A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)

Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.

Development of standard indicators to assess use of electronic health record systems implemented in low-and medium-income countries

Background

Electronic Health Record Systems (EHRs) are being rolled out nationally in many low- and middle-income countries (LMICs) yet assessing actual system usage remains a challenge. We employed a nominal group technique (NGT) process to systematically develop high-quality indicators for evaluating actual usage of EHRs in LMICs.

Methods

An initial set of 14 candidate indicators were developed by the study team adapting the Human Immunodeficiency Virus (HIV) Monitoring, Evaluation, and Reporting indicators format. A multidisciplinary team of 10 experts was convened in a two-day NGT workshop in Kenya to systematically evaluate, rate (using Specific, Measurable, Achievable, Relevant, and Time-Bound (SMART) criteria), prioritize, refine, and identify new indicators. NGT steps included introduction to candidate indicators, silent indicator ranking, round-robin indicator rating, and silent generation of new indicators. 5-point Likert scale was used in rating the candidate indicators against the SMART components.

Results

Candidate indicators were rated highly on SMART criteria (4.05/5). NGT participants settled on 15 final indicators, categorized as system use (4); data quality (3), system interoperability (3), and reporting (5). Data entry statistics, systems uptime, and EHRs variable concordance indicators were rated highest.

Conclusion

This study describes a systematic approach to develop and validate quality indicators for determining EHRs use and provides LMICs with a multidimensional tool for assessing success of EHRs implementations.

Impact of conflict on maternal and child health service delivery - how and how not: a country case study of conflict affected areas of Pakistan

INTRODUCTION

In conflict affected countries, healthcare delivery remains a huge concern. Pakistan is one country engulfed with conflict spanning various areas and time spans. We aimed to explore the effect of conflict on provision of reproductive, maternal, newborn, child and adolescent health and nutrition (RMNCAH&N) services and describe the contextual factors influencing the prioritization and implementation in conflict affected areas of Pakistan (Balochistan and FATA).

METHOD

We conducted a secondary quantitative and a primary qualitative analysis. For the quantitative analysis, we stratified the various districts/agencies of Balochistan and FATA into the conflict categories of minimal-, moderate- and severe based on accessibility to health services through a Delphi methodology with local stakeholders and implementing agencies and also based on battle-related deaths (BRD) information from Uppsala Conflict Data Program (UCDP). The coverage of RMNCAH&N indicators across the continuum of care were extracted from the demographic and health surveys (DHS) and district health information system (DHIS). We conducted a stratified descriptive analysis and multivariate analysis using STATA version 15. The qualitative data was captured by conducting key informant interviews of stakeholders working in government, NGOs, UN agencies and academia. All the interviews were audiotaped which were transcribed, translated, coded and analyzed on Nvivo software version 10.

RESULTS

The comparison of the various districts based on the severity of conflict through Delphi process showed that the mean coverage of various RMNCAH&N indicators in Balochistan were significantly lower in severe- conflict districts when compared to minimal conflict districts, while there was no significant difference between moderate and severe conflict areas. There was no reliable quantitative data available for FATA. Key factors identified through qualitative analysis, which affected the prioritization and delivery of services included planning at the central level, lack of coordination amongst various hierarchies of the government and various stakeholders. Other factors included unavailability of health workforce especially female workers, poor quality of healthcare services, poor data keeping and monitoring, lack of funds and inconsistent supplies. Women and child health is set at a high priority but capacity gap at service delivery, resilience from health workers, insecurity and poor infrastructure severely hampers the delivery of quality healthcare services.

CONCLUSION

Conflict has severely hampered the delivery of health services and a wholesome effort is desired involving coordination amongst various stakeholders. The multiple barriers in conflict contexts cannot be fully mitigated, but efforts should be made to negate these as much as possible with good governance, planning, efficiency and transparency in utilization of available resources.

'They Say HIV is a Punishment from God or from Ancestors': Cross-Cultural Adaptation and Psychometric Assessment of an HIV Stigma Scale for South African Adolescents Living with HIV (ALHIV-SS)

Sub-Saharan Africa is home to 90 % of the world's adolescents living with HIV (ALHIV). HIV-stigma and the resultant fear of being identified as HIV-positive can compromise the survival of these youth by undermining anti-retroviral treatment initiation and adherence. To date, no HIV-stigma measures have been validated for use with ALHIV in Sub-Saharan Africa. This paper reports on a two-stage study in the Eastern Cape, South Africa. Firstly, we conducted a cross-cultural adaptation of an HIV stigma scale, previously used with US ALHIV. One-on-one semi-structured cognitive interviews were conducted with 9 urban and rural ALHIV. Three main themes emerged: 1) participants spoke about experiences of HIV stigma specific to a Southern African context, such as anticipating stigma from community members due to 'punishment from God or ancestors'; 2) participants' responses uncovered discrepancies between what the items intended to capture and how they understood them and 3) participants' interpretation of wording uncovered redundant items. Items were revised or removed in consultation with participants. Secondly, we psychometrically assessed and validated this adapted ALHIV stigma scale (ALHIV-SS). We used total population sampling in 53 public healthcare facilities with community tracing. 721 ALHIV who were fully aware of their status were identified and interviewed for the psychometric assessment. Confirmatory factor analysis confirmed a 3-factor structure of enacted, anticipated and internalized stigma. The removal of 3 items resulted in a significant improvement in model fit (Chi²(df) = 189.83 (33), p < .001) and the restricted model fitted the data well (RMSEA = .017; CFI/TLI = .985/.980; SRMR = .032). Standardized factor loadings of indicators onto the latent variable were acceptable for all three measures (.41-.96). Concurrent criterion validity confirmed hypothesized relationships. Enacted stigma was associated with higher AIDS symptomatology (r = .146, p < .01) and depression (r = .092, p < .01). Internalized stigma was correlated with higher depression (r = .340, p < .01), higher AIDS symptomatology (r = .228, p < .01) and low social support (r = -.265, p < .01). Anticipated stigma was associated with higher depression (r = .203, p < .01) and lower social support (r = -.142, p < .01). The resulting ALHIV-SS has 10 items capturing all three HIV stigma mechanisms experienced by ALHIV. ALHIV-SS will be valuable for evaluating rates and types of stigma, as well as effectiveness of stigma-reduction interventions among ALHIV in Southern Africa.

Prevalence and determinants of hypertension in Myanmar - a nationwide cross-sectional study

BACKGROUND

Non-communicable diseases (NCDs), malaria and tuberculosis dominate the disease pattern in Myanmar. Due to urbanization, westernized lifestyle and economic development, it is likely that NCDs such as cerebrovascular disease and ischemic heart disease are on a rise. The leading behavioral- and metabolic NCDs risk factors are tobacco smoke, dietary risks and alcohol use, and high blood pressure and body mass index, respectively. The study aimed at estimating the prevalence and determinants of hypertension, including metabolic-, behavioral- and socio-demographic risk factors.

METHODS

A nationwide, cross-sectional study of 7429 citizens of Myanmar aged 15-64 years were examined in 2009, using the WHO STEPS methodology. In separate analyses by gender, odds radios (ORs) and 95 % confidence intervals (CIs) for determinants of hypertension were estimated using logistic regression analyses. Confounders included in analyses were chosen based on Directed acyclic graphs (DAGs).

RESULTS

The prevalence of hypertension was 30.1 % (95 % CI: 28.4-31.8) in males and 29.8 % (28.5-31.1) in females. The mean BMI was 21.7 (SD 4.3) kg/m(2) for males and 23.0 (5.1) kg/m(2) for females. In fully adjusted analyses, we found in both genders increased OR for hypertension if the participants had high BMI (males: OR = 2.6; 95 % CI 2.1-3.3, females: OR = 2.3; 2.0-2.7) and high waist circumference (males: OR = 3.4; 1.8-6.8, females: OR = 2.7; 2.2-3.3). In both sexes, associations were also found between hypertension and low physical activity at work, or living in urban areas or the delta region. Being underweight and use of sesame oil in cooking was associated with lower odds for hypertension.

CONCLUSIONS

The prevalence of hypertension was high and associated with metabolic-, behavioral- and socio-demographic factors. Due to expected rapid economic growth in Myanmar we recommend similar studies in the future to follow up and describe trends in the risk factors, especially modifiable factors, which will most likely be on rise. Studies on effectiveness on interventions are needed, and policies to reduce the burden of NCD risk factors should be implemented if proven effective in similar settings.