Dataset Information

Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

ABSTRACT: The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.

SUBMITTER: Sahadeo NSD

PROVIDER: S-EPMC10022082 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

Sahadeo Nikita S D NSD Nicholls Soren S Moreira Filipe R R FRR O'Toole Áine Á Ramkissoon Vernie V Whittaker Charles C Hill Verity V McCrone John T JT Mohammed Nicholas N Ramjag Anushka A Brown Jordan Arianne A Hill Sarah C SC Singh Risha R Nathaniel-Girdharrie Sue-Min SM Hinds Avery A Ramkissoon Nuala N Parag Kris V KV Nandram Naresh N Parasram Roshan R Khan-Mohammed Zobida Z Edghill Lisa L Indar Lisa L Andrewin Aisha A Sealey-Thomas Rhonda R McMillan Pearl P Oyinloye Ayoola A George Kenneth K Potter Irad I Lee John J Johnson David D Charles Shawn S Singh Narine N Bisesor-McKenzie Jacquiline J Laws Hazel H Belmar-George Sharon S Keizer-Beache Simone S Greenaway-Duberry Sharra S Ashwood Nadia N Foster Jerome E JE Georges Karla K Naidu Rahul R Ivey Marsha M Giddings Stanley S Haraksingh Rajini R Ramsubhag Adesh A Jayaraman Jayaraj J Chinnadurai Chinnaraja C Oura Christopher C Pybus Oliver G OG St John Joy J Gonzalez-Escobar Gabriel G Faria Nuno R NR Carrington Christine V F CVF

PLOS global public health 20230222 2

The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore s ...[more]

PMID: 36963002

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Project description:BACKGROUND:To develop effective and sustainable simulation training programs in low-resource settings, it is critical that facilitators are thoroughly trained in debriefing, a critical component of simulation learning. However, large knowledge gaps exist regarding the best way to train and evaluate debrief facilitators in low-resource settings. METHODS:Using a mixed methods approach, this study explored the feasibility of evaluating the debriefing skills of nurse mentors in Bihar, India. Videos of obstetric and neonatal post-simulation debriefs were assessed using two known tools: the Center for Advanced Pediatric and Perinatal Education (CAPE) tool and Debriefing Assessment for Simulation in Healthcare (DASH). Video data was used to evaluate interrater reliability and changes in debriefing performance over time. Additionally, twenty semi-structured interviews with nurse mentors explored perceived barriers and enablers of debriefing in Bihar. RESULTS:A total of 73 debriefing videos, averaging 18 min each, were analyzed by two raters. The CAPE tool demonstrated higher interrater reliability than the DASH; 13 of 16 CAPE indicators and two of six DASH indicators were judged reliable (ICC > 0.6 or kappa > 0.40). All indicators remained stable or improved over time. The number of 'instructors questions,' the amount of 'trainee responses,' and the ability to 'organize the debrief' improved significantly over time (p < 0.01, p < 0.01, p = 0.04). Barriers included fear of making mistakes, time constraints, and technical challenges. Enablers included creating a safe learning environment, using contextually appropriate debriefing strategies, and team building. Overall, nurse mentors believed that debriefing was a vital aspect of simulation-based training. CONCLUSION:Simulation debriefing and evaluation was feasible among nurse mentors in Bihar. Results demonstrated that the CAPE demonstrated higher interrater reliability than the DASH and that nurse mentors were able to maintain or improve their debriefing skills overtime. Further, debriefing was considered to be critical to the success of the simulation training. However, fear of making mistakes and logistical challenges must be addressed to maximize learning. Teamwork, adaptability, and building a safe learning environment enhanced the quality enhanced the quality of simulation-based training, which could ultimately help to improve maternal and neonatal health outcomes in Bihar.

Project description:Background Failing to account for the resources required to successfully implement public health interventions can lead to an underestimation of costs and budget impact, optimistic cost-effectiveness estimates, and ultimately a disconnect between published evidence and public health decision-making. Methods We developed a conceptual framework for assessing implementation costs. We illustrate the use of this framework with case studies involving interventions for tuberculosis and HIV/AIDS in resource-limited settings. Results Costs of implementing public health interventions may be conceptualized as occurring across three phases: design, initiation, and maintenance. In the design phase, activities include developing intervention components and establishing necessary infrastructure (e.g., technology, standard operating procedures). Initiation phase activities include training, initiation of supply chains and quality assurance procedures, and installation of equipment. Implementation costs in the maintenance phase include ongoing technical support, monitoring and evaluation, and troubleshooting unexpected obstacles. Within each phase, implementation costs can be incurred at the site of delivery (“site-specific” costs) or more centrally (“above-service” or “central” costs). For interventions evaluated in the context of research studies, implementation costs should be classified as programmatic, research-related, or shared research/program costs. Purely research-related costs are often excluded from analysis of programmatic implementation. Conclusions In evaluating public health interventions in resource-limited settings, accounting for implementation costs enables more realistic estimates of budget impact and cost-effectiveness and provides important insights into program feasibility, scale-up, and sustainability. Assessment of implementation costs should be planned prospectively and performed in a standardized manner to ensure generalizability.

Project description:BackgroundAlthough laparoscopic surgery has made remarkable progress and become the standard approach for various surgical procedures worldwide over the past 30 years, its establishment in low-resource settings, particularly in public hospitals, has been challenging. The lack of equipment and trained expertise has hindered its widespread adoption in these settings. Cholecystectomy is one of the most commonly performed procedures using laparoscopy world wide AIM: The aim of the study is to determine whether laparoscopic cholecystectomy is feasible in a resource challenged setting METHODS: The research focused on individuals who underwent laparoscopic or open cholecystectomies at Yekatit 12 Hospital in Addis Ababa, Ethiopia, over a one-year period. Comprehensive data collection was conducted prospectively, encompassing both intraoperative and postoperative parameters. Follow-up was carried out via phone calls. The surgical procedures employed innovative techniques, including the reuse of sterilized single-use equipment and the utilization of local resources. The evaluation involved a comparison of demographic information, intraoperative details (such as critical view determination and operative duration), and postoperative complications, including assessments of pain and wound infections RESULTS: From August 2021 to September 2022, 119 patients were assessed. Among these patients, 65 (54.6%) underwent open cholecystectomies, while the remaining 54 (45.4%) underwent laparoscopic cholecystectomies. The average duration of the laparoscopic cholecystectomies was 90.7 min, which is 17.7 min behind the open. Patients in the laparoscopy group had significantly shorter hospital stays than the open group, and 94% were discharged by post operative day 2. The conversion rate from laparoscopic to open surgery was determined to be 3.3% CONCLUSION: To sum up, the safe execution of laparoscopic cholecystectomies is feasible in public hospitals and settings with limited resources, given adequate training and resource distribution. The study findings showcased superior outcomes, including reduced hospitalization duration and fewer complications, while maintaining comparable levels of operative duration and patient satisfaction in both groups.

Dataset Information

Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

Publications

Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

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