SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents (preprint)

Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain inconsistent. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly plus lineage and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,346 (89.8%) had a lineage identified. Omicron lineages dominated, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based analysis platform like GPAS addresses bioinformatics bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic and pandemic preparedness.

Trends in buprenorphine treatment disparities during the COVID pandemic in Massachusetts.

Background: Racial, sex, and age disparities in buprenorphine treatment have previously been demonstrated. We evaluated trends in buprenorphine treatment disparities before and after the onset of the COVID pandemic in Massachusetts. Methods: This cross-sectional study used data from an integrated health system comparing 12-months before and after the March 2020 Massachusetts COVID state of emergency declaration, excluding March as a washout period. Among patients with a clinical encounter during the study periods with a diagnosis of opioid use disorder or opioid poisoning, we extracted outpatient buprenorphine prescription rates by age, sex, race and ethnicity, and language. Generating univariable and multivariable Poisson regression models, we calculated the probability of receiving buprenorphine. Results: Among 4,530 patients seen in the period before the COVID emergency declaration, 57.9% received buprenorphine. Among 3,653 patients seen in the second time period, 55.1% received buprenorphine. Younger patients (<24) had a lower likelihood of receiving buprenorphine in both time periods (adjusted prevalence ratio (aPR), 0.56; 95% CI, 0.42-0.75 before vs. aPR, 0.76; 95% CI, 0.60-0.96 after). Male patients had a greater likelihood of receiving buprenorphine compared to female patients in both time periods (aPR: 1.05; 95% CI, 1.00-1.11 vs. aPR: 1.09; 95% CI, 1.02-1.16). Racial disparities emerged in the time period following the COVID pandemic, with non-Hispanic Black patients having a lower likelihood of receiving buprenorphine compared to non-Hispanic white patients in the second time period (aPR, 0.85; 95% CI, 0.72-0.99). Conclusions: Following the onset of the COVID pandemic in Massachusetts, ongoing racial, age, and gender disparities were evident in buprenorphine treatment with younger, Black, and female patients less likely to be treated with buprenorphine across an integrated health system.

Baseline Marine Litter Surveys along Vietnam Coasts Using Citizen Science Approach

Marine litter is a significant threat to the marine environment, human health, and the economy. In this study, beach litter surveys along Vietnamese coasts were conducted in a local context to quantify and characterize marine litter using the modified GESAMP marine litter monitoring guideline. A total of 21,754 items weighing 136,820.2 g was recorded across 14 surveys from September 2020 to January 2021. Plastic was the most abundant type of litter by both quantity (20,744 items) and weight (100,371.2 g). Fishing gear 1 (fishing plastic rope, net pieces, fishing lures and lines, hard plastic floats) and soft plastic fragments were the most frequently observed items (17.65% and 17.24%, respectively). This study not only demonstrates the abundance and composition of marine litter in Vietnam, it also provides valuable information for the implementation of appropriate preventive measures, such as the redesign of collection, reuse, and recycling programs, and informs policy and priorities, with a focus on action and investment in Vietnam. Moreover, insights from this study indicate that citizen science is a useful approach for collecting data on marine litter in Vietnam.

How Digital Natives Learn and Thrive in the Digital Age: Evidence from an Emerging Economy

As a generation of ‘digital natives,’ secondary students who were born from 2002 to 2010 have various approaches to acquiring digital knowledge. Digital literacy and resilience are crucial for them to navigate the digital world as much as the real world;however, these remain under-researched subjects, especially in developing countries. In Vietnam, the education system has put considerable effort into teaching students these skills to promote quality education as part of the United Nations-defined Sustainable Development Goal 4 (SDG4). This issue has proven especially salient amid the COVID−19 pandemic lockdowns, which had obliged most schools to switch to online forms of teaching. This study, which utilizes a dataset of 1061 Vietnamese students taken from the United Nations Educational, Scientific, and Cultural Organization (UNESCO)’s “Digital Kids Asia Pacific (DKAP)” project, employs Bayesian statistics to explore the relationship between the students’ background and their digital abilities. Results show that economic status and parents’ level of education are positively correlated with digital literacy. Students from urban schools have only a slightly higher level of digital literacy than their rural counterparts, suggesting that school location may not be a defining explanatory element in the variation of digital literacy and resilience among Vietnamese students. Students’ digital literacy and, especially resilience, also have associations with their gender. Moreover, as students are digitally literate, they are more likely to be digitally resilient. Following SDG4, i.e., Quality Education, it is advisable for schools, and especially parents, to seriously invest in creating a safe, educational environment to enhance digital literacy among students.

Lay social workers implementing a task-sharing approach to managing depression in Vietnam.

BACKGROUND: While depression is a leading contributor to burden of disease in Vietnam, there is a critical gap in depression care due to the shortage of mental health specialists and extremely limited mental health services in general health care settings. We have previously reported the effectiveness of a supported self-management (SSM) task-sharing intervention for depression, delivered by social collaborators (lay social workers). The purpose of this study was to identify factors influencing the effectiveness of delivery of SSM by social collaborators and delineate areas for further attention that are relevant for scale-up. METHODS: A hundred and ten (110) key informant interviews were conducted with three stakeholder groups (patients, social collaborators, experts) from eight provinces in Vietnam. Participants were identified through records from a recently completed randomized trial that showed the effectiveness of SSM in community-based settings in Vietnam. Qualitative descriptive methods and thematic analysis were used to examine the interviews. A coding framework and corresponding themes were developed deductively, based on the findings from the randomized trial and the literature, and through inductive analysis, to describe the contextual factors that impacted the social collaborators' role in successfully implementing the SSM intervention. RESULTS: Our analysis identified the following benefits of working with social collaborators: (1) increased awareness of mental health in the family and community; (2) reduced stigma; (3) a better understanding that depression is treatable; (4) increased help-seeking; and (5) improved access to care. There were also significant challenges, including social collaborator characteristics (age, education, pre-existing training and skills) and contextual factors influencing their work (roles and responsibilities, training, compensation, support from government). CONCLUSIONS: Engaging social collaborators in the delivery of SSM in the community can help fill a critical gap in depression care in Vietnam. However, several contextual challenges that are an impediment to increased engagement and sustainable integration into health and social systems need to be resolved through policy change to regulate their practice, define their scope of work, and provide adequate remuneration.

Dataset of Vietnamese teachers' perspectives and perceived support during the COVID-19 pandemic.

The COVID-19 pandemic has caused unprecedented damage to the educational system worldwide. Besides the measurable economic impacts in the short-term and long-term, there is intangible destruction within educational institutions. In particular, teachers - the most critical intellectual resources of any schools - have to face various types of financial, physical, and mental struggles due to COVID-19. To capture the current context of more than one million Vietnamese teachers during COVID-19, we distributed an e-survey to more than 2,500 randomly selected teachers from two major teacher communities on Facebook from 6th to 11th April 2020. From over 373 responses, we excluded the observations which violated our cross-check questions and retained 294 observations for further analysis. This dataset includes: (i) Demographics of participants; (ii) Teachers' perspectives regarding the operation of teaching activities during the pandemic; (iii) Teachers' received support from their schools, government bodies, other stakeholders such as teacher unions, and parents' associations; and (iv) teachers' evaluation of school readiness toward digital transformation. Further, the dataset was supplemented with an additional question on the teachers' primary source of professional development activities during the pandemic.

How Digital Natives Learn and Thrive in the Digital Age: Evidence from an Emerging Economy

As a generation of ‘digital natives,’secondary students who were born from 2002 to 2010 have various approaches to acquiring digital knowledge. Digital literacy and resilience are crucial for them to navigate the digital world as much as the real world;however, these remain under-researched subjects, especially in developing countries. In Vietnam, the education system has put considerable effort into teaching students these skills to promote quality education as part of the United Nations-defined Sustainable Development Goal 4 (SDG4). This issue has proven especially salient amid the COVID−19 pandemic lockdowns, which had obliged most schools to switch to online forms of teaching. This study utilizes a dataset of 1061 Vietnamese students taken from the United Nations Educational, Scientific, and Cultural Organization (UNESCO)’s “Digital Kids Asia Pacific (DKAP)”project and employed Bayesian statistics to explore the relationship between the students’background and their digital abilities. Results show that economic status and parents’level of education are positively correlated with digital literacy. Students from urban schools have only a slightly higher level of digital literacy than their rural counterparts, suggesting that school location may not be a defining explanatory element in the variation of digital literacy and resilience among Vietnamese students. Students’digital literacy and, especially resilience, also have associations with their gender. Moreover, as students are digitally literate, they are more likely to be digitally resilient. Following SDG4, i.e., Quality Education, it is advisable for schools, and especially parents, to seriously invest in creating a safe, educational environment to enhance digital literacy among students.