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.

Development of a machine learning model for early prediction of plasma leakage in suspected dengue patients.

BACKGROUND: At least a third of dengue patients develop plasma leakage with increased risk of life-threatening complications. Predicting plasma leakage using laboratory parameters obtained in early infection as means of triaging patients for hospital admission is important for resource-limited settings. METHODS: A Sri Lankan cohort including 4,768 instances of clinical data from N = 877 patients (60.3% patients with confirmed dengue infection) recorded in the first 96 hours of fever was considered. After excluding incomplete instances, the dataset was randomly split into a development and a test set with 374 (70%) and 172 (30%) patients, respectively. From the development set, five most informative features were selected using the minimum description length (MDL) algorithm. Random forest and light gradient boosting machine (LightGBM) were used to develop a classification model using the development set based on nested cross validation. An ensemble of the learners via average stacking was used as the final model to predict plasma leakage. RESULTS: Lymphocyte count, haemoglobin, haematocrit, age, and aspartate aminotransferase were the most informative features to predict plasma leakage. The final model achieved the area under the receiver operating characteristics curve, AUC = 0.80 with positive predictive value, PPV = 76.9%, negative predictive value, NPV = 72.5%, specificity = 87.9%, and sensitivity = 54.8% on the test set. CONCLUSION: The early predictors of plasma leakage identified in this study are similar to those identified in several prior studies that used non-machine learning based methods. However, our observations strengthen the evidence base for these predictors by showing their relevance even when individual data points, missing data and non-linear associations were considered. Testing the model on different populations using these low-cost observations would identify further strengths and limitations of the presented model.

Prevalence of diabetes and pre-diabetes in Sri Lanka: a new global hotspot-estimates from the Sri Lanka Health and Ageing Survey 2018/2019.

INTRODUCTION: This study's objective was to produce robust, comparable estimates of the prevalence of diabetes and pre-diabetes in the Sri Lankan adult population, where previous studies suggest the highest prevalence in South Asia. RESEARCH DESIGN AND METHODS: We used data on 6661 adults from the nationally representative 2018/2019 first wave of the Sri Lanka Health and Ageing Study (SLHAS). We classified glycemic status based on previous diabetes diagnosis, and either fasting plasma glucose (FPG), or FPG and 2-hour plasma glucose (2-h PG). We estimated crude and age-standardized prevalence of pre-diabetes and diabetes and by major individual characteristics weighting the data to account for study design and subject participation. RESULTS: Crude prevalence of diabetes in adults was 23.0% (95% CI 21.2% to 24.7%) using both 2-h PG and FPG, and age-standardized prevalence was 21.8% (95% CI 20.1% to 23.5%). Using only FPG, prevalence was 18.5% (95% CI 7.1% to 19.8%). Previously diagnosed prevalence was 14.3% (95% CI 13.1% to 15.5%) of all adults. The prevalence of pre-diabetes was 30.5% (95% CI 28.2% to 32.7%). Diabetes prevalence increased with age until ages ≥70 years and was more prevalent in female, urban, more affluent, and Muslim adults. Diabetes and pre-diabetes prevalence increased with body mass index (BMI) but was as high as 21% and 29%, respectively, in those of normal weight. CONCLUSIONS: Study limitations included using only a single visit to assess diabetes, relying on self-reported fasting times, and unavailability of glycated hemoglobin for most participants. Our results indicate that Sri Lanka has a very high diabetes prevalence, significantly higher than previous estimates of 8%-15% and higher than current global estimates for any other Asian country. Our results have implications for other populations of South Asian origin, and the high prevalence of diabetes and dysglycemia at normal body weight indicates the need for further research to understand the underlying drivers.

Prevalence and Associations of Hypertension in Sri Lankan Adults: Estimates from the SLHAS 2018-19 Survey Using JNC7 and ACC/AHA 2017 Guidelines.

Background: Sri Lanka lacks robust estimates of hypertension (HTN) prevalence owing to few national studies, hindering optimization of control strategies. Evidence on how the revised 2017 American College of Cardiology/American Heart Association (ACC/AHA) HTN definition affects prevalence in low- and middle-income countries (LMICs) is also limited. Objectives: To make robust estimates of HTN prevalence in the Sri Lankan adult population, and to assess impact of the ACC/AHA 2017 definitions. Methods: Data were sourced from the 2018-2019 first wave of the Sri Lanka Health and Ageing Study (SLHAS), a nationally representative longitudinal study of the noninstitutionalized adult population. After excluding those with missing data and aged <18 years, 6,342 participants (95.1%) were included in the analysis. HTN was defined using either the traditional threshold of systolic BP (SBP) ≥140 mmHg or a diastolic BP (DBP) ≥90 mmHg, or the ACC/AHA 2017 threshold of SBP ≥130 mmHg or DBP ≥80 mmHg, or if taking antihypertensive medication. Results: Estimated prevalence of HTN in all Sri Lankan adults was 28.2% using the traditional definition, and it doubled to 51.3% when applying the ACC/AHA 2017 definition. Of those classified as hypertensive according to the older and ACC/AHA 2017 definitions, 53.4% and 31.2%, respectively, were previously diagnosed. Of the 23.2% of adults reclassified as hypertensive by the ACC/AHA 2017 definition, 16.6% had a history of CVD or diabetes. Increased prevalence was associated with urban residence, socioeconomic status, obesity, and Muslim ethnicity. Prevalence increased with age, but the increase was steeper in women from their 30s. Conclusions: Nearly one in three adult Sri Lankans are hypertensive, requiring antihypertensive treatment. Applying the ACC/AHA 2017 definitions almost doubles numbers, but many of those reclassified would require treatment under recent WHO guidelines. Study findings also suggest that design effects in HTN surveys may be higher than usually assumed.

Plasma leakage in dengue: a systematic review of prospective observational studies.

Plasma leakage is a precursor to life-threatening complications of dengue, but this group is poorly defined and not often reported in literature. Patients with Dengue haemorrhagic fever (DHF) as defined in the 1997 World Health Organization classification are often reported, and they all have plasma leakage, but some patients with plasma leakage do not meet the definition of DHF. The study aims to estimate the frequency of plasma leakage and DHF (as a surrogate of plasma leakage) in dengue and its variations based on virus serotype, geography, patient gender and pre-existing immunity to dengue. PUBMED, Scopus, EMBASE, CINAHL and Web of Science were searched for prospective observational studies reporting on plasma leakage or DHF. Quality of data was assessed using the NIH quality assessment tool for cohort studies. Forty-three studies that recruited 15,794 confirmed dengue patients were eligible. Cumulative frequency of plasma leakage was 36.8% (15 studies, 1642/4462, 95% CI 35.4-38.2%), but surprisingly the estimated cumulative frequency of DHF was higher (45.7%, 32 studies, 4758/10417, 95% CI 44.7-46.6%), indicating that current medical literature over-reports DHF or under-reports plasma leakage. Therefore, a reliable estimate for the proportion of dengue patients developing plasma leakage cannot be derived from existing medical literature even after applying rigorous inclusion criteria to select homogenous studies. Plasma leakage is an important marker of "at-risk" dengue patients and standardizing its definition, diagnosis and reporting should be a priority in research and global policy.

Direct costs of managing in-ward dengue patients in Sri Lanka: A prospective study.

INTRODUCTION: The cost in managing hospitalised dengue patients varies across countries depending on access to healthcare, management guidelines, and state sponsored subsidies. For health budget planning, locally relevant, accurate costing data from prospective studies, is essential. OBJECTIVE: To characterise the direct costs of managing hospitalised patients with suspected dengue infection in Sri Lanka. METHODS: Colombo Dengue Study is a prospective single centre cohort study in Sri Lanka recruiting suspected hospitalised dengue fever patients in the first three days of fever and following them up until discharge. The diagnosis of dengue is retrospectively confirmed and the cohort therefore has a group of non-dengue fever patients with a phenotypically similar illness, managed as dengue while in hospital. The direct costs of hospital admission (base and investigation costs, excluding medication) were calculated for all recruited patients and compared between dengue and non-dengue categories as well as across subgroups (demographic, clinical or temporal) within each of these categories. We also explored if excluding dengue upfront, would lead to an overall cost saving in several hypothetical scenarios. RESULTS: From October 2017 to February 2020, 431 adult dengue patients and 256 non-dengue fever patients were recruited. The hospitalisation costs were USD 18.02 (SD: 4.42) and USD 17.55 (SD: 4.09) per patient per day for dengue and non-dengue patients respectively (p>0.05). Laboratory investigations (haematological, biochemical and imaging) accounted for more than 50% of the total cost. The costs were largely homogenous in all subgroups within or across dengue and non-dengue categories. Excluding dengue upfront by subsidised viral genomic testing may yield overall cost savings for non-dengue patients. CONCLUSION: As non-dengue patients incur a similar cost per day as the dengue patients, confirming dengue diagnosis using subsidised tests for patients presenting in the first three days of fever may be cost-efficient.

A scoping review of registry captured indicators for evaluating quality of critical care in ICU.

BACKGROUND: Excess morbidity and mortality following critical illness is increasingly attributed to potentially avoidable complications occurring as a result of complex ICU management (Berenholtz et al., J Crit Care 17:1-2, 2002; De Vos et al., J Crit Care 22:267-74, 2007; Zimmerman J Crit Care 1:12-5, 2002). Routine measurement of quality indicators (QIs) through an Electronic Health Record (EHR) or registries are increasingly used to benchmark care and evaluate improvement interventions. However, existing indicators of quality for intensive care are derived almost exclusively from relatively narrow subsets of ICU patients from high-income healthcare systems. The aim of this scoping review is to systematically review the literature on QIs for evaluating critical care, identify QIs, map their definitions, evidence base, and describe the variances in measurement, and both the reported advantages and challenges of implementation. METHOD: We searched MEDLINE, EMBASE, CINAHL, and the Cochrane libraries from the earliest available date through to January 2019. To increase the sensitivity of the search, grey literature and reference lists were reviewed. Minimum inclusion criteria were a description of one or more QIs designed to evaluate care for patients in ICU captured through a registry platform or EHR adapted for quality of care surveillance. RESULTS: The search identified 4780 citations. Review of abstracts led to retrieval of 276 full-text articles, of which 123 articles were accepted. Fifty-one unique QIs in ICU were classified using the three components of health care quality proposed by the High Quality Health Systems (HQSS) framework. Adverse events including hospital acquired infections (13.7%), hospital processes (54.9%), and outcomes (31.4%) were the most common QIs identified. Patient reported outcome QIs accounted for less than 6%. Barriers to the implementation of QIs were described in 35.7% of articles and divided into operational barriers (51%) and acceptability barriers (49%). CONCLUSIONS: Despite the complexity and risk associated with ICU care, there are only a small number of operational indicators used. Future selection of QIs would benefit from a stakeholder-driven approach, whereby the values of patients and communities and the priorities for actionable improvement as perceived by healthcare providers are prioritized and include greater focus on measuring discriminable processes of care.

Increased Intensity Of PCR Testing Reduced COVID-19 Transmission Within Countries During The First Pandemic Wave.

Experts agree that reverse transcription-polymerase chain reaction (PCR) testing is critical in controlling coronavirus disease 2019 (COVID-19), but decision makers disagree on how much testing is optimal. Controlling for interventions and ecological factors, we used linear regression to quantify testing's impact on COVID-19's average reproduction number, which represents transmissibility, in 173 countries and territories (which account for 99 percent of the world's COVID-19 cases) during March-June 2020. Among interventions, PCR testing had the greatest influence: a tenfold increase in the ratio of tests to new cases reported reduced the average reproduction number by 9 percent across a range of testing levels. Our results imply that mobility reductions (for example, shelter-in-place orders) were less effective in developing countries than in developed countries. Our results help explain how some nations achieved near-elimination of COVID-19 and the failure of lockdowns to slow COVID-19 in others. Our findings suggest that the testing benchmarks used by the World Health Organization and other entities are insufficient for COVID-19 control. Increased testing and isolation may represent the most effective, least costly alternative in terms of money, economic growth, and human life for controlling COVID-19.

Single molecule, near full-length genome sequencing of dengue virus.

Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process is laborious, costly and requires at least 10 primers per serotype, thus increasing the likelihood of PCR bias. We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation "nanopore" technology without fragmenting and use the sequence data to differentiate within-host viral variants with a bioinformatics tool (Nano-Q). The new assay successfully generated near full-length amplicons from DENV serotypes 1, 2 and 3 samples which were sequenced with nanopore technology. Consensus DENV sequences generated by nanopore sequencing had over 99.5% pairwise sequence similarity to Illumina generated counterparts provided the coverage was > 100 with both platforms. Maximum likelihood phylogenetic trees generated from nanopore consensus sequences were able to reproduce the exact trees made from Illumina sequencing with a conservative 99% bootstrapping threshold (after 1000 replicates and 10% burn-in). Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host.

Carica papaya extract in dengue: a systematic review and meta-analysis.

BACKGROUND: Carica papaya (CP) extract is becoming popular as an unlicensed herbal remedy purported to hasten recovery in dengue infection, mostly based on observations that it may increase platelet counts. This systematic review and meta-analysis aims to critically analyze the evidence from controlled clinical trials on the efficacy and safety of CP extract in the treatment of dengue infection. METHODS: PubMed, LILACS and Google Scholar were searched for randomized or non-randomized trials enrolling patients with suspected or confirmed dengue where CP extract was compared, as a treatment measure, against standard treatment. Recovery of platelet counts as well as other clinical indicators of favourable outcome (duration of hospital stay, prevention of plasma leakage, life threatening complications, and mortality) were assessed. RESULTS: Nine studies (India-6, Pakistan-1, Indonesia-1, Malaysia-1) met the inclusion criteria. Seven studies showed an increase in platelet counts in patients receiving CP extract, while one study showed no significant difference between the two groups, and direct comparison was not possible in the remaining study. Serious adverse events were not reported. CP extract may reduce the duration of hospital stay (mean difference - 1.98 days, 95% confidence interval - 1.83 to - 2.12, 3 studies, 580 participants, low quality evidence), and cause improvement in mean platelet counts between the first and fifth day of treatment (mean difference 35.45, 95% confidence interval 23.74 to 47.15, 3 studies, 129 participants, low quality evidence). No evidence was available regarding other clinical outcomes. CONCLUSIONS: The clinical value of improvement in platelet count or early discharge is unclear in the absence of more robust indicators of favourable clinical outcome. Current evidence is insufficient to comment on the role of CP extract in dengue. There is a need for further well designed clinical trials examining the effect of CP on platelet counts, plasma leakage, other serious manifestations of dengue, and mortality, with clearly defined outcome measures.

A short, structured skills training course for critical care physiotherapists in a lower-middle income country.

OBJECTIVES: The aim of this article is to describe the delivery and acceptability of a short, structured training course for critical care physiotherapy and its effects on the knowledge and skills of the participants in Sri Lanka, a lower-middle income country. METHODS: The two-day program combining short didactic sessions with small group workshops and skills stations was developed and delivered by local facilitators in partnership with an overseas specialist physiotherapist trainer. The impact was assessed using pre/post-course self-assessment, pre/post-course multiple-choice-question (MCQ) papers, and an end-of-course feedback questionnaire. RESULTS: Fifty-six physiotherapists (26% of critical care physiotherapists in Sri Lanka) participated. Overall confidence in common critical care physiotherapy skills improved from 11.6% to 59.2% in pre/post-training self-assessments, respectively. Post-course MCQ scores (mean score = 63.2) and percentage of passes (87.5%) were higher than pre-course scores (mean score = 36.6; percentage of passes = 12.5%). Overall feedback was very positive as 75% of the participants were highly satisfied with the course's contribution to improved critical care knowledge. CONCLUSIONS: This short, structured, critical care focused physiotherapy training has potential benefit to participating physiotherapists. Further, it provides an evidence that collaborative program can be planned and conducted successfully in a resource poor setting. This sustainable short course model may be adaptable to other resource-limited settings.

A data platform to improve rabies prevention, Sri Lanka.

PROBLEM: In Sri Lanka, rabies prevention initiatives are hindered by fragmented and delayed information-sharing that limits clinicians' ability to follow patients and impedes public health surveillance. APPROACH: In a project led by the health ministry, we adapted existing technologies to create an electronic platform for rabies surveillance. Information is entered by trained clinical staff, and both aggregate and individual patient data are visualized in real time. An automated short message system (SMS) alerts patients for vaccination follow-up appointments and informs public health inspectors about incidents of animal bites. LOCAL SETTING: The platform was rolled out in June 2016 in four districts of Sri Lanka, linking six rabies clinics, three laboratories and the public health inspectorate. RELEVANT CHANGES: Over a 9-month period, 12 121 animal bites were reported to clinics and entered in the registry. Via secure portals, clinicians and public health teams accessed live information on treatment and outcomes of patients started on post-exposure prophylaxis (9507) or receiving deferred treatment (2614). Laboratories rapidly communicated the results of rabies virus tests on dead mammals (328/907 positive). In two pilot districts SMS reminders were sent to 1376 (71.2%) of 1933 patients whose contact details were available. Daily SMS reports alerted 17 public health inspectors to bite incidents in their area for investigation. LESSONS LEARNT: Existing technologies in low-resource countries can be harnessed to improve public health surveillance. Investment is needed in platform development and training and support for front-line staff. Greater public engagement is needed to improve completeness of surveillance and treatment.

Capacity building for critical care training delivery: Development and evaluation of the Network for Improving Critical care Skills Training (NICST) programme in Sri Lanka.

OBJECTIVES: To deliver and evaluate a short critical care nurse training course whilst simultaneously building local training capacity. RESEARCH METHODOLOGY: A multi-modal short course for critical care nursing skills was delivered in seven training blocks, from 06/2013-11/2014. Each training block included a Train the Trainer programme. The project was evaluated using Kirkpatrick's Hierarchy of Learning. There was a graded hand over of responsibility for course delivery from overseas to local faculty between 2013 and 2014. SETTING: Sri Lanka. MAIN OUTCOME MEASURES: Participant learning assessed through pre/post course Multi-Choice Questionnaires. RESULTS: A total of 584 nurses and 29 faculty were trained. Participant feedback was consistently positive and each course demonstrated a significant increase (p≤0.0001) in MCQ scores. There was no significant difference MCQ scores (p=0.186) between overseas faculty led and local faculty led courses. CONCLUSIONS: In a relatively short period, training with good educational outcomes was delivered to nearly 25% of the critical care nursing population in Sri Lanka whilst simultaneously building a local faculty of trainers. Through use of a structured Train the Trainer programme, course outcomes were maintained following the handover of training responsibility to Sri Lankan faculty. The focus on local capacity building increases the possibility of long term course sustainability.

Physical inactivity among physiotherapy undergraduates: exploring the knowledge-practice gap.

BACKGROUND: Physical inactivity is a common risk factor for several non-communicable diseases (NCDs). Increasing physical activity could reduce the burden of disease due to major NCDs and increase life expectancy. Undergraduate physiotherapy students represent a group of young-adults expected to have a good knowledge of physical activity. We evaluated physical activity levels of undergraduate physiotherapy students of University of Colombo, Sri Lanka and determined their motives and barriers for participation in physical activity. METHODS: All physiotherapy undergraduates studying at the University of Colombo, Sri Lanka in 2013 were invited for the study. Phase one was a quantitative study to evaluate the physical activity levels and phase two was a qualitative study to identify motives and barriers for physical activity and sports in the same cohort. Physical activity levels (phase 1) were assessed using the interviewer administered International Physical Activity Questionnaire (long-version). The qualitative study (phase 2) was conducted in the same population using Focus Group Discussions (n = 3) and individual In-depth Interviews (n = 5). RESULTS: Sample size in phase 1 and phase 2 were 113 (response rate = 98%; [N-115]) and 87 (response rat = 97%; [N-90]) respectively. Mean age (±SD) of participants was 23.4 ± 1 years. The mean weekly total MET minutes (±SD) of the study population was 1791.25 ± 3097. According to the IPAQ categorical score a higher percentage of participants were 'inactive' (48.7%), while only 15.9% were in the 'Highly active' group. Lack of support and encouragement received during childhood to engage in sports activity seem to have played an important role in continuing their exercise behavior through to the adult life. Academic activities were given priority by both parents and teachers. The environment and support from teachers, family and friends were important to initiate and adhere to sports and physical activity. CONCLUSIONS: A higher percentage of participants were 'inactive', in spite of belonging to a group which is presumed to be knowledgeable regarding the benefits of physical activity. A significant negative attitude towards physical activity was observed in this cohort of young-adults. This seems to stem from earlier in life, due to lack of support and motivation for physical exercise and sports, received during primary and secondary schooling. This negative attitude has become a significant 'internal' barrier, which has not been changed in spite of their education.

Nursing intensive care skills training: a nurse led, short, structured, and practical training program, developed and tested in a resource-limited setting.

PURPOSE: To assess the impact of a nurse-led, short, structured training program for intensive care unit (ICU) nurses in a resource-limited setting. METHODS: A training program using a structured approach to patient assessment and management for ICU nurses was designed and delivered by local nurse tutors in partnership with overseas nurse trainers. The impact of the course was assessed using the following: pre-course and post-course self-assessment, a pre-course and post-course Multiple Choice Questionnaire (MCQ), a post-course Objective Structured Clinical Assessment station, 2 post-course Short Oral Exam (SOE) stations, and post-course feedback questionnaires. RESULTS: In total, 117 ICU nurses were trained. Post-MCQ scores were significantly higher when compared with pre-MCQ (P < .0001). More than 95% passed the post-course Objective Structured Clinical Assessment (patient assessment) and SOE 1 (arterial blood gas analysis), whereas 76.9% passed SOE 2 (3-lead electrocardiogram analysis). The course was highly rated by participants, with 98% believing that this was a useful experience. CONCLUSIONS: Nursing Intensive Care Skills Training was highly rated by participants and was effective in improving the knowledge of the participants. This sustainable short course model may be adaptable to other resource-limited settings.