SARS-CoV-2 is caused by a pathogenic and highly transmissible beta coronavirus leading to severe infections in immuno-compromised individuals. This study first evaluates the primers used in the Reverse Transcription Polymerase Chain Reaction (RT-PCR) to detect SARS-CoV-2 by understanding how mutations might affect the primer efficiency with the SARS-CoV-2 sequences. Mutations on the Spike protein of SARS-CoV-2 are the most important as the spike protein mediates the viral entry into host cells. This study tracks the course of mutations on the spike protein by focusing on the haplogroups of the sequences across the world. A comprehensive database linking three important, currently available databases is curated as part of this study to fill the gaps caused by sequencing errors. Further, this study exploits the data generated by the Illumina and Oxford Nanopore next generation sequencing methods to study the evolution of mutations in a single Septuagenarian patient over an infection period of 102 days using the gene analysis software Geneious Prime. / Master of Science / A novel corona virus named Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken down the entire world by causing Covid-19 pandemic. Initially detected in Wuhan, China, the virus has now made its way to more than 200 countries with a heavy death toll. Understanding the virus through mutation tracking and improving diagnostics and vaccine design have now become the top priority of researchers. Most of these researchers depend on quality viral sequence datasets to identify and track mutations. One aim of this study is to provide a comprehensive dataset linking the GISAID (Global Initiative on Sharing All Influenza Data), NCBI (National Center for Biological Information) and the SRA (Sequence Read Archive) sequences. The dataset can be used for genome analysis and mutation tracking which can provide important insights for vaccine design and in improving diagnostic assays. In addition, this study provides an analysis of viral mutations in in the genomic regions targeted by commonly used primers in the RT-PCR tests for SARS-CoV-2 that may affect the efficiency of detection. This study also uses the haplogroup information of people across the world to track the D614G mutation on the S gene of SARS-CoV-2 as it may be associated with increased transmissibility. To track the course of mutations in SARS-CoV-2, it is important to analyze the sequencing data provided by the Illumina and Oxford Nanopore next generation sequencing methods. We present a case study to investigate the course of SARS-CoV-2 mutations in a single septuagenarian patient over a period of 102days using the Sequence Read Archive (SRA) data generated by two Next Generation Sequencing methods and compare the advantages that one has over the other.

This dissertation is comprised of two manuscripts that explore various contestations and representations of knowledge about the highly pathogenic avian influenza H5N1virus. In the first manuscript, I explore three narratives that have been produced to describe the 20-year journey of the virus. The journey begins in 1996 when the virus was a singular localized animal virus but then over the next 20 years multiplied its ontological status through a (de)stabilized global network of science and politics that promoted both fears of contagion and politics of otherness. Written by and for powerful actors and institutions in the global North, the narratives focused on technical solutions and outbreak fears. In doing so, the narratives produced policies and practices of biopower that obscured alternative considerations for equity, social justice, and wellbeing for the marginalized groups most directly affected by the H5N1 virus. The second manuscript explores a unique aspect of the H5N1 virus's journey as an emerging infectious disease -- its representation as a potential weapon for bioterrorists. The US government's recent attempt to secure what constitutes H5N1 knowledge produced a global debate between scientists and policy makers over how to balance the nation-state's desire for security with the life science's tradition of openly shared research. Known as the dual-use dilemma, this debate set up binaries of impossible reconciliation between the two groups. This dissertation argues that the dual-use dilemma obscures larger questions of justice. I propose a new concept of justice, knowledge justice, as an alternate more globally inclusive framework for exploring ways out of the dilemma. The concept is premised on the assertion that if knowledge is framed to obscure justice issues, then the justice questions of owning that knowledge can be used as a way out of the dual-use dilemma. Thus, knowledge becomes a question of justice that should be as important to policy makers as more traditional justice considerations of inequities in distribution, recognition, representation, and fairness. / Ph. D.

The COVID-19 Pandemic exacerbated a multitude of systems in the United States in 2020 up to current day. The structure of non-profit organizations across the country weakened as demands escalated for free food resources with specific pressure placed on food banks and food recovery organizations. There were citizens who had not previously relied on free food services who found themselves in drive through pickups, waiting for pre-packaged food boxes or the occasional you-pick operation to feed their families and themselves. The increase in demand for free food services was reacted to by those leading and directing the free food distribution sites through a time of crisis. This qualitative study serves to analyze food recovery organization (FRO) leadership strategies and principles that guided their decision making and problem-solving skills in response to food shortages and supply chain issues. The merge of the eight pillars of transformational and servant leadership theory provided propositional pillars that were tested in practice through interviews with FRO leaders in Appalachia. The discovery of how these leadership strategies were enacted during a time of crisis will guide the development of a training curriculum for nonprofit leaders in the future. / Master of Science in Life Sciences / The COVID-19 Pandemic exacerbated a multitude of systems in the United States in 2020 up to current day. The structure of non-profit organizations across the country weakened as demands escalated for free food resources with specific pressure placed on food banks and food recovery organizations. There were citizens who had not previously relied on free food services who found themselves in drive through pickups, waiting for pre-packaged food boxes or the occasional you-pick operation to feed their families and themselves. The increase in demand for free food services was reacted to by those leading and directing the free food distribution sites through a time of crisis. This qualitative study serves to analyze food recovery organization (FRO) leadership strategies and principles that guided their decision making and problem-solving skills in response to food shortages and supply chain issues. The merge of the eight pillars of transformational and servant leadership theory provided propositional pillars that were tested in practice through interviews with FRO leaders in Appalachia. The discovery of how these leadership strategies were enacted during a time of crisis will guide the development of a training curriculum for nonprofit leaders in the future.

In recent years, rare catastrophic disasters have triggered pharmaceutical supply chain disruptions, resulting in product shortages and other problems that have negatively impacted healthcare delivery. Since the health sector is part of many nations’ critical infrastructure, ensuring minimal disruption in the supporting supply chains is an essential aspect of national security. While traditional risk management approaches have proven adequate for handling independent routine operational risks, these methods are inadequate for infrequent disruptive risks that propagate further risks, producing a domino effect in complex systems. Since today’s pharmaceutical supply chains have many characteristics of complex systems, elucidating the disruptive risks and required resilience capabilities, through knowledge gained from actual disasters, can be valuable in developing mitigation strategies. This research aims to investigate two catastrophic disasters that disrupted pharmaceutical supply chains in recent years. The first case explores the impact of a localized Category IV hurricane that hit Puerto Rico and disrupted the supply chain for saline, an essential product used in the treatment of many illnesses. The risk events that propagated from the disaster are identified and modeled using a Bayesian network to determine where resilience should be strengthened. In accordance with ISO 31000 risk management guidelines, Bayesian networks have been identified as appropriate tools for modeling complex system risks. The second case employs a qualitative research study on the vaccine supply chain supporting mass immunization during the COVID-19 pandemic. A content analysis is conducted to extract the insights of over 100 professionals on disruptors and resilience capability requirements of the COVID-19 vaccine supply chain. The results indicate that a large and diverse set of risk factors and resilience capabilities are pertinent to pharmaceutical supply chains during localized severe weather and global pandemic disasters. Furthermore, to mitigate the impacts of severe weather risk in the case of Puerto Rico, the predominant type of resilience required is absorptive capacity, while in the case of the mass immunization vaccine supply chain, adaptive capacity is key. These findings should be useful to national leaders, pharmaceutical supply chain and healthcare sourcing managers, disaster preparedness officers, and others charged with pharmaceutical supply chain resilience.

Students and educators around the world faced many challenges when returning to the physical school building and environment after the disruption to our educational systems throughout the height of the COVID-19 pandemic. Educational leaders across the U.S. have expressed concerns over the substantially higher levels of anxiety and chronic absenteeism among adolescents. This study examined middle school adolescents' abilities to use coping skills for managing anxiety in the school environment post-pandemic. Qualitative data were collected from eight middle school counselors through one-on-one semi-structured interviews. Findings indicated an increase in the number of students presenting with symptoms of anxiety and the severity of symptoms. Middle school counselors noted an increase in school refusal and self-harm and indicated that the majority of their direct service time is spent with individual students. In order to better support students with managing anxiety, middle school counselors expressed the need for explicit coping skills instruction and additional mental health staffing in the school buildings. / Doctor of Education / Students and educators around the world faced many challenges when returning to the physical school building and environment after the disruption to our educational systems throughout the height of the COVID-19 pandemic. Educational leaders across the U.S. have expressed concerns over the substantially higher levels of anxiety and student absenteeism among adolescents. In this study, a total of eight middle school counselors who served as counselors prior to the pandemic and in the 2023-2024 school year participated in one-on-one interviews. Counselors were asked to describe their observations of adolescent coping strategies for managing anxiety in the school environment and share any differences in how they were working to support adolescents presenting with symptoms of anxiety. Middle school counselors reported an increase in the number of students presenting with symptoms of anxiety and the severity of symptoms. They also noted an increase in school refusal and self-harm and indicated that the majority of their time is spent with individual students. In order to better support students managing anxiety, middle school counselors expressed the need for explicit coping skills instruction and additional mental health staffing in the school buildings.

Yes / Planetary health sees neoliberal capitalism as a key mediator of socioecological crises, a position that is echoed in much COVID-19 commentary. In this Personal View, I set out an economic theory that emphasises some of the ways in which neoliberal capitalism's conceptualisation of value has mediated responses to COVID-19. Using the intersection of ecological, feminist, and Marxist economics, I develop an analysis of neoliberal capitalism as a specific historical form of the economy. I identify the accumulation of exchange value as a central tendency of neoliberal capitalism and argue that this tendency creates barriers to the production of other forms of value. I then analyse the implications of this tendency in the context of responses to COVID-19. I argue that resources and labour flow to the production of exchange value, at the expense of production of other value forms. Consequently, the global capitalist economy has unprecedented productive capacity but uses little of this capacity to create the conditions that improve and maintain people's health. To be more resilient to coming crises, academics, policy makers, and activists should do theoretical work that enables global economies to recognise multiple forms of value and political work that embeds these theories in societal institutions.

Yes / We interviewed people with dementia and carers from the IDEAL cohort to find out how the COVID-19 lockdown and continuing restrictions affected those living with dementia. Some people with dementia coped well, while others coped with difficulty or were only just coping. The additional stress of COVID-19 exacerbated pre-existing coping difficulties. For many, social isolation increased anxiety. Some felt that lack of activity or lack of social contact caused a decline in their abilities to manage everyday tasks. Confusion about COVID-19 rules or difficulty remembering what to do led to anxiety when leaving the house. People felt that members of the public might not understand their particular needs. While some carers felt they were coping well, others experienced stress when having to leave the home because the person with dementia might not be safe if left alone. Some experienced increased strain in the caring relationship compounded by an uncertainty about future availability of respite. Some were concerned about the complex health needs of the person with dementia alongside COVID-19 risk and lack of personalised information. Both people with dementia and carers talked about the importance of access to safe outdoor space. People were anxious about how others would react or behave towards them regarding keeping a distance if they went out. Being connected to friends, family and wider community or support groups was important to help combat the effects of isolation. People from BAME communities worried about their increased vulnerability to the virus. A lack of trust in Government guidance and in health care services added to their anxiety. However, some benefitted from strong community and faith group involvement. What might be helpful for people with dementia? • Reablement to help regain or maintain skills • Personalised health advice regarding managing COVID-19 risk and the opportunity to ask questions. • Identification of people with dementia who live alone and an assessment of their needs. What might be helpful for carers? • Needs assessment in regard to respite. • Novel forms of respite care that incorporate social distancing. What might be helpful for both carers and people with dementia? • Access to COVID-safe outdoor spaces. • Continuation and expansion of ‘just checking’ services. • Support to get online and use the internet. • Communication and information through non-digital means. • Community COVID-19 ‘dementia awareness’ initiatives. What might be helpful for people from Black and minority ethnic groups? • Addressing concerns about their increased risk of COVID-19. • Directing information and support through existing community and faith groups. / This report presents independent research funded by the National Institute for Health Research Policy Research Unit in Older People and Frailty.

Yes / Healthcare system resilience is a conceptual approach that seeks to explore how health services adapt and respond to variability in demand and resources. As has been witnessed since the beginning of the COVID-19 pandemic, healthcare services have undergone many reconfigurations. One understudied aspect of how the 'system' is able to adapt and respond is the contribution of key stakeholders-patients and families, and in the context of the pandemic, the general public as a whole. This study aimed to understand what people were doing during the first wave of the pandemic to protect the safety of their health, and the health of others from COVID-19, and the resilience of the healthcare system. Social media (Twitter) was used as a method of recruitment due to its ability for social reach. Twenty-one participants took part in 57 semistructured interviews over three time points from June to September 2020. The included an initial interview and invitation to two follow-up interviews after 3 and 6 weeks. Interviews were conducted virtually using Zoom-an encrypted secure video conferencing software. A reflexive thematic analysis approach to analysis was used. Three themes, each with its own subthemes were identified in the analysis: (1) A 'new safety normal'; (2) Existing vulnerabilities and heightened safety and (3) Are we all in this together? This study found that the public had a role in supporting the resilience of healthcare services and systems during the first wave of the pandemic by adapting their behaviour to protect themselves and others, and to avoid overwhelming the National Health Service. People who had existing vulnerabilities were more likely to experience safety gaps in their care, and be required to step in to support their safety, despite it being more difficult for them to do so. It may be that the most vulnerable were previously required to do this extra work to support the safety of their care and that the pandemic has just illuminated this issue. Future research should explore existing vulnerabilities and inequalities, and the heightened safety consequences created by the pandemic. The National Institute for Health Research (NIHR) Yorkshire and Humber Patient Safety Translational Research Centre (NIHR Yorkshire and Humber PSTRC), Patient and Public Involvement and Engagement Research Fellow and NIHR Yorkshire and Humber PSTRC Patient Involvement in Patient Safety theme lay leader are involved in the preparation of a lay version of the findings within this manuscript.

This study employed Kirkpatrick's training evaluation model to better examine the reactions and learning experiences of a group of pharmaceutical industry sales professionals who participated in pandemic-related virtual compliance training in spring 2020. The field of learning technologies has few examples and limited knowledge regarding the evaluation of virtual training in the context of pandemic-related compliance training in the biopharmaceutical sector. This qualitative study employed semi-structured interviews to collect data from industry participants, allowing an examination of their experiences relative to the first three stages of Kirkpatrick's training evaluation framework, namely the reactions of the trainees, the knowledge transferred to the trainees, and the performance as it relates to the trainees' changed behaviors because of their participation in virtually delivered training.

This qualitative descriptive case study examines the pedagogical teaching and instructional practices of fifth, sixth and eighth grade Texas public school English/reading teachers. This study shares the description of each teachers' English and Reading pedagogy, instructional practices, and their successes and/or challenges prior to and during the pandemic. The participants of the study were from two different school districts in Texas. The study utilized surveys and semi-structured interviews as sources of data that revealed reading pedagogy and a self-assessment of reading pedagogy practices prior to and during the COVID-19 pandemic. Three conclusive themes emerged after analysis of the data: importance of social emotional wellness of students, teaching and learning became a one size fits all approach, and varied levels of student engagement. Recommendations from this study for educational practitioners include a need to value the importance of the teacher-student relationship and the powerful role it plays in each student's emotional wellness and learning. Practitioners will need to reflect on what the COVID-19 pandemic taught the educational system about digital platforms and learning. Practitioners in the field should consider how the lingering effects of the COVID-19 pandemic will impact instructional design, teaching, content pedagogy, student academic gaps and academic progress or lack thereof for years to come. Implications for future research include more descriptive reading pedagogy studies that replicate this study and are inclusive of a larger sampling population of teachers, inclusive of students' and parents' experiences throughout more districts in the state of Texas post the COVID-19 pandemic.