Genomic Surveillance of Recent Dengue Outbreaks in Colombo, Sri Lanka.

All four serotypes of the dengue virus (DENV1-4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of disproportionate magnitude. A phylogenetic analysis was conducted on near full length DENV genomes sequenced from serum collected from a prospective cohort study from the Colombo district, Sri Lanka during a 28-month period using Oxford nanopore technology, and the consensus sequences were analyzed using maximum likelihood and Bayesian evolutionary analysis. From 523 patients, 328 DENV sequences were successfully generated (DENV1: 43, DENV2: 219, DENV3:66). Most circulating sequences originated from a common ancestor that was estimated to have existed from around 2010 for DENV2 and around 2015/2016 for DENV1 and DENV3. Four distinct outbreaks coinciding with monsoon rain seasons were identified during the observation period mostly driven by DENV2 cosmopolitan genotype, except for a large outbreak in 2019 contributed by DENV3 genotype I. This serotype switch did not result in a more clinically severe illness. Phylogeographic analyses showed that all outbreaks started within Colombo city and then spread to the rest of the district. In 2019, DENV3 genotype I, previously, rarely reported in Sri Lanka, is likely to have contributed to a disease outbreak. However, this did not result in more severe disease in those infected, probably due to pre-existing DENV3 immunity in the community. Targeted vector control within Colombo city before anticipated seasonal outbreaks may help to limit the geographic spread of outbreaks.

A Diagnostic Scoring Model for Leptospirosis in Resource Limited Settings.

BACKGROUND: Leptospirosis is a zoonotic infection with significant morbidity and mortality. The clinical presentation of leptospirosis is known to mimic the clinical profile of other prevalent tropical fevers. Laboratory confirmation of leptospirosis is based on the reference standard microscopic agglutination test (MAT), direct demonstration of the organism, and isolation by culture and DNA detection by polymerase chain reaction (PCR) amplification. However these methods of confirmation are not widely available in resource limited settings where the infection is prevalent, and reliance is placed on clinical features for provisional diagnosis. In this prospective study, we attempted to develop a model for diagnosis of leptospirosis, based on clinical features and standard laboratory test results. METHODS: The diagnostic score was developed based on data from a prospective multicentre study in two hospitals in the Western Province of Sri Lanka. All patients presenting to these hospitals with a suspected diagnosis of leptospirosis, based on the WHO surveillance criteria, were recruited. Confirmed disease was defined as positive genus specific MAT (Leptospira biflexa). A derivation cohort and a validation cohort were randomly selected from available data. Clinical and laboratory manifestations associated with confirmed leptospirosis in the derivation cohort were selected for construction of a multivariate regression model with correlation matrices, and adjusted odds ratios were extracted for significant variables. The odds ratios thus derived were subsequently utilized in the criteria model, and sensitivity and specificity examined with ROC curves. RESULTS: A total of 592 patients were included in the final analysis with 450 (180 confirmed leptospirosis) in the derivation cohort and 142 (52 confirmed leptospirosis) in the validation cohort. The variables in the final model were: history of exposure to a possible source of leptospirosis (adjusted OR = 2.827; 95% CI = 1.517-5.435; p = 0.001) serum creatinine > 150 micromol/l (adjusted OR = 2.735; 95% CI = 1.374-4.901; p = 0.001), neutrophil differential percentage > 80.0% of total white blood cell count (adjusted OR 2.163; 95% CI = 1.309-3.847; p = 0.032), serum bilirubin > 30 micromol/l (adjusted OR = 1.717; 95% CI 0.938-3.456; p = 0.049) and platelet count < 85,000/mm3 (adjusted OR = 2.350; 95% CI = 1.481-4.513; p = 0.006). Hosmer-Lemeshow test for goodness of fit was 0.931. The Nagelkerke R2 was 0.622. The area under the curve (AUC) was noted as 0.762. A score value of 14 reflected a sensitivity of 0.803, specificity of 0.602, a PPV of 0.54, NPV of 0.84, a positive LR of 2.01 and a negative LR of 0.32. CONCLUSIONS: The above diagnostic model for diagnosis of leptospirosis is suggested for use in clinical settings. It should be further validated in clinical practice.

Clinical and laboratory associations of severity in a Sri Lankan cohort of patients with serologically confirmed leptospirosis: a prospective study.

BACKGROUND: Leptospirosis results in significant morbidity and mortality. This study elucidates markers of severity in a cohort of Sri Lankan patients. METHODS: Patients presenting to three healthcare institutions in the Western province of Sri Lanka with leptospirosis serological confirmed by the microscopic agglutination test (MAT) were included. Prospective data regarding demographic, clinical and laboratory parameters was extracted. Univariate associations and subsequent multivariate logistic regression models were constructed. RESULTS: The study included 232 patients, with 68.5% (159) demonstrating severe disease. Significant associations of severe disease at a significance level of p<0.05 were fever >38.8°C on presentation, age >40 years, muscle tenderness, tachycardia on admission, highest white cell count >12 350/mm(3) and <7900/mm(3), highest neutrophil percentage >84%, haemoglobin >11.2 g/dL and <10.2 g/dL, packed cell volume (PCV) >33.8% and <29.8%, lowest platelet count <63 500/mm(3), highest alanine transaminase (ALT) >70 IU/L and hyponatremia with sodium <131 mEq/L. On multivariate analysis, PCV <29.8% (p=0.011; OR 3.750; CI: 1.394-10.423), ALT >70 IU/L (p=0.044; OR 2.639; CI: 1.028-6.774) and hyponatremia <131 mEq/L (p=0.019; OR 6.413; CI: 1.353-30.388) were independent associations of severe disease. CONCLUSIONS: Severity associations were demonstrated with both clinical and laboratory parameters. There is a need for novel biomarkers for prediction of severity in leptospirosis.

Knowledge seeking behaviours of pre interns and early career doctors in Sri Lanka: a cross sectional study.

BACKGROUND: Use of reference sources for medical knowledge has changed dramatically over the last two decades with the introduction of online sources of information. This study analyses the medical knowledge seeking behaviours of pre interns and early career doctors in Sri Lanka. METHODS: This cross sectional survey with a convenience sample was conducted at two sites targeting two groups; pre-intern doctors graduated from the Faculty of Medicine, University of Colombo and early career doctors following a postgraduate course at the National Hospital of Sri Lanka. The data collection tool was an online self-administered questionnaire (paper based questionnaires used on request) that probed the patterns of using reference sources for medical knowledge. RESULTS AND DISCUSSION: The respondents comprised of 52 pre-interns and 34 early career doctors. A majority (98 %) had internet access. Early career doctors preferred online resources significantly more than the pre-interns. However, the utilization of online resources for evidence synthesis and planning research was unsatisfactory in both groups. A significant proportion (35 %) responded that they had never read a systematic review. Only one person in the entire sample had co-authored a review article. CONCLUSION: The use of online resources by participants seems to be satisfactory with a majority shifting to reliable online resources as a reference point for medical knowledge. However, a closer look at the usage patterns reveal that online resources that can be used for more innovative tasks such as evidence synthesis are grossly under-utilized.

Corticosteroids in the treatment of dengue shock syndrome.

Dengue infection causes significant morbidity and mortality in over 100 countries worldwide, and its incidence is on the rise. The pathophysiological basis for the development of severe dengue, characterized by plasma leakage and the "shock syndrome" are poorly understood. No specific treatment or vaccine is available, and careful monitoring and judicious administration of fluids forms the mainstay of management at present. It is postulated that vascular endothelial dysfunction, induced by cytokine and chemical mediators, is an important mechanism of plasma leakage. Although corticosteroids are potent modulators of the immune system, their role in pharmacological doses in modulating the purported immunological effects that take place in severe dengue has been a subject of controversy. The key evidence related to the role of corticosteroids for various manifestations of dengue are reviewed here. In summary, there is currently no high-quality evidence supporting the beneficial effects of corticosteroids for treatment of shock, prevention of serious complications, or increasing platelet counts. Non-randomized trials of corticosteroids given as rescue medication for severe shock have shown possible benefit. Nonetheless, the evidence base is small, and good-quality trials are lacking. We reiterate the need for well-designed and adequately powered randomized controlled trials of corticosteroids for the treatment of dengue shock.