness-onset of fever ≥ 38.0°C and cough in prior 7 days. Enrolled patients were administered a structured questionnaire, physical examination, and nasal/nasopharyngeal sampling for rapid influenza A/B testing. Influenza test results were released only during phase 2 (January-October 2014). We enrolled 571 patients with ILI-316 in phase 1 and 241 in phase 2. The proportion positive for influenza was 46.5% in phase 1 and 28.6% in phase 2, P < 0.001. Between phases, antibiotic prescriptions decreased from 81.3% to 69.3% (P = 0.001) among all patients and from 83.7% to 62.3% (P = 0.001) among influenza-positive patients. On multivariable analysis, a positive influenza result during phase 2 was associated with lower odds of antibiotic prescriptions (OR = 0.50, 95% CI = 0.26-0.95). This prospective study suggests that providing access to rapid influenza testing may reduce unnecessary antibiotic prescriptions in resource-limited settings.
- Published
- 2015
50. Insights into HLA-Restricted T Cell Responses in a Novel Mouse Model of Dengue Virus Infection Point toward New Implications for Vaccine Design
- Author
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Aruna D. De Silva, Ravi Kolla, Michael A. Angelo, Lauren E. Yauch, Aravinda M. de Silva, Jason A. Greenbaum, Alessandro Sette, John Sidney, Bjoern Peters, Daniela Weiskopf, Howard M. Grey, Daisy V. John, and Sujan Shresta
- Subjects
T-Lymphocytes ,viruses ,T cell ,Immunology ,Epitopes, T-Lymphocyte ,Dengue Vaccines ,Mice, Transgenic ,Human leukocyte antigen ,Dengue virus ,Biology ,medicine.disease_cause ,Article ,Epitope ,Mice ,Histocompatibility Antigens ,medicine ,Animals ,Humans ,Immunology and Allergy ,Dengue vaccine ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,Virology ,Histocompatibility ,HLA-A ,Mice, Inbred C57BL ,Disease Models, Animal ,Epitope mapping ,medicine.anatomical_structure ,Epitope Mapping - Abstract
The frequency of dengue virus (DENV) infection has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. To date, a convenient murine system to study human T cell responses to DENV has not been available. Mice transgenic for HLA are widely used to model human immune responses, and it has been shown that mouse-passaged DENV is able to replicate to significant levels in IFN-α/βR−/− mice. To cover a wide range of HLA phenotypes, we backcrossed IFN-α/βR−/− mice with HLA A*0201, A*0101, A*1101, B*0702, and DRB1*0101-transgenic mice. A DENV proteome-wide screen identified a total of 42 epitopes across all HLA-transgenic IFN-α/βR−/− strains tested. In contrast, only eight of these elicited responses in the corresponding IFN-α/βR+/+ mice. We were able to identify T cell epitopes from 9 out of the 10 DENV proteins. However, the majority of responses were derived from the highly conserved nonstructural proteins NS3 and NS5. The relevance of this model is further demonstrated by the fact that most of the epitopes identified in our murine system are also recognized by PBMC from DENV-exposed human donors, and a dominance of HLA B*0702-restricted responses has been detected in both systems. Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design.
- Published
- 2011
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