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Fulltext Integrated genomic view of SARS-CoV-2 in India

Kumar P, Pandey R, Sharma P, Dhar MS, A V, Uppili B, et al.

Wellcome Open Res, 2020;5:184.
PMID: 32995557 DOI: 10.12688/wellcomeopenres.16119.1

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
Fulltext Understanding the impact of the COVID-19 outbreak on vulnerable populations in Malaysia through an ethical lens: A study of non-state actors involved in aid distribution

Nungsari M, Hui Yin C, Fong N, Pillai V

Wellcome Open Res, 2021;6:263.
PMID: 35111977 DOI: 10.12688/wellcomeopenres.17239.2

Background: Globally, vulnerable populations have been disproportionately affected by the COVID-19 pandemic and subsequent responses, such as lockdown measures and mass vaccinations. Numerous ethical challenges have arisen at different levels, be it at the policy-making level or on the ground. For example, policymakers have to contain a highly contagious disease with high morbidity using scarce resources, while minimizing the medium- to long-term social and economic impacts induced by containment measures. This study explores the impact of COVID-19 on vulnerable populations in Malaysia by using an intersectional framework that accounts for overlapping forms of marginalization. Methods: This study utilizes in-depth qualitative data obtained from 34 individuals and organizations to understand the impact of the COVID-19 outbreak on vulnerable populations in Malaysia. We utilize four principles of ethics to guide our coding and interpretation of the data - namely beneficence, non-maleficence, justice and autonomy. We utilize a frequency analysis to roughly understand the types of ethical issues that emerged. Using hermeneutic content analysis (HCA), we then explore how the principles interact with each other. Results: Through the frequently analysis, we found that although beneficence was very prevalent in our dataset, so was a significant amount of harm - as perpetuated through injustice, the removal or lack of autonomy and maleficence. We also unearthed a worrying landscape of harm and deep systemic issues associated with a lack of support for vulnerable households - further exacerbated during the pandemic. Conclusions: Policy recommendations for aid organizations and society to mitigate these ethical problems are presented, such as long overdue institutional reforms and stronger ethical practices rooted in human rights principles, which government agencies and aid providers can then use in the provision of aid to vulnerable populations.
Performance evaluation of a multinational data platform for critical care in Asia

Collaboration for Research, Implementation and Training in Critical Care - Asia Investigators, Pisani L, Rashan T, Shamal M, Ghose A, Kumar Tirupakuzhi Vijayaraghavan B, et al.

Wellcome Open Res, 2021;6:251.
PMID: 35141427 DOI: 10.12688/wellcomeopenres.17122.1

Background: The value of medical registries strongly depends on the quality of the data collected. This must be objectively measured before large clinical databases can be promoted for observational research, quality improvement, and clinical trials. We aimed to evaluate the quality of a multinational intensive care unit (ICU) network of registries of critically ill patients established in seven Asian low- and middle-income countries (LMICs). Methods: The Critical Care Asia federated registry platform enables ICUs to collect clinical, outcome and process data for aggregate and unit-level analysis. The evaluation used the standardised criteria of the Directory of Clinical Databases (DoCDat) and a framework for data quality assurance in medical registries. Six reviewers assessed structure, coverage, reliability and validity of the ICU registry data. Case mix and process measures on patient episodes from June to December 2020 were analysed. Results: Data on 20,507 consecutive patient episodes from 97 ICUs in Afghanistan, Bangladesh, India, Malaysia, Nepal, Pakistan and Vietnam were included. The quality level achieved according to the ten prespecified DoCDat criteria was high (average score 3.4 out of 4) as was the structural and organizational performance -- comparable to ICU registries in high-income countries. Identified strengths were types of variables included, reliability of coding, data completeness and validation. Potential improvements included extension of national coverage, optimization of recruitment completeness validation in all centers and the use of interobserver reliability checks. Conclusions: The Critical Care Asia platform evaluates well using standardised frameworks for data quality and equally to registries in resource-rich settings.
Fulltext An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

MalariaGEN, Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, et al.

Wellcome Open Res, 2022;7:136.
PMID: 35651694 DOI: 10.12688/wellcomeopenres.17795.1

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network) II: protocol for case based antimicrobial resistance surveillance

Mo Y, Ding Y, Cao Y, Hopkins J, Ashley EA, Waithira N, et al.

Wellcome Open Res, 2023;8:179.
PMID: 37854055 DOI: 10.12688/wellcomeopenres.19210.2

Background: Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods: A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion: ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an example, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.
Fulltext Invisibility in global health: A case for disturbing bioethical frameworks

Alenichev A, Suwalowska H, Faure MC, Ng SH, Modlin C, Ambrogi I, et al.

Wellcome Open Res, 2023;8:191.
PMID: 38313470 DOI: 10.12688/wellcomeopenres.19346.2

In recent years, the global health community has increasingly reported the problem of 'invisibility': aspects of health and wellbeing, particularly amongst the world's most marginalized and impoverished people, that are systematically overlooked and ignored by people and institutions in relative positions of power. It is unclear how to realistically manage global health invisibility within bioethics and other social science disciplines and move forward. In this letter, we reflect on several case studies of invisibility experienced by people in Brazil, Malaysia, West Africa and other transnational contexts. Highlighting the complex nature of invisibility and its interconnectedness with social, political and economic issues and trends, we argue that while local and targeted interventions might provide relief and comfort locally, they will not be able to solve the underlying causes of invisibility. Building from the shared lessons of case study presentations at an Oxford-Johns Hopkins Global Infectious Disease Ethics Collaborative (GLIDE), we argue that in dealing with an intersectional issue such as invisibility, twenty-first century global health bioethics could pursue a more 'disturbing' framework, challenging the narrow comforting solutions which take as a given the sociomaterial inequalities of the status quo. We highlight that comforting and disturbing bioethical frameworks should not be considered as opposing sides, but as two approaches working in tandem in order to achieve the internationally set global health milestones of providing better health and wellbeing for everyone. Insights from sociology, anthropology, postcolonial studies, history, feminist studies and other styles of critical reasoning have long been disturbing to grand narratives of people and their conditions. To rediscover the ethos of the WHO Alma Ata Declaration-a vision of "health for all by the year 2000"-these thinking tools will be necessary aids in developing cooperation and support beyond the narrow market logic that dominates the landscape of contemporary global health.
Fulltext Perspectives on public health interventions in the management of the COVID-19 pandemic in Thailand

Pan-Ngum W, Poomchaichote T, Peerawaranun P, Kulpijit N, Osterrieder A, Waithira N, et al.

Wellcome Open Res, 2020;5:245.
PMID: 34345714 DOI: 10.12688/wellcomeopenres.16293.3

Background: Any government needs to react quickly to a pandemic and make decisions on healthcare interventions locally and internationally with little information regarding the perceptions of people and the reactions they may receive during the implementation of restrictions. Methods: We report an anonymous online survey in Thailand conducted in May 2020 to assess public perceptions of three interventions in the Thai context: isolation, quarantine and social distancing. A total of 1,020 participants, of whom 52% were women, responded to the survey. Results: Loss of income was the main concern among respondents (>80% for all provinces in Thailand). Traditional media and social media were important channels for communication during the pandemic. A total of 92% of respondents reported that they changed their social behaviour even before the implementation of government policy with 94% reporting they performed social distancing, 97% reported using personal protective equipment such as masks and 95% reported using sanitizer products. Conclusions: This study showed a high level of compliance from individuals with government enforced or voluntarily controls such as quarantine, isolation and social distancing in Thailand. The findings from this study can be used to inform future government measures to control the pandemic and to shape communication strategies.
Fulltext Social, ethical and behavioural aspects of COVID-19

Pan-Ngum W, Poomchaichote T, Cuman G, Cheah PK, Waithira N, Mukaka M, et al.

Wellcome Open Res, 2020;5:90.
PMID: 32704548 DOI: 10.12688/wellcomeopenres.15813.2

Introduction: Vaccines and drugs for the treatment and prevention of COVID-19 require robust evidence generated from clinical trials before they can be used. Decisions on how to apply non-pharmaceutical interventions such as quarantine, self-isolation, social distancing and travel restrictions should also be based on evidence. There are some experiential and mathematical modelling data for these interventions, but there is a lack of data on the social, ethical and behavioural aspects of these interventions in the literature. Therefore, our study aims to produce evidence to inform (non-pharmaceutical) interventions such as communications, quarantine, self-isolation, social distancing, travel restrictions and other public health measures for the COVID-19 pandemic. Methods: The study will be conducted in the United Kingdom, Italy, Malaysia, Slovenia and Thailand. We propose to conduct 600-1000 quantitative surveys and 25-35 qualitative interviews per country. Data collection will follow the following four themes: (1) Quarantine and self-isolation (2) social distancing and travel restrictions (3) wellbeing and mental health (4) information, misinformation and rumours. In light of limitations of travel and holding in-person meetings, we will primarily use online/remote methods for collecting data. Study participants will be adults who have provided informed consent from different demographic, socio-economic and risk groups. Discussion: At the time of the inception of the study, United Kingdom, Italy, Malaysia, Slovenia and Thailand have initiated strict public health measures and varying degrees of "lockdowns" to curb the pandemic. These public health measures will change in the coming weeks and months depending on the number of cases of COVID-19 in the respective countries. The data generated from our study could inform these strategies in real time.
Migration health ethics in Southeast Asia: a scoping review

Ng SH, Kaur S, Cheah PY, Ong ZL, Lim J, Voo TC

Wellcome Open Res, 2023;8:391.
PMID: 38595706 DOI: 10.12688/wellcomeopenres.19572.2

BACKGROUND: Asia hosts the second-largest international migrant population in the world. In Southeast Asia (SEA), key types of migration are labour migration, forced migration, and environmental migration. This scoping review seeks to identify key themes and gaps in current research on the ethics of healthcare for mobile and marginalised populations in SEA, and the ethics of research involving these populations.
METHODS: We performed a scoping review using three broad concepts: population (stateless population, migrants, refugees, asylum seekers, internally displaced people), issues (healthcare and ethics), and context (11 countries in SEA). Three databases (PubMed, CINAHL, and Web of Science) were searched from 2000 until May 2023 over a period of four months (February 2023 to May 2023). Other relevant publications were identified through citation searches, and six bioethics journals were hand searched. All searches were conducted in English, and relevant publications were screened against the inclusion and exclusion criteria. Data were subsequently imported into NVivo 14, and thematic analysis was conducted.
RESULTS: We identified 18 papers with substantial bioethical analysis. Ethical concepts that guide the analysis were 'capability, agency, dignity', 'vulnerability', 'precarity, complicity, and structural violence' (n=7). Ethical issues were discussed from the perspective of research ethics (n=9), clinical ethics (n=1) and public health ethics (n=1). All publications are from researchers based in Singapore, Thailand, and Malaysia. Research gaps identified include the need for more research involving migrant children, research from migrant-sending countries, studies on quality of migrant healthcare, participatory health research, and research with internal migrants.
CONCLUSIONS: More empirical research is necessary to better understand the ethical issues that exist in the domains of research, clinical care, and public health. Critical examination of the interplay between migration, health and ethics with consideration of the diverse factors and contexts involved is crucial for the advancement of migration health ethics in SEA.
Mixed methods study protocol for combining stakeholder-led rapid evaluation with near real-time continuous registry data to facilitate evaluations of quality of care in intensive care units

Collaboration for Research, Implementation and Training in Critical Care in Asia and Africa (CCAA), Rashan A, Beane A, Ghose A, Dondorp AM, Kwizera A, et al.

Wellcome Open Res, 2023;8:29.
PMID: 37954925 DOI: 10.12688/wellcomeopenres.18710.3

BACKGROUND: Improved access to healthcare in low- and middle-income countries (LMICs) has not equated to improved health outcomes. Absence or unsustained quality of care is partly to blame. Improving outcomes in intensive care units (ICUs) requires delivery of complex interventions by multiple specialties working in concert, and the simultaneous prevention of avoidable harms associated with the illness and the treatment interventions. Therefore, successful design and implementation of improvement interventions requires understanding of the behavioural, organisational, and external factors that determine care delivery and the likelihood of achieving sustained improvement. We aim to identify care processes that contribute to suboptimal clinical outcomes in ICUs located in LMICs and to establish barriers and enablers for improving the care processes.
METHODS: Using rapid evaluation methods, we will use four data collection methods: 1) registry embedded indicators to assess quality of care processes and their associated outcomes; 2) process mapping to provide a preliminary framework to understand gaps between current and desired care practices; 3) structured observations of processes of interest identified from the process mapping and; 4) focus group discussions with stakeholders to identify barriers and enablers influencing the gap between current and desired care practices. We will also collect self-assessments of readiness for quality improvement. Data collection and analysis will be led by local stakeholders, performed in parallel and through an iterative process across eight countries: Kenya, India, Malaysia, Nepal, Pakistan, South Africa, Uganda and Vietnam.
CONCLUSIONS: The results of our study will provide essential information on where and how care processes can be improved to facilitate better quality of care to critically ill patients in LMICs; thus, reduce preventable mortality and morbidity in ICUs. Furthermore, understanding the rapid evaluation methods that will be used for this study will allow other researchers and healthcare professionals to carry out similar research in ICUs and other health services.

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