COVID-19 Commons^™

Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A–D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key …

Increasing Covid-19 Testing And Vaccination Uptake In The Take Care Texas Community-Based Randomized Trial: Adaptive Geospatial Analysis, Kehe Zhang, Jocelyn V Hunyadi, Marcia C De Oliveira Otto, Miryoung Lee, Zitong Zhang, Ryan Ramphul, Jose-Miguel Yamal, Ashraf Yaseen, Alanna C Morrison, Shreela Sharma, Mohammad Hossein Rahbar, Xu Zhang, Stephen Linder, Dritana Marko, Rachel White Roy, Deborah Banerjee, Esmeralda Guajardo, Michelle Crum, Belinda Reininger, Maria E Fernandez, Cici Bauer

Faculty, Staff and Student Publications

BACKGROUND: Geospatial data science can be a powerful tool to aid the design, reach, efficiency, and impact of community-based intervention trials. The project titled Take Care Texas aims to develop and test an adaptive, multilevel, community-based intervention to increase COVID-19 testing and vaccination uptake among vulnerable populations in 3 Texas regions: Harris County, Cameron County, and Northeast Texas.

OBJECTIVE: We aimed to develop a novel procedure for adaptive selections of census block groups (CBGs) to include in the community-based randomized trial for the Take Care Texas project.

METHODS: CBG selection was conducted across 3 Texas regions over a 17-month period …

Quantitative Characterization And Prediction Of The Binding Determinants And Immune Escape Hotspots For Groups Of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling Of The Sars-Cov-2 Spike Complexes With Antibodies, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning of SARS-CoV-2 spike residues, and binding free energy computations for two distinct groups …

One Center's Experience Of Pulmonary Embolism After Covid-19: Impact Of Vaccination Status, Cara Gose, Kaylee Dixon, Andrea M. Bodine Md

Advances in Clinical Medical Research and Healthcare Delivery

Background: The incidence of pulmonary embolism (PE) has increased since the outbreak of the COVID-19 pandemic and may be due to the observed hypercoagulable state. There is conflicting evidence that thromboembolism risk increases after vaccination and that vaccines decrease the probability of having a thromboembolic event. This study aimed to explore how vaccination status impacts occurrence of PE after a positive COVID-19 test. The hypothesis was that vaccinated, immunocompetent patients have a lower incidence of PE after COVID-19 compared to unvaccinated patients.

Methods: This was a retrospective chart review at a teaching hospital in New England from 1/01/2021 to 3/31/2023 …

A Randomized, Double-Blind, Placebo-Controlled Trial Of Il-7 In Critically Ill Patients With Covid-19, Manu Shankar-Hari, Bruno Francois, Kenneth E Remy, Cristina Gutierrez, Stephen Pastores, Thomas Daix, Robin Jeannet, Jane Blood, Andrew H Walton, Reinaldo Salomao, Georg Auzinger, David Striker, Robert S Martin, Nitin J Anand, James Bosanquet, Teresa Blood, Scott Brakenridge, Lyle L Moldawer, Vidula Vachharajani, Cassian Yee, Felipe Dal-Pizzol, Michel Morre, Frederique Berbille, Marcel Van Den Brink, Richard Hotchkiss

Faculty, Staff and Student Publications

Background: Lymphopenia and failure of lymphocytes to mount an early IFN-γ response correlate with increased mortality in COVID-19. Given the essential role of CD4 helper and CD8 cytotoxic cells in eliminating viral pathogens, this profound loss in lymphocytes may impair patients' ability to eliminate the virus. IL-7 is a pleiotropic cytokine that is obligatory for lymphocyte survival and optimal function.

Methods: We conducted a prospective, double-blind, randomized, placebo-controlled trial of CYT107, recombinant human IL-7, in 109 critically ill, patients with lymphopenia who have COVID-19. The primary endpoint was to assess CYT107's effect on lymphocyte recovery with secondary clinical endpoints including …

Examining Health Insurance And Non-Medical Challenges Among Vietnamese Americans In Texas During The Covid-19 Pandemic, Alexander Le, Saba Siddiqi, Celine Nguyen, Ben King, Paul Gerardo Yeh, Jannette Diep, Lauren Gilbert, Bich-May Nguyen

Faculty, Staff and Student Publications

When COVID-19 data on Asian Americans are available, they are frequently aggregated, concealing community-specific concerns. Consequently, there is limited COVID-19 literature on Vietnamese Americans. In this study, we investigated the association between health insurance coverage and non-medical challenges during the COVID-19 pandemic, in Vietnamese Americans in Texas. The NIH Community Engagement Alliance (CEAL) Common Survey 2 was administered electronically in English and Vietnamese and contained 23 questions about non-medical drivers of health, COVID-19 vaccination, and research participation. Vietnamese American adults in Texas were recruited between September 2021 and March 2022 via partnerships with community organizations. Responses were compared and analyzed …

Coronavirus Disease 2019 (Covid-19) Real World Data Infrastructure: A Big-Data Resource For Study Of The Impact Of Covid-19 In Patient Populations With Immunocompromising Conditions, James M. Crawford, Lynne Penberthy, Ligia A. Pinto, Keri N. Althoff, Magdalene M. Assimon, Oren Cohen, Laura Gillim, Tracy L. Hammonds, Shilpa Kapur, Harvey W. Kaufman, David Kwasny, Jean W. Liew, William A. Meyer 3rd, Shannon L. Reynolds, Cheryl B. Schleicher, Suki Subbiah, Catherine Theruviparampil, Zachary S. Wallace, Jeremy L. Warner, Suhyeon Yoon, Yonah C. Ziemba

School of Medicine Faculty Publications

Background. We developed a United States–based real-world data resource to better understand the continued impact of the coronavirus disease 2019 (COVID-19) pandemic on immunocompromised patients, who are typically underrepresented in prospective studies and clinical trials. Methods. The COVID-19 Real World Data infrastructure (CRWDi) was created by linking and harmonizing de-identified HealthVerity medical and pharmacy claims data from 1 December 2018 to 31 December 2023, with severe acute respiratory syndrome coronavirus 2 virologic and serologic laboratory data from major commercial laboratories and Northwell Health; COVID-19 vaccination data; and, for patients with cancer, 2010 to 2021 National Cancer Institute Surveillance, Epidemiology, and …

Decriminalizing Disease: A Health Justice Approach To Infectious Diseases And Criminal Law, Sean E. Bland

Arkansas Law Review

Infectious diseases, also called communicable diseases, are largely a public health issue and should not be criminalized. This Article seeks to re-frame the discussion around the legal framework for infectious diseases in a way that moves beyond a punishment mindset and toward a health justice mindset. The focus in this Article is on health justice rather than traditional understandings of public health, defined as the science and practice of improving the health of people and their communities. The Article makes three novel contributions. First, it applies a health justice framework to the critique of infectious disease criminalization. Second, the Article …

What Factors Influenced Covid-19 Vaccine Hesitancy? Evidence From Social Media, Huseyin Zeyd Koytak

Population Health Research Brief Series

Vaccine hesitancy is one of the most significant threats to global public health efforts. Despite the rapid development and deployment of effective vaccines, resistance to vaccination has persisted in many communities, undermining collective immunity and prolonging health crises, including most recently the COVID-19 pandemic. This brief summarizes findings from a study that used data from over 50 million tweets (later rebranded as X) from 2020 to 2022 to investigate the patterns, justifications, and socioeconomic roots of vaccine hesitancy in the United States. The authors find that Twitter users in states with lower levels of education, higher poverty and unemployment rates, …

Uncovering The Binding Mechanism Of Mutated Omicron Variants Via Computational Strategies, Sajjad Haider, Nadeem Ahmad, Muhammad Shafiq, Ali Raza Siddiqui, Mohammad Nur-E-Alam, Aftab Ahmed, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

The COVID-19 pandemic, triggered by the SARS-CoV-2 virus, has resulted in nearly 630 million cases and 6.60 million fatalities globally, as of November 2022. SARS-CoV-2, a species of the Coronaviridae family, has a single-stranded positive-sense RNA genome as well as four main structural proteins (S, E, M, and N) required for viral entrance into target cells. The spike protein (S) influences this entry through interactions with human angiotensin-converting enzyme 2 (hACE2) receptor. The World Health Organization (WHO) recognized numerous variants of concern (VOCs) that involve Alpha, Beta, Gamma, Delta, and Omicron, having multiple mutations within the spike protein, altering infection …

Dissecting The Binding Affinity Of Anti-Sars-Cov-2 Compounds To Human Transmembrane Protease, Serine 2: A Computational Study, Yue-Hui Shi, Jian-Xin Shen, Yan Tao, Yuan-Ling Xia, Zhi-Bi Zhang, Yun-Xin Fu, Ke-Qin Zhang, Shu-Qun Liu

Faculty, Staff and Student Publications

The human transmembrane protease, serine 2 (TMPRSS2), essential for SARS-CoV-2 entry, is a key antiviral target. Here, we computationally profiled the TMPRSS2-binding affinities of 15 antiviral compounds. Molecular dynamics (MD) simulations for the docked complexes revealed that three compounds exited the substrate-binding cavity (SBC), suggesting noncompetitive inhibition. Of the remaining compounds, five charged ones exhibited reduced binding stability due to competing electrostatic interactions and increased solvent exposure, while seven neutral compounds showed stronger binding affinity driven by van der Waals (vdW) interactions compensating for unfavorable electrostatic effects (including electrostatic interactions and desolvation penalties). Positive and negative hotspot residues were identified …

Lessons Learned From The Covid-19 Pandemic Crisis Management In The Gaza Strip: A Qualitative Study., Belal Aljamal

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

Aims of the study: The main aim of this study was to discover the lessons learned from the COVID-19 pandemic crisis management from health policymakers' perspective in the Gaza Strip. Methods: The researcher used a qualitative design, targeting 25health policymakers using a purposeful sampling technique and face-to-face semi-structured interviews to collect data. To analyze the interview data, the directed qualitative content analysis approach was used.

Results: All interviewees agreed that the Palestinian Ministry of Health (MoH) managed the COVID-19pandemic well despite the insufficient resources and lack of experience. More specifically, the average of most participants’ assessments of Palestinian MoH “Preparedness” …

A Regularized Bayesian Dirichlet-Multinomial Regression Model For Integrating Single-Cell-Level Omics And Patient-Level Clinical Study Data, Yanghong Guo, Lei Yu, Lei Guo, Lin Xu, Qiwei Li

Faculty, Staff and Student Publications

The abundance of various cell types can vary significantly among patients with varying phenotypes and even those with the same phenotype. Recent scientific advancements provide mounting evidence that other clinical variables, such as age, gender, and lifestyle habits, can also influence the abundance of certain cell types. However, current methods for integrating single-cell-level omics data with clinical variables are inadequate. In this study, we propose a regularized Bayesian Dirichlet-multinomial regression framework to investigate the relationship between single-cell RNA sequencing data and patient-level clinical data. Additionally, the model employs a novel hierarchical tree structure to identify such relationships at different cell-type …

Covid-19 Vaccine Hesitancy Among Black Women In The Us, Brittany C Slatton, Farrah G Cambrice, Serwaa S Omowale

Faculty, Staff and Student Publications

IMPORTANCE: COVID-19 vaccine hesitancy among Black women is a critical public health concern, potentially exacerbating existing health disparities and impacting community-wide vaccination efforts.

OBJECTIVE: To explore the factors associated with COVID-19 vaccine hesitancy among Black women in the US and identify the specific concerns and experiences shaping hesitant attitudes toward vaccination.

DESIGN, SETTING, AND PARTICIPANTS: Qualitative study using in-depth, semistructured interviews conducted virtually between June and November 2021. Thematic analysis was used to identify key themes from the interview data. Participants were recruited through social media platforms and word-of-mouth referrals from various regions of the US. Interviews were conducted remotely …

Covid-19 Taking Aim At The Heart Of Public Education, Jeremy James Pyle

Theses, Dissertations and Capstones

The COVID-19 pandemic, distinguished by both its duration and widespread impact, stands apart from other crises typically faced by schools, such as natural disasters, school violence, or isolated traumatic incidents. Unlike these shorter-term events, the pandemic fundamentally altered the educational landscape, reshaping both school climate and instructional practices. This non-experimental, descriptive study employed a phenomenological research approach to examine the lived experiences of teachers during and after the pandemic. The central aim was to explore how pandemic-related stressors influenced teachers’ decisions to remain in or leave the profession, as well as to identify the supports educators perceived as necessary for …

Evaluating The Effectiveness Of Teledermatology For Undeserved Populations During And Post-Covid-19, Jakob Gibbs, Sean Hanshaw

Theses, Dissertations and Capstones

Introduction: Teledermatology, a subset of telemedicine, has gained prominence as a means to increase access to dermatologic care while reducing costs and improving patient satisfaction. The swift expansion of teledermatology during the COVID-19 pandemic was driven by the necessity to limit physical contact and adapt to public health restrictions. This technological shift aimed to address longstanding disparities in dermatology access, especially in rural and underserved populations, and to respond to the rising demand for dermatologic services amid provider shortages.

Purpose of the Study: The purpose of this study was to analyze the effects that teledermatology following the COVID-19 pandemic had …

The Birth Experience During The First Wave Of Covid-19 Lockdown In New York Hospitals: A Qualitative Study, Emily Morse Small M.S.

Selected Full Text Dissertations, 2011-

In 2020, alongside the onset of the SARS-CoV-2 (COVID-19) pandemic, 209,338 births occurred in New York State (Osterman et al., 2022). While much of the public adjusted to working or learning in a virtual world, many hospitals in New York remained open to treat those in need of care. Women nearing the end of their pregnancy, many of whom felt that they had no other choice, found themselves headed to the hospital—to the labor and delivery unit. Many studies completed outside of the United States on the birth experience during the pandemic found an increase in the likelihood of negative …

A Teacher Preparation Program's Stakeholders' Perceptions Since Campus Closure Due To Covid-19, Laurie J. Mccormick

Theses, Dissertations and Capstones

COVID-19 closed colleges and forced faculty and students to learn a new way of teaching and learning. Like most institutions, Marshall University’s College of Education and Professional Development struggled to provide the practicum experience required for teacher preparation when most public schools shifted to remote learning. This qualitative study investigated the reactions of, and ongoing impact on, a university’s college of education’s administrators, faculty, undergraduates, the institution’s instructional designers, and the Counseling Center’s director when the campus closed spring of 2020 due to the pandemic. Initial and ongoing challenges faced, and strategies implemented were categorized by the four themes that …

Building Place-Based Experiential Learning Into The Honors Curriculum At Ohio University, Geoffrey L. Buckley, Nicole Finnicum, Michelle O'Malley, Jennifer Bowie, Yolonda Youngs

Honors in Practice Online Archive

Observing the demand for interdisciplinary experiential learning opportunities post-COVID, authors present a place-based curriculum in honors. Workshop-style special topics classes provide students with an immersive and flexible learning environment, energize faculty, and engage alumni and community partners. Coursework, fieldwork, internships, and study abroad opportunities all contribute to the development of an informed and engaged citizenry. Authors address challenges in funding, access, and equity, and they suggest ways these challenges might be met.

Resilience And Reality: Exploring The Lived Experiences Of People Living With Hiv In Texas During The Covid-19 Pandemic – A Qualitative Study., Ahmed F. Alanazi

Social Work Dissertations - Archive

This study investigated the lived experiences of individuals living with HIV (PLWH) in the Dallas-Fort Worth (DFW) area of Texas during the COVID-19 pandemic, using an Interpretative Phenomenological Analysis (IPA) framework. The research examined the intersection of health, social dynamics, and psychological resilience among PLWH, who faced compounded vulnerabilities due to systemic inequities and the dual public health crises of HIV and COVID-19. Through semi-structured interviews with ten participants from diverse backgrounds, the study captured the profound impacts of disrupted healthcare systems, heightened stigma, and social isolation on this marginalized population. The findings reveal that the pandemic exacerbated existing inequities …

Early, Standardised, And Precise Treatment Of Copd Exacerbations And Covid-19, Sanjay Ramakrishnan

Theses: Doctorates and Masters

Background: Background Chronic Obstructive Pulmonary Disease (COPD) is a common chronic condition causing significant morbidity and mortality. Patients with COPD report sudden episodes of deteriorating respiratory symptoms called exacerbations, often presumed to be precipitated by infections. COPD is in the top 5 causes of death globally. COPD exacerbations drive a large proportion of these deaths. Despite this, there is no standardised model of care for the sickest patients who need hospitalisations for exacerbations. Meanwhile, treatment for COPD exacerbations continues to be guided by symptoms, instead of underlying biology. Most patients are treated with unnecessary and harmful systemic corticosteroids. During the …

Metadata Makes Big Data Useful For Ai/Ml-Ready, Equitable Pandemic Response, Sudarshan Anand, Miae Lee, Seshadri S. Vasan

Research outputs 2022 to 2026

While genomic data helps understand the pathogen and its evolution, patient metadata is critical to get the host side of the picture, so that the pandemic response is effective and equitable.

Clinical Relevance: We highlight the importance of patient stratification and metadata to help develop diagnostics, therapies and vaccines as the pathogen (virus) evolves.

Understanding The Impact Of The Care Connect Washington Program, Hannah Cohen-Cline, Dan Fish, Taylor Doren, Abby Bush

Articles, Abstracts, and Reports

No abstract provided.

Association Between Lifetime Interpersonal Violence And Post– Covid-19 Condition Among Women In Kentucky, 2020-2022, Ayşe Güler, Heather M. Bush, Katie Schill, Nurlan Kussainov, Ann L. Coker

Biostatistics Faculty Publications

Objective: The COVID-19 pandemic increased the risk of interpersonal violence. We investigated the association between lifetime interpersonal violence experience and risk of post–COVID-19 condition (the persistence of symptoms of COVID-19 and severity of health problems associated with COVID-19 that last a few weeks, months, or years) among women with lifetime interpersonal violence experience.   Methods: Women participants aged ≥18 years in Kentucky’s Wellness, Health & You—COVID-19 study completed online quantitative surveys about the impacts of the pandemic, developing COVID-19, and symptoms of post–COVID-19 condition. We conducted cross-sectional analyses estimating rate ratios of developing COVID-19 and symptoms of post–COVID-19 condition during the …

Changes In Cancer Diagnosis And Survival In The United States During The Covid-19 Pandemic, Justin T. Burus

Theses and Dissertations--Epidemiology and Biostatistics

The COVID-19 Pandemic led to global societal disruptions as political leaders and public health authorities attempted to control the spread of the newly discovered SARS- CoV-2 virus. While these measures were designed to lessen morbidity and mortality from a novel pathogen, their impact was also felt in many other, often unintended ways. The purpose of this dissertation is to use cancer surveillance research methods to examine the association between COVID-19 Pandemic-related disruptions and changes in the normal diagnosis and care of cancer in the United States.

The first two studies of this dissertation analyzed reductions in cancer diagnoses in the …

An Analysis Of Covid-19 Vaccine Hesitancy In The U.S., Hieu Trung Bui, Sandra Eksioglu, Ruben Proano, Sarah Nurre Pinkley

Industrial Engineering Faculty Publications and Presentations

Reluctance or refusal to get vaccinated, commonly known as Vaccine Hesitancy (VH), poses a significant challenge to COVID-19 vaccination campaigns. Understanding the factors contributing to VH is essential for shaping effective public health strategies. This study proposes a novel framework for combining machine learning with publicly available data to generate a proxy metric that evaluates the dynamics of VH faster than the currently used survey methods. The metric is input to descriptive classification models that analyze a wide array of data, aiming to identify key factors associated with VH at the county level in the U.S. during the COVID-19 pandemic …

Structural And Interpersonal Determinants Of Covid-19 Vaccine Uptake In Vulnerable Populations Of The United States, Alyea Wood

Capstone Showcase

Since its introduction in late 2020, the uptake of the COVID-19 vaccine has had the lowest rates in marginalized populations like minorities, elderly, and those of low socioeconomic status. Decreased rates of vaccination uptake in these groups has resulted in increased burden of disease and subsequently higher rates of hospitalization and death. Many inequities in poor COVID-19 health outcomes can be explained by examining common predictive factors that determine vaccination rates in these United States populations. This special article research aims to explore these various predictive factors with the goal to provide targeted strategies to boost COVID-19 vaccination rates, especially …

Focus Group Interview: Perspectives Of Virtual Dietary Counseling Methods Post Covid-19 Pandemic, Maria R. Mendoza

All Master's Theses

In response to the prevalence of morbidity and mortality, studies to avert these conditions in a cost-effective and accessible manner are also increasing. Developing new methods to provide nutrition education that are more accessible is critical to reaching individuals who may experience socioeconomic barriers impacting their ability to access healthcare. The purpose of this study is to examine the perceptions related to different delivery methods of dietary counseling. This qualitative research study will examine the perceptions related to different methods of dietary counseling (telephone calls, video calls, or face-to-face visits). Focus group one contained provider participants (N = 7), which …

Evolution Of Stressors For Healthcare Workers Over The Covid-19 Pandemic, F. Labrèche, Q. Durand-Moreau, A. Adisesh, J.-M. Galarneau, Shannon Ruzycki, Tanis Zadunayski, Nicola Cherry

Études primaires

Background:

Many studies have documented exposure to psychosocial factors in healthcare workers (HCWs) during the COVID-19 pandemic. Few have done it prospectively with open-ended questions.

Aims:

To describe the evolution of stress factors reported by HCWs during the pandemic.

Methods:

A prospective cohort of 4964 HCWs (physicians, nurses, healthcare aides, personal support workers), from four Canadian provinces, received four online questionnaires between the springs 2020 and 2022. Responses to an open-ended question on stressful events were coded into 25 stressors. Multilevel logistic regressions assessed trends in stressors, and the effect of gender, occupation, and age.

Results:

In 2020, 91% of …

Expériences Vécues Et Perceptions De Personnes Étudiantes Internationales Sur Les Mesures Et Les Services Offerts Par Les Universités Québécoises Pendant La Pandémie De Covid-19 = Experiences And Perceptions Of International Students Regarding Measures And Services Offered By Quebec Universities During The Covid-19 Pandemic, Farrah Bérubé, Jessica Dubé, Jorge Frozzini, Daniel Côté

Études primaires

Cet article fait état d’une partie des résultats d’une recherche menée auprès de personnes étudiantes internationales (PÉI) qui fréquentaient des universités québécoises pendant la pandémie de COVID-19. La recherche portait sur les usages sociaux des technologies de l’information et de la communication (TIC) et sur la qualité de vie des PÉI en période de confinement. Les résultats présentés et discutés dans cet article se rapportent plus spécifiquement aux expériences et perceptions des PÉI sur les mesures et les services offerts par les universités en contexte de confinement. Afin de répondre à cet objectif, des entretiens semi-dirigés, menés auprès de 40 …