Dengue type 1 viruses circulating in humans are highly infectious and poorly neutralized by human antibodies.

The four dengue virus (DENV) serotypes are mosquito-borne flaviviruses of humans. The interactions between DENVs and the human host that lead to asymptomatic, mild, or severe disease are poorly understood, in part, because laboratory models are poor surrogates for human DENV disease. Virologists are interested in how the properties of DENVs replicating in people compare with virions propagated on laboratory cell lines, which are widely used for research and vaccine development. Using clinical samples from a DENV type 1 epidemic in Sri Lanka and new ultrasensitive assays, we compared the properties of DENVs in human plasma and after one passage on laboratory cell lines. DENVs in plasma were 50- to 700-fold more infectious than cell culture-grown viruses. DENVs produced by laboratory cell lines were structurally immature and hypersensitive to neutralization by human antibodies compared with DENVs circulating in people. Human plasma and cell culture-derived virions had identical genome sequences, indicating that these phenotypic differences were due to the mature state of plasma virions. Several dengue vaccines are under development. Recent studies indicate that vaccine-induced antibodies that neutralized DENVs in cell culture assays were not sufficient for protecting people from DENV infections. Our results about structural differences between DENVs produced in humans versus cell lines may be key to understanding vaccine failure and developing better models for vaccine evaluation.

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.

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.

A case report of co-infection of Melioidosis and cutaneous Leishmaniasis.

BACKGROUND: Leishmaniasis and melioidosis are frequently reported from the North Central Province of Sri Lanka. However, only one case of co-infection of the two diseases has been reported to date over the world. This is a case report of a patient who had co-infection with cutaneous leishmaniasis and melioidosis and was successfully treated and recovered from the illness. CASE PRESENTATION: A 61 year old female patient with diabetes mellitus presented with fever for one month's duration and was found to have hepatosplenomegaly and an ulcer over the left arm. She had elevated inflammatory markers and blood culture grew Burkholderia pseudomallei and serum was highly positive for melioidosis antibodies. A slit skin smear of the ulcer showed Leishmania amastigotes. CONCLUSION: Melioidosis and leishmaniasis are emerging infectious diseases in endemic countries and can be severe. The high prevalence rates in Sri Lanka should keep the treating physicians' threshold for suspicion low for these two diseases.

HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses.

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.

EVALUATION OF A COMMERCIAL RAPID TEST KIT FOR DETECTION OF ACUTE DENGUE INFECTION.

Early diagnosis is important for clinical management of dengue disease. While classic laboratory tests are often tedious and time consuming, point of care devices offer a rapid, cost-effective and user-friendly alternative provided their accuracy is acceptable. This study evaluated the sensitivity, specificity and efficiency of SD BIOLINE Dengue Duo® rapid NS1, IgM and IgG test kit for diagnosis of acute dengue virus infection. Standard laboratory diagnostics, RT-PCR, IgM and IgG capture ELISAs were carried out on 143 suspected dengue patient samples obtained from a Sri Lankan population. Using the results of these standard laboratory tests as reference, the sensitivity and specificity of the SD Dengue Duo® NS1 test was 57% and 87%, respectively, and those of the IgM test was 50% and 84%, respectively. The combined sensitivity and specificity of the SD Dengue Duo® NS1/ IgM test was 72% and 80%, respectively. The SD Dengue Duo® NS1 test detected NS1 for up to 9 days from onset of fever. Primary and secondary dengue cases were classified according to the IgG test, of which the kit identified 88% and 26% of primary and of secondary infection, respectively. Although the SD Dengue Duo® kit was not as accurate as the standard tests, it still can serve the useful reference for initial screening of suspected dengue cases, especially in poor resource hospital settings and aid in clinical disease management of dengue infection.

Identifying the strains of dengue circulating in the western province of Sri Lanka during 2019-2022.

A study conducted from July 2019 to May 2022 at several hospitals in the Western Province, Sri Lanka, focused on dengue virus strains during the COVID-19 pandemic. Among 417 febrile patients, 47% were PCR-positive for dengue. Serotyping revealed DENV-1 (12.8%), DENV-2 (46.4%), DENV-3 (37.2%), and DENV-4 (3.6%). Sequencing identified two genotypically distinct variants of DENV-3 and two genotypically distinct variants of DENV-1, while DENV-2 showed a single genotype cluster. Notably, the study found concurrent circulation of two DENV-3 and two DENV-1 genotypes, along with DENV-2, during the pandemic in the area. This data suggests the presence of multiple dengue strains, including several DENV-1 and DENV-3 variants, without major epidemic outbreaks reported in the Western Province. Continuous monitoring and research are essential to understand the dynamics of these dengue strains in the context of the COVID-19 pandemic.

Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka.

Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

Mild venom-induced consumption coagulopathy associated with thrombotic microangiopathy following a juvenile Russell's viper (Daboia russelii) envenoming: A case report.

Russell's viper envenoming causes venom-induced consumption coagulopathy (VICC) within hours of a bite, which is associated with thrombotic microangiopathy (TMA) and acute kidney injury (AKI) in a proportion of cases. We report a juvenile Russell's viper bite in which a patient developed mild VICC after the usual 24-h observation period, which was subsequently associated with severe AKI due to TMA. This shows the clinical importance of detecting and treating mild VICC, which may be delayed or not detected with bedside clotting tests.

First Complete Cytochrome B Sequences and Molecular Taxonomy of Bat Species from Sri Lanka.

This is the first report on the molecular identification and phylogeny of the Rousettus leschenaultii Desmarest, 1810, Rhinolophus rouxii Temminck, 1835, Hipposideros speoris Schneider, 1800, Hipposideros lankadiva Kelaart, 1850, and Miniopterus fuliginosus Kuhl, 1817, bat species in Sri Lanka, inferred from analyses by mitochondrially encoded cytochrome b gene sequences. Recent research has indicated that bats show enormous cryptic genetic diversity. Moreover, even within the same species, the acoustic properties of echolocation calls and morphological features such as fur color could vary in different populations. Therefore, we have used molecular taxonomy for the accurate identification of five bat species recorded in one of the largest cave populations in Sri Lanka. The bats were caught using a hand net, and saliva samples were collected non-invasively from each bat by using a sterile oral swab. Nucleic acids were extracted from the oral swab samples, and mitochondrial DNA was amplified by using primers targeting the mitochondrially encoded cytochrome b gene. This study reports the first molecular evidence for the identification of five bat species in Sri Lanka. Our findings will contribute to future conservation and systematic studies of bats in Sri Lanka. This study will also provide the basis for a genetic database of Sri Lankan bats which will contribute significantly to the investigation of potentially zoonotic bat viruses.

Paramyxovirus Diversity within One Population of Miniopterus fuliginosus Bats in Sri Lanka.

Bats are known as typical reservoirs for a number of viruses, including viruses of the family Paramyxoviridae. Representatives of the subfamily Orthoparamyxovirinae are distributed worldwide and can cause mild to fatal diseases when infecting humans. The research on Paramyxoviruses (PMVs) from different bat hosts all over the world aims to understand the diversity, evolution and distribution of these viruses and to assess their zoonotic potential. A high number of yet unclassified PMVs from bats are recorded. In our study, we investigated bat species from the families Rhinolophidae, Hipposiderae, Pteropodidae and Miniopteridae that are roosting sympatrically in the Wavul Galge cave (Koslanda, Sri Lanka). The sampling at three time points (March and July 2018; January 2019) and screening for PMVs with a generic PCR show the presence of different novel PMVs in 10 urine samples collected from Miniopterus fuliginosus. Sequence analysis revealed a high similarity of the novel strains among each other and to other unclassified PMVs collected from Miniopterus bats. In this study, we present the first detection of PMVs in Sri Lanka and the presence of PMVs in the bat species M. fuliginosus for the first time.

A Population of CD4+CD8+ Double-Positive T Cells Associated with Risk of Plasma Leakage in Dengue Viral Infection.

According to the WHO 2009 classification, dengue with warning signs is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which can be a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4+CD8+ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4+CD8+ DP cells were distinct from CD4+ Single Positive (SP) T cells but co-clustered with CD8+ SP cells, indicating a largely similar transcriptional profile. Twenty significant differentially expressed (DE) genes were identified between CD4+CD8+ DP and CD8+ SP cells. These genes encode OX40 and CCR4 proteins as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, and PTPRK). While comparing the profile of gene expression in CD4+CD8+ DP cells from patients with and without warning signs of plasma leakage, similar expression profile was observed, implying a role of CD4+CD8+ DP cells in plasma leakage through a quantitative increase rather than functional alteration. This study provided novel insight into the host immune response during the acute febrile phase of DENV infection and the role of CD4+CD8+ DP T cells in the pathogenesis of plasma leakage.

Full Genome of batCoV/MinFul/2018/SriLanka, a Novel Alpha-Coronavirus Detected in Miniopterus fuliginosus, Sri Lanka.

Coronaviruses (CoV) are divided into the genera α-CoVs, ß-CoVs, γ-CoVs and δ-CoVs. Of these, α-CoVs and ß-CoVs are solely capable of causing infections in humans, resulting in mild to severe respiratory symptoms. Bats have been identified as natural reservoir hosts for CoVs belonging to these two genera. Consequently, research on bat populations, CoV prevalence in bats and genetic characterization of bat CoVs is of special interest to investigate the potential transmission risks. We present the genome sequence of a novel α-CoV strain detected in rectal swab samples of Miniopterus fuliginosus bats from a colony in the Wavul Galge cave (Koslanda, Sri Lanka). The novel strain is highly similar to Miniopterus bat coronavirus 1, an α-CoV located in the subgenus of Minunacoviruses. Phylogenetic reconstruction revealed a high identity of the novel strain to other α-CoVs derived from Miniopterus bats, while human-pathogenic α-CoV strains like HCoV-229E and HCoV-NL63 were more distantly related. Comparison with selected bat-related and human-pathogenic strains of the ß-CoV genus showed low identities of ~40%. Analyses of the different genes on nucleotide and amino acid level revealed that the non-structural ORF1a/1b are more conserved among α-CoVs and ß-CoVs, while there are higher variations in the structural proteins known to be important for host specificity. The novel strain was named batCoV/MinFul/2018/SriLanka and had a prevalence of 50% (66/130) in rectal swab samples and 58% (61/104) in feces samples that were collected from Miniopterus bats in Wavul Galge cave. Based on the differences between strain batCoV/MinFul/2018/SriLanka and human-pathogenic α-CoVs and ß-CoVs, we conclude that there is a rather low transmission risk to humans. Further studies in the Wavul Galge cave and at other locations in Sri Lanka will give more detailed information about the prevalence of this virus.

Transcriptomics of Acute DENV-Specific CD8+ T Cells Does Not Support Qualitative Differences as Drivers of Disease Severity.

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.

Predictive value of hepatic transaminases during febrile phase as a predictor of a severe form of Dengue: analysis of adult Dengue patients from a tertiary care setting of Sri Lanka.

OBJECTIVES: Dengue viral infection is an ongoing epidemic in Sri Lanka, causing significant mortality and morbidity. A descriptive-analytical study was carried out using serologically confirmed Dengue patients during a 6 month period. The relationship between the elevation of hepatic enzymes and severity of Dengue was assessed after stratifying recorded maximum AST/ALT (SGOT/SGPT) values 2-15 times elevated and by the phases of the illness. Sensitivity, specificity, predictive values, and ROC curves were assessed using maximum values for AST and ALT. RESULTS: Out of 255 patients, 107(42%) were females. The majority (52.9%) were in the 20-39 year age group. Only 19.6% had DHF. No statistically significant difference was noticed in the values of maximum transaminases during the febrile phase among DF and DHF patients. Higher sensitivity and low specificity with the 1-5 times elevation range was noticed, and a higher cut-off level of more than 5 times elevation showed low sensitivity and higher specificity. The combination of both transaminases cut-offs with age and sex also does not show clinically significant predictability of severe disease. The AST and ALT elevations are not showing discriminatory predictive value on dengue severity. As different serotypes cause different epidemics, it is important to carry out large-scale specific studies considering the serotypes.

Detection of Alpha- and Betacoronaviruses in Miniopterus fuliginosus and Rousettus leschenaultii, two species of Sri Lankan Bats.

Bats are known to be potential reservoirs of numerous human-pathogenic viruses. They have been identified as natural hosts for coronaviruses, causing Severe Acute Respiratory Syndrome (SARS) in humans. Since the emergence of SARS-CoV-2 in 2019 interest in the prevalence of coronaviruses in bats was newly raised. In this study we investigated different bat species living in a sympatric colony in the Wavul Galge cave (Koslanda, Sri Lanka). In three field sessions (in 2018 and 2019), 395 bats were captured (Miniopterus, Rousettus, Hipposideros and Rhinolophus spp.) and either rectal swabs or fecal samples were collected. From these overall 396 rectal swab and fecal samples, the screening for coronaviruses with nested PCR resulted in 33 positive samples, 31 of which originated from Miniopterus fuliginosus and two from Rousettus leschenaultii. Sanger sequencing and phylogenetic analysis of the obtained 384-nt fragment of the RNA-dependent RNA polymerase revealed that the examined M. fuliginosus bats excrete alphacoronaviruses and the examined R. leschenaultii bats excrete betacoronaviruses. Despite the sympatric roosting habitat, the coronaviruses showed host specificity and seemed to be limited to one species. Our results represent an important basis to better understand the prevalence of coronaviruses in Sri Lankan bats and may provide a basis for pursuing studies on particular bat species of interest.

Genetic risk for dengue hemorrhagic fever and dengue fever in multiple ancestries.

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.

Spleen modulation of cytoadherence properties of Plasmodium falciparum.

Cytoadherence to CD36 and ICAM-1 and var gene expression of P. falciparum parasites from a splenectomized patient were studied. These parasites lacked cytoadherence and showed expression of a non-coding cDNA sequence. Hence the spleen's modulation of parasite cytoadherence by mechanisms that affect the parasite's surface antigen expression is suggested.

Circulating T cell-monocyte complexes are markers of immune perturbations.

Our results highlight for the first time that a significant proportion of cell doublets in flow cytometry, previously believed to be the result of technical artifacts and thus ignored in data acquisition and analysis, are the result of biological interaction between immune cells. In particular, we show that cell:cell doublets pairing a T cell and a monocyte can be directly isolated from human blood, and high resolution microscopy shows polarized distribution of LFA1/ICAM1 in many doublets, suggesting in vivo formation. Intriguingly, T cell-monocyte complex frequency and phenotype fluctuate with the onset of immune perturbations such as infection or immunization, reflecting expected polarization of immune responses. Overall these data suggest that cell doublets reflecting T cell-monocyte in vivo immune interactions can be detected in human blood and that the common approach in flow cytometry to avoid studying cell:cell complexes should be re-visited.

Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-producing CD4 T Cells and Their Association with Dengue Disease.

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.

Positive melioidosis serology in a patient with adult onset Still's disease: a case report of a diagnostic dilemma.

BACKGROUND: Autoimmune disorders are known to produce false positives in serological tests for infections. Aetiological association between infections and autoimmunity, increased susceptibility to infectious and autoimmune disorders with immune dysregulation and non-specific polyclonal expansion of B cells with autoimmunity may cause confusion in diagnosis and patient management. We report a patient with Adult Onset Still's Disease (AOSD) presenting with rising melioidosis antibody titres that caused diagnostic confusion. CASE PRESENTATION: A forty-nine-year-old female presented with prolonged fever, sore-throat, large joint arthritis, lymphadenopathy, hepatomegaly and transient rash. She had elevated inflammatory markers and a rising melioidosis antibody titre. The patient responded poorly to prolonged course of appropriate antimicrobials but showed rapid and sustained improvement with glucocorticoids. CONCLUSION: Positive melioidosis serology could have been due to a co-infection or false positive antibody reaction due to non-specific B cell expansion or an indicator of true infection that triggered the immune dysregulation to develop AOSD.