Biology subjects

Malavige, G. N.

Publications and source records attributed to Malavige, G. N..

8 recordsLinked to original sources

bioRxiv2026

Myeloperoxidase (MPO) exacerbates dengue-associated liver injury and contributes to disease pathogenesis in mouse models

Severe dengue can damage the liver through unestablished mechanisms. We investigated the role of myeloperoxidase (MPO), a neutrophil enzyme, in dengue through patients, fatal liver samples, and mouse infection models. Observations from two independent clinical cohorts revealed elevated plasma MPO levels in dengue and, in one cohort, MPO was further linked to liver injury markers during the critical phase of disease, whereas livers from dengue fatal cases revealed MPO build-up in the vicinity of CD177+ activated neutrophils. In mice, dengue led to MPO overexpression, oxidative damage, and broad activation of innate and systemic inflammatory pathways in livers. Blocking MPO activity alleviated these and improved survival in one model and delayed disease progression without preventing death in another. These findings establish MPO as a functional mediator of severe dengue-associated liver injury and inflammation, which warrants further preclinical investigation into its hepatic pathogenic mechanism and its validity as target for therapeutic intervention.

pathology↗

bioRxiv2026

biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes

Genomic epidemiology workflows typically require expert curation of multiple specialized tools, extensive manual parameter tuning, and access to heterogeneous compute infrastructure. While standard generative AI models often hallucinate in complex biological domains, we introduce biomeStat: an autonomous AI agent that functions as a strict deterministic orchestrator. By automatically writing code to execute established bioinformatics tools in sandboxed environments, biomeStat dynamically provisions compute resources (CPU and GPU) and guarantees reproducibility, making it immediately useful for scientists without requiring command-line expertise. To demonstrate the platform, we performed a fully autonomous genomic epidemiology and structural analysis of 1,000 Dengue virus (DENV) genomes sampled from 16 Asian countries between 2000 and 2025. The agent seamlessly orchestrated phylogenetic reconstruction (IQ-TREE, TreeTime), Bayesian phylodynamics (BEAST2 via NVIDIA H200 GPU), selection pressure analysis (HyPhy), and structural mapping (PyMOL). The analysis was completed in under 24 hours of wall-clock time, revealing endemic stability (R_e [~]1.0) and identifying 1,869 candidate immune escape sites structurally colocalized with B-cell and T-cell epitopes. Furthermore, the agent validated 176 highly conserved drug target residues across the viral replication complex, confirming that resistance-associated positions for emerging antivirals JNJ-1802 and NITD-688 remain absolutely conserved across all four serotypes. By bridging the gap between natural language intent and deterministic computational execution, biomeStat reduces weeks of expert effort into a single-session analysis with full methodological transparency.

bioinformatics↗

bioRxiv2025

Remodelled cholesteryl ester enriched lipid droplets fuel flavivirus morphogenesis

Flaviviruses such as dengue and Zika viruses extensively remodel host cell membranes to create specialised replication organelles, but the role of lipid metabolism to generate them remain poorly understood. Through systematic screens of fatty acyl transferase enzymes (MBOAT and zDHHC families) and complementary approaches including CRISPR/Cas9 gene deletions, pharmacological inhibition, proteomics, and photo-crosslinkable cholesterol analogues, we identified cholesteryl ester-enriched lipid droplets (CE-LDs) as critical host components required for flavivirus infection. CE-LD formation is mediated by Sterol O-acyltransferases 1 and 2 (SOAT1/SOAT2), whose activities were upregulated early during infection, coinciding with increased CE-LD formation and transition to liquid crystalline phases. Genetic deletion or pharmacological inhibition of either enzyme resulted in a dramatic [~]100-fold reduction in viral production. Mechanistically, CE-LDs display distinct proteomic signatures, enriched in fatty acid remodelling enzymes, GTPases, and lipid transport proteins. Photo-crosslinking experiments demonstrated direct interactions between LD-derived cholesterol and viral prM, capsid and NS1. Disrupting CE-LD formation via SOAT1/2-deficiency resulted in defective, viral RNA-free replication organelles and complete absence of immature virions. Supporting the physiological and clinical relevance of viral LD exploitation, analysis in iPSC-derived macrophages mirrored findings in Huh7 cells, and dengue patients from a Sri Lankan cohort revealed that central obesity significantly increased the risk of severe dengue haemorrhagic fever. This study establishes CE-LDs as essential host metabolic hubs that enable flavivirus morphogenesis and identifies host LD metabolism as a promising therapeutic target for combating flavivirus infections.

cell biology↗

bioRxiv2020

Development and validation of an assay for detection of Japanese Encephalitis virus specific antibody responses

BackgroundAlthough immune responses to the Japanese Encephalitis virus (JEV), and the dengue viruses (DENV) have a potential to modulate the immune responses to each other, this has been poorly investigated. Therefore, we developed an ELISA to identify JEV specific, DENV non cross-reactive antibody responses by identifying JEV specific, highly conserved regions of the virus and proceeded to investigate if the presence of JEV specific antibodies associate with dengue disease severity. Methodology/Principal findings20 JEV specific peptides were identified from highly conserved regions of the virus and the immunogenicity and specificity of these peptides were assessed in individuals who were non-immune to JEV and DENV (JEV-DENV-, N=30), those who were only immune to the JEV and not DENV (JEV+DENV-, N=30), those who were only immune to DENV(JEV-DENV+, N=30) and in those who were immune to both viruses (JEV+DENV+, N=30). 7/20 peptides were found to be highly immunogenic and specific and these 7 peptides were used as a pool to further evaluate JEV-specific responses. All 30/30 JEV+DENV-and 30/30 JEV+DENV+individuals, and only 3/30 (10%) JEV-DENV+individuals responded to this pool. We further evaluated this pool of 7 peptides in patients following primary and secondary dengue infection during the convalescent period and found that the JEV-specific peptides, were unlikely to cross react with DENV IgG antibodies. We further compared this in-house ELISA developed with the peptide pool with an existing commercial JEV IgG assay to identify JEV-specific IgG following vaccination, and our in-house ELISA was found to be more sensitive. We then proceeded to investigate if the presence of JEV-specific antibodies were associated with dengue disease severity, and we found that those who had past severe dengue (n=175) were significantly more likely (p<0.0001) to have JEV-specific antibodies than those with past non-severe dengue (n=175) (OR 5.3, 95% CI 3.3 to 8.3). Conclusions/SignificanceAs our data show that this assay is highly sensitive and specific for detection of JEV-specific antibody responses, it would be an important tool to determine how JEV seropositivity modulate dengue immunity and disease severity when undertaking dengue vaccine trials. Author summaryBoth Japanese Encephalitis virus (JEV), and the dengue viruses (DENV) co-circulate in the same geographical region and have a potential to modulate the immune responses to each other. However, due to the difficulty in identifying antibody responses specific to either virus due to the highly cross-reactive nature of virus-specific antibodies, this has been poorly investigated. Therefore, we developed an ELISA to identify JEV-specific, DENV non cross-reactive antibody responses by identifying JEV-specific, highly conserved regions of the virus and proceeded to investigate if the presence of JEV-specific antibodies associates with dengue disease severity. 20 JEV-specific peptides were identified from highly conserved regions of the virus and the immunogenicity and specificity of these peptides were assessed. We found that seven peptides were highly immunogenic and specific to the JEV and we further evaluated the usefulness of an ELISA developed using these pools of peptides. We found that our in-house ELISA was found to be significantly more sensitive some of the existing commercial assays. As this assay appears to be highly sensitive and specific for detection of JEV-specific antibody responses, it would be an important tool to determine how JEV seropositivity modulate dengue immunity and disease severity when undertaking dengue vaccine trials.

immunology↗

bioRxiv2019

Phenotype and functionality of follicular helper T cells in patients with acute dengue infection

BackgroundThe association of functionality and phenotype of follicular helper T cells (Tfh) with dengue virus (DENV) specific antibody responses and clinical disease severity is has not been well studied.\n\nMethodology/Principal findingsWe investigated the phenotype and functionality of Tfhs in adult patients (DF = 18, DHF = 22) with acute dengue of varying severity using multiparametric flowcytometry. We determined if the properties of Tfhs were correlated with viraemia, disease severity, plasmablast responses and DENV-specific serum antibody responses. We further evaluated the changes in neutralizing antibodies (Neut50) with viraemia and clinical disease severity in a different cohort of patients with acute secondary DENV1 (DF=12, DHF=10) and DENV2 infection (DF=8, DHF=9).\n\nTfhs (especially those producing IL-21 and co-expressing PD-1 and ICOS) were found to be significantly expanded (p<0.0001) and highly activated in patients with DHF compared to those with DF. The frequency of Tfh cells significantly correlated with DENV-specific IgG, NS1-specific antibodies and Neut50 antibody titres, which were also significantly higher in patients with DHF. Although the Neut50 titres increased during the course of acute secondary DENV infection, they showed differences based on serotype. For instance, the Neut50 titres were significantly higher during the latter part of illness in patients with DF compared DHF in DENV1 infection, while in DENV2, patients with DHF had significantly higher titres. The viral loads during early illness did not correlate with the subsequent rise in the Neut50 antibody titres during time point of illness.\n\nConclusions/SignificanceThe expansion of Tfhs is associated with DHF and DENV-specific IgG, NS1-specific and neutralising antibodies. Neut50 titres did not associate with disease severity or viraemia at the point of first presentation during the febrile phase, but later titres do show differential association with severity in patients with DENV1 compared to DENV2.\n\nAuthor summaryFollicular helper T cells (Tfh cells) are a subset of T cells which are important in activation of germinal centre T cells and induction of long-lasting virus specific antibodies. The association of the functional status and phenotype of Tfh cells in relation to dengue virus (DENV) specific antibodies, clinical disease severity and the degree of viraemia in patients with acute dengue has not been extensively studied. Here we show that the Tfh cells are significantly expanded in patients with severe clinical disease and associate with levels of serum DENV envelop specific IgG, NS1-specific antibodies and neutralising antibodies (Neu50). Although DENV Neu50 antibody titres are thought to associate with protection, the Neut50 antibody titres were similar in patients who proceeded to develop mild or severe clinical disease and also the increase in their titres showed significant variation based on infecting DENV serotype and clinical disease severity. Therefore, although Tfh cells are expanded in patients with more severe forms of disease, and associate with DENV-specific antibody responses, they do not appear to have a protective role.

immunology↗

bioRxiv2019

Association of the gut microbiota with colorectal cancer in a South Asian cohort of patients

BackgroundAs the gut microbiome is thought to play a role in the pathogenesis of colorectal carcinoma (CRC) and affected by the diet and the genetic composition, we sought to investigate the patterns of gut microbiota that associate with CRC in a South Asian cohort of patients with CRC.\n\nMethodologyThe relative abundance of 45 types of gut microbial species were determined in faecal samples of CRC patients (n=24), DM (n=20) and healthy age matched controls (n=44), using a PCR array. Data was analyzed using the specific software for analysis of bacterial DNA quantification.\n\nResultsThe species Bacteroides fragilis (23.9-fold), Bacteroides thetaiotaomicron (8-fold) and Akkermansia muciniphila (5.9 fold) were several-fold over expressed in patients with CRC compared to healthy individuals, whereas bacterial species of the Phylum Proteobactria were under expressed. There was no difference in the abundance of these 3 species of bacteria with tumour stage or gender and age of patients. Aeromonas species, Enterococcus faecium and Shigella dysenteriae (Proteobacteria) were over 100-fold over abundant in those with DM compared to healthy individuals. Although 70.83% of those with CRC also had diabetes, the relative abundance of microbiota in CRC patients were different to those who had diabetes and no CRC.\n\nConclusionsPatients with CRC and DM harbor a markedly different gut microbiota patterns compared to their healthy counterparts. Similar patterns of gut microbial dysbiosis that associate with CRC and DM appear be seen in South Asian populations, compared to Western countries, despite differences in the diet and ethnicity.

microbiology↗

bioRxiv2018

Emergence of a Dengue virus serotype 2 causing the largest ever dengue epidemic in Sri Lanka

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.\n\nMethodology/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 (p<0.0001, median= 3, days) when compared to those with a DENV1 infection (median 5 days) and were more likely to develop significant bleeding and to require blood transfusions. Furthermore, patients with DENV2 were more likely to have significantly lower platelet counts during day 3, 4 and 5 since onset of illness.\n\nWhole 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.\n\nConclusions/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.\n\nAuthor 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<0.0001, median= 3, days) when compared to those with a DENV1 infection (median 5 days) and were more likely to develop significant bleeding. Whole genome sequencing showed that these DENV-2 isolates belonged to cosmopolitan strain and was genetically more distant to the DENV-2 strains that circulated from 1981 to 2004 in Sri Lanka.

epidemiology↗

bioRxiv2018

Quantification of dengue virus specific T cell responses and correlation with viral load and clinical disease severity in acute dengue infection

BackgroundIn order to understand the role of dengue virus (DENV) specific T cell responses that associate with protection, we studied their frequency and phenotype in relation to clinical disease severity and resolution of viraemia in a large cohort of patients with varying severity of acute dengue infection.\n\nMethodology/Principal findingsUsing ex vivo IFN{gamma} ELISpot assays we determined the frequency of dengue viral peptide (DENV)-NS3, NS1 and NS5 responsive T cells in 74 adult patients with acute dengue infection and examined the association of responsive T cell frequency with the extent of viraemia and clinical disease severity. We found that total DENV-specific and DENV-NS3-specific T cell responses, were higher in patients with dengue fever (DF), when compared to those with dengue haemorrhagic fever (DHF). In addition, early appearance of DENV-specific T cell responses was significantly associated with milder clinical disease (p=0.02). DENV peptide specific T cell responses inversely correlated with the degree of viraemia, which was most significant for DENV-NS3 specific T cell responses (Spearmans r = -0.47, p=0.0003). The frequency of T cell responses to NS1, NS5 and pooled DENV peptides, correlated with the degree of thrombocytopenia but had no association with levels of liver transaminases. In contrast, DENV-IgG inversely correlated with the degree of thrombocytopenia and levels of liver transaminases.\n\nConclusions/significanceEarly appearance of DENV-specific T cell IFN{gamma} responses appears to associate with milder clinical disease and resolution of viraemia, suggesting a protective role in acute dengue infection.

immunology↗