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Genomic Analysis Of The Sars-Cov-2 Variants Circulated In The Philippines, 2020–2024, Arnie Dimaano, Kiana Dominique Carreon, Giselle Sophia Camaya, Irvin Rondolo, Jarel Elgin Tolentino

Biology Faculty Publications

Purpose

Genomic sequencing has been an invaluable tool to determine the evolution of SARS-CoV-2. In the present study, we provided a comprehensive description of the SARS-CoV-2 variants circulated in the Philippines.

Methods

The dataset from the human COVID-19 infections was acquired by downloading the sequences and their associated metadata spanning from March 2020 to April 2024. Then, we executed several filtering criteria to acquire the final dataset for the Philippine samples and performed spatial distribution analysis and phylogenetic tree construction of the reported SARS-CoV-2 sequences.

Results

A total of 16,679,203 SARS-CoV sequences were obtained, of which 17,393 (0.10 %) were …

Navigating Physical Activity Promotion And Policy In The Post-Covid-19-Pandemic Era, Justin Richards, Katja Siefken, Michael Pratt, Adrian Bauman, Juliana Mejía-Grueso, Catherine B Woods, Wanda Wendel-Vos, Erica Hinckson, Deborah Salvo, Pedro C Hallal, Andrea Ramírez Varela

Faculty, Staff and Student Publications

Background: There is limited evidence on the priorities and opportunities associated with promoting population physical activity (PA) participation for the post-COVID-19-pandemic future.

Purpose: This study assessed government-led PA promotion efforts before and during the COVID-19 pandemic, along with post-COVID-19-pandemic priorities and recommendations.

Methods: Two separate cross-sectional surveys conducted in 2023. Survey 1 was targeted at the Global Observatory for Physical Activity (GoPA!) Country Contacts. Survey 2 also included key international informants representing influential stakeholders in PA policy implementation.

Results: There were 68 respondents to Survey 1, collectively representing 61 countries. An additional 37 people, including representatives from 14 key international …

Finding Them Before They Find Us: Solving The Emerging Infectious Disease Crisis, Daniel R. Brooks

MANTER: Journal of Parasite Biodiversity

The human population grows daily, it’s on the move, and it’s carving a deep technological footprint on our planet. We alter landscapes and perturb ecosystems, inserting ourselves and other species into novel regions of the world, leading to potentially irreversible changes in the biosphere. This is not news. More than 75 years ago, Charles Elton, one of the founders of modern ecology, wrote, “We must make no mistake; we are seeing one of the greatest historical convulsions in the world’s fauna and flora.” We are also in the midst of a public health and epidemiological crisis. Climate change alters movements …

Norovirus Acute Gastroenteritis Amongst Us And European Travellers To Areas Of Moderate To High Risk Of Travellers’ Diarrhoea: A Prospective Cohort Study, Martin Alberer, Christine L Moe, Christoph Hatz, Kerstin Kling, Amy E Kirby, Lisa Lindsay, Hans D Nothdurft, Margarita Riera-Montes, Robert Steffen, Thomas Verstraeten, Henry M Wu, Herbert L Dupont

Faculty, Staff and Student Publications

BACKGROUND: Acute gastroenteritis (AGE) is a major medical condition for travellers worldwide, particularly travellers to low- and middle-income countries. Norovirus (NoV) is the most common cause of viral AGE in older children and adults, but data on prevalence and impact amongst travellers is limited.

METHODS: Prospective, multi-site, observational cohort study conducted 2015-2017, amongst adult international travellers from the US and Europe to areas of moderate to high risk of travel-acquired AGE. Participants provided self-collected pre-travel stool samples and self-reported AGE symptoms whilst travelling. Post-travel stool samples were requested from symptomatic subjects and a sample of asymptomatic travellers within 14 days …

Trajectories Of Diabetes-Related Sequelae For Identifying Transition Probabilities, And Optimal Timepoints For Prevention Of Ulceration, Infection, And Amputation, Daniel C. Jupiter, Yuanyi Zhang, Naohiro Shibuya

School of Podiatric Medicine Publications

To reduce diabetes-related complications and to avoid futile procedures, foot and ankle surgeons need to understand the relative timings of catastrophic events, their incidence, and probabilities of transitions between disease states in diabetes in different patient populations. For this study, we tracked medical events (including an initial diagnosis of diabetes, ulcer, wound care, osteomyelitis, amputation, and reamputation, in order of severity) and the time between each such event in patients with diabetes, stratifying by sex, race, and ethnicity. We found that the longest average duration between the different lower extremity states was a diagnosis of diabetes to the occurrence of …

Leptospirosis In The Platypus (Ornithorhynchus Anatinus) In Australia: Who Is Infecting Whom?, Richard J. Whittington, Thomas R. Grant, Jarrad Mckercher, Monica Suann, Keith Hart, Kathrine A. Handasyde, James Macgregor, Mark E. Westman, Joanne H. Connolly

Research outputs 2022 to 2026

The platypus (Ornithorhynchus anatinus) is an amphibious, egg-laying mammal of high conservation value that is found only in Australia. The zoonotic bacterium Leptospira interrogans serovar Hardjo was discovered in platypuses in prior studies, but little is known about its epidemiology. Samples in the Platypus Serum Bank were tested in 2023 and the results were combined with historical records. Antibodies against L. interrogans serovar Hardjo were found in 50% of 464 serum samples from 411 platypuses collected from 14 river basins in southeastern Australia between 1981 and 2012; prevalence remained high over three decades in the Shoalhaven River population. Seroprevalence increased …

Do Patients Infected With Human Coronavirus Before The Covid-19 Pandemic Have Less Risk Of Being Infected With Covid-19?, Gamze Şanlidağ İşbi̇len, Ayça Aydin Uysal, Seli̇n Yi̇ği̇t, Özgür Appak, Hi̇lal Si̇pahi̇, Gülendam Bozdayi, Arzu Sayiner, Candan Çi̇çek, Özlem Güzel Tunçcan, Oğuz Reşat Si̇pahi̇

Turkish Journal of Medical Sciences

Background/aim: Although seasonal human coronaviruses (HCoVs) have long been recognized as respiratory tract viruses, the newly identified SARS-CoV-2 caused a pandemic associated with severe respiratory failure. We aimed to evaluate the incidence of COVID-19 infection in patients diagnosed in three tertiary teaching hospitals, both with and without prior confirmed HCoV infection, and to compare these cohorts in terms of COVID-19 contraction.Materials and methods: In our study, we examined HCoV PCR-positive cases obtained retrospectively between January 2014 and March 2020 from three University Hospital Microbiology Laboratories (Cohort 1), as well as PCR-negative patients detected in the same PCR cycle as the …

Antimicrobial Resistance In Equines: A Growing Threat To Horse Health And Beyond-A Comprehensive Review., Ajran Kabir, Bibek Lamichhane, Tasmia Habib, Alexis Adams, Hossam El-Sheikh Ali, Nathan M Slovis, Mats H. T. Troedsson, Yosra A. Helmy

Veterinary Science Faculty Publications

The equine industry holds substantial economic importance not only in the USA but worldwide. The occurrence of various infectious bacterial diseases in horses can lead to severe health issues, economic losses, and restrictions on horse movement and trade. Effective management and control of these diseases are therefore crucial for the growth and sustainability of the equine industry. While antibiotics constitute the primary treatment strategy for any bacterial infections in horses, developing resistance to clinically important antibiotics poses significant challenges to equine health and welfare. The adverse effects of antimicrobial overuse and the escalating threat of resistance underscore the critical importance …

The Role Of Sexual Network Core Groups In Disease Epidemics, Jason Janeaux

LSU Doctoral Dissertations

Sexually transmitted infections (STIs) remain an economic and social burden, non-discriminately affecting sexually active individuals worldwide. The unique transmission of STIs is dependent upon host and pathogen life histories, as well as the underlying network structure of the host population. Within a population there is a group of individuals, the core group, that maintains STI presence and helps sustain ongoing transmission both within the core group and in the surrounding population. While the presence of these core groups is well documented, the criteria for inclusion into a sexual core group is not. In this dissertation, I explore common factors that …

Associations Between Longer Leukocyte Telomere Length And Increased Lung Cancer Risk Among Never Smokers In Urban China, Jason Y Y Wong, Xiao-Ou Shu, Wei Hu, Batel Blechter, Jianxin Shi, Kevin Wang, Richard Cawthon, Qiuyin Cai, Gong Yang, Mohammad L Rahman, Bu-Tian Ji, Yutang Gao, Wei Zheng, Nathaniel Rothman, Qing Lan

Faculty, Staff and Student Publications

BACKGROUND: The complex relationship between measured leukocyte telomere length (LTL), genetically predicted LTL (gTL), and carcinogenesis is exemplified by lung cancer. We previously reported associations between longer pre-diagnostic LTL, gTL, and increased lung cancer risk among European and East Asian populations. However, we had limited statistical power to examine the associations among never smokers by gender and histology.

METHODS: To investigate further, we conducted nested case-control analyses on an expanded sample of never smokers from the prospective Shanghai Women's Health Studies (798 cases and 792 controls) and Shanghai Men's Health Studies (161 cases and 162 controls). We broke the case-control …

Modeling Fast Information And Slow(Er) Disease Spreading: A Geometric Analysis, Iulia Martina Bulai, Mattia Sensi, Sara Sottile

Biology and Medicine Through Mathematics Conference

No abstract provided.

Dual-Domain Clustering Of Spatiotemporal Infectious Disease Data, Samuel R. Thornton, Erin C.S. Acquesta, Patrick D. Finley, Mansoor A. Haider

Biology and Medicine Through Mathematics Conference

No abstract provided.

Graphing The Curve: A Mathematical Expedition Into Social Distancing's Role In The South African Covid-19 Narrative, Chidozie Williams Chukwu

Biology and Medicine Through Mathematics Conference

No abstract provided.

Information Feedback Delays Within Epidemic Models And Their Effect On Model Dynamics., Maria K. Bouka, Christopher Strickland Dr

Biology and Medicine Through Mathematics Conference

No abstract provided.

Associations Between Polycystic Ovary Syndrome (Pcos) And Antibiotic Use: Results From The Uaehfs, Nirmin F. Juber, Abdishakur Abdulle, Amar Ahmad, Fatme Alanouti, Tom Loney, Youssef Idaghdour, Yvonne Valles, Raghib Ali

All Works

Women with polycystic ovary syndrome (PCOS) have a higher susceptibility to infections compared to those without PCOS. Studies evaluating antibiotic use based on PCOS status are scarce. Therefore, we aimed to (i) assess the associations between self-reported PCOS and antibiotic use, and (ii) whether PCOS treatment and the age at PCOS diagnosis modified the associations above. This cross-sectional analysis used the United Arab Emirates Healthy Future Study (UAEHFS) conducted from February 2016 to March 2023 involving 2063 Emirati women aged 18–62 years. We performed ordinal logistic regressions under unadjusted and demographic-health-characteristic-adjusted models to obtain the odds ratios (ORs) and 95% …

One Year Follow Up Of A Cross-Sectional Study Of Hookworm Infection And Response To Deworming In Beposo, Ghana, Taylor Clarkson

Capstone Experience: Master of Public Health

Hookworms are soil-transmitted helminths that infect over 500 million people worldwide, primarily those in low-income countries. Infection with hookworm can cause anemia, malnutrition, and stunted physical and cognitive development. Deworming campaigns have attempted to combat hookworm infections in endemic areas for decades. However, there is growing variability in the effectiveness of deworming drugs, and post-treatment reinfections are abundant. There are significant gaps in our understanding of critical host-parasite factors that mediate hookworm infection, reinfection, and response to deworming treatment in endemic communities. A five-year prospective study was undertaken to better understand drivers of hookworm infection in rural Ghana and thus …

Defining The Phylogenetics And Resistome Of The Major Clostridioides Difficile Ribotypes Circulating In Australia, Keeley O’Grady, Stacey Hong, Papanin Putsathit, Narelle George, Christine Hemphill, Peter G. Huntington, Tony M. Korman, Despina Kotsanas, Monica Lahra, Rodney Mcdougall, Andrew Mcglinchey, Avram Levy, Casey V. Moore, Graeme Nimmo, Louise Prendergast, Jennifer Robson, David J. Speers, Lynette Waring, Michael C. Wehrhahn, Gerhard F. Weldhagen, Richard M. Wilson, Thomas V. Riley, Daniel R. Knight

Research outputs 2022 to 2026

Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 …

Identifying The Multilevel Factors Influencing Provider Recommendations For Adolescent Vaccines, Mallory Kathryn Ellingson

Yale Graduate School of Arts and Sciences Dissertations

Health care provider (HCP) recommendations are a key predictor of vaccineacceptance among parents of adolescents. However, HCP recommendations for adolescent vaccines are not universal. In order to address disparities in HCP recommendations, we must first understand why recommendations vary. The factors that influence a HCP recommendation are multilevel. At the individual level, a HCP’s own knowledge, attitudes and beliefs about a vaccine can influence how or if they recommend the vaccine to a patient. At the interpersonal level, the characteristics of the patient can impact how a HCP perceives disease risk or need for a vaccine in their patient. At …

Utilizing Meta-Analytical And Causal Inference Methods To Evaluate The Impacts Of Environmental Risk Factors On Non-Hodgkin Lymphoma, Xiaoting Shi

Yale Graduate School of Arts and Sciences Dissertations

Non-Hodgkin lymphoma (NHL) is one of the most common hematologic malignancies in the world. Despite substantial efforts to identify causes and risk factors for NHL over the past few decades, the etiology of NHL is largely unclear. The overarching goal of this three-part dissertation is to use different meta-analytical and causal inference methods to identify and evaluate potential environmental risk factors for NHL. For the first project of this dissertation, we conducted an umbrella review to summarize the range, strength, and consistency of all associations between environmental risk factors and NHL reported in published meta-analyses. We identified 85 meta-analyses of …

Exploring The Associations Between Drug Resistant Mutations, Low-Level Viremia, And Virological Failure In Persons With Hiv In Florida, Adriana Campos

USF Tampa Graduate Theses and Dissertations

Virologic suppression is an essential part to a successful regimen for Persons with HIV (PWH) and the 95-95-95 initiative. Yet, PWH experiencing episodes of low-level viremia (LLV) may be more prone to experience virological failure (VF). Currently, studies debate the clinical relevance of LLV and its effect on virological outcomes, but none have explored its interconnectedness with drug resistant mutations (DRM) and antiretroviral treatment (ART) adherence – all integral elements in predicting virological outcomes.

The goal of the proposed study was to contribute to the knowledge gap regarding the interconnectivity of drug resistant mutations, low-level viremia, adherence, and virological failure …

The Prevalence Of Gram-Negative Bacteria With Difficult-To-Treat Resistance And Utilization Of Novel Β-Lactam Antibiotics In The Southeastern United States, Y. Vivian Tsai, P. Brandon Bookstaver Pharm.D., Joseph Kohn, Julie Ann Justo, Darrell Childress, Stefanie Stramel, Douglas Slain, Patrick Tu, Mary Joyce B. Wingler, Bruce M. Jones, Daniel T. Anderson, Megan M. Seddon, David A. Cretella, Joshua Eudy, Hana Winders, Kayla Antosz Pharm.D., Pamela Bailey, Majdi N. Al-Hasan

Faculty Publications

Objective:

To evaluate temporal trends in the prevalence of gram-negative bacteria (GNB) with difficult-to-treat resistance (DTR) in the southeastern United States. Secondary objective was to examine the use of novel β-lactams for GNB with DTR by both antimicrobial use (AU) and a novel metric of adjusted AU by microbiological burden (am-AU). Design:

Retrospective, multicenter, cohort. Setting:

Ten hospitals in the southeastern United States. Methods:

GNB with DTR including Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter spp. from 2015 to 2020 were tracked at each institution. Cumulative AU of novel β-lactams including ceftolozane/tazobactam, ceftazidime/avibactam, meropenem/vaborbactam, imipenem/cilastatin/relebactam, and cefiderocol in days of therapy (DOT) …

Health Status In An Urban-Dwelling, Subtropical Frog Species (Lithobates Sphenocephalus) And Its Relation To Ranavirus And Hemoparasites, Gabrielle M. Wickersham

USF Tampa Graduate Theses and Dissertations

Urbanization poses significant challenges to wildlife, including amphibians. The present study uses a multi-parameter approach that incorporates veterinary techniques to investigate the current health status of the adult southern leopard frogs (Lithobates sphenocephalus) in Tampa Bay, Florida, amidst urban stressors including nutrient loading, fragmented habitats, and light and noise pollution. Novel values for fluctuating asymmetry (e.g., variation between left and right bilateral traits; FA), body condition (CF), stress (e.g., neutrophil:lymphocyte (N:L) ratio), and inflammation (e.g., neutrophil morphologic abnormalities, parasite load) are reported. I also investigate the relationship of overall health with ranavirus presence and hemoparasite infections. Ranavirus was absent in …

Sexual Orientation And Gender Identity Measures And Viral Suppression For People Living With Hiv: A Protocol For A Population-Based Cohort Study, Xueying Yang, Bankole Olatosi Ph.D., Sharon Weissman, Xiaoming Li Ph.D., Jiajia Zhang Ph.D.

Faculty Publications

Introduction The measure of sexual orientation and gender identity (SOGI) data in electronic health records (EHR) has been critical for addressing health disparities and inequalities, especially for HIV care. Given that gender and sexual minorities (eg, transgender, men who have sex with men and intersex) are key groups in people living with HIV (PLWH), SOGI data can facilitate a more accurate understanding about the HIV outcomes (eg, viral suppression) among this key group and then lead to tailored therapeutic services. The two-step SOGI collection method as an emerging gender measurement can be used to measure SOGI status in medical settings. …

Association Between Malaria Educational Message Exposure And Malaria Prevalence Among Children In Nigeria, Eberechukwu Jacob Ajiwe

Walden Dissertations and Doctoral Studies

No abstract provided.

The Color Of Disease: Race Science, Pandemic Influenza, And The Rise Of Epidemiology In The Segregated South, Andrew Kishuni

Graduate Thesis and Dissertation 2023-2024

This thesis evaluates the relationship between race science and eugenics, statistical epidemiology and Southern public health thought, African American health, and the 1918-1920 influenza pandemic. Historians have neglected the flu as an important epidemiological event in Southern history and historiography. To demonstrate the significance of the flu, this thesis makes several arguments based on research from new qualitative and quantitative evidence. The chief argument is that African Americans suffered disproportionately compared to whites in the South, challenging the consensus that the flu affected both races equally. Segregation did not protect African Americans from the flu. In some cases, African Americans …

Impacts Of Climate Change On Vector-Borne Disease Burden In The United States: Exploring The Epidemiological Evidence, Leah V. Loetman

Honors Theses

Climate change models predict shifts in vector-borne diseases (VBDs) around the world, including in the United States. However, to my knowledge there has yet to be a comprehensive descriptive epidemiological study examining prevalence, geographic distribution, and trends for all tick- and mosquito-borne diseases in the United States. I compiled data from the U.S. Centers for Disease Control (CDC), which publishes yearly case numbers for 17 vector-borne diseases. However, these publications depend on a scattered framework of state regulations regarding disease reporting. I compiled data from the CDC to determine the current geographic distribution, prevalence, and trends of tick- and mosquito-borne …

Investigating Tuberculosis Dynamics Using Surveillance Data And Statistical Modeling: Studies In Three High Burden Settings, Melanie Hunter Chitwood

Yale Graduate School of Arts and Sciences Dissertations

Tuberculosis (TB) is a leading cause of death from infectious disease globally, despite the availability of effective antibiotic treatment. Control efforts focus on the rapid diagnosis and treatment of individuals with TB, which reduces both disease-related morbidity and mortality and onward transmission. In addition to passive case finding, the World Health Organization recommends active case finding for high-risk individuals and their contacts. Expanding these activities to populations in which there is evidence of recent transmission may be a suitable strategy to reduce TB burden, but identifying these populations is a persistent challenge. Statistical analyses, informed by high quality surveillance data, …

Estimating Modeling Parameters For Covid-19 Spread On Campus, Aviel S. Crigger

Honors Undergraduate Theses

Understanding the true burden of community transmission of communicable diseases like COVID-19 is crucial for effective public health response. Clinical cases, while important, only represent a fraction of the actual disease prevalence within a population. In this thesis, we investigate methods to estimate parameters that link clinical cases to the true disease prevalence using a modified compartmental model known as SICR (Susceptible, Infected, Cases, Recovered). We employ Bayesian inference and ensemble Markov chain Monte Carlo (MCMC) simulations to analyze clinical case data provided by the University of Central Florida Health Center from 2020 to 2022. Our goal is to estimate …

The Influence Of Social And Spatial Processes On The Epidemiology Of Environmentally Transmitted Pathogens In Wildlife: Implications For Management, Aakash Pandey, Chris Wojan, Abigail Feuka, Meggan E. Craft, Kezia Manlove, Kim M. Pepin

United States Department of Agriculture Wildlife Services: Staff Publications

Social and spatial structures of host populations play important roles in pathogen transmission. For environmentally transmitted pathogens, the host space use interacts with both the host social structure and the pathogen’s environmental persistence (which determines the timelag across which two hosts can transmit). Together, these factors shape the epidemiological dynamics of environmentally transmitted pathogens. While the importance of both social and spatial structures and environmental pathogen persistence has long been recognized in epidemiology, they are often considered separately. A better understanding of how these factors interact to determine disease dynamics is required for developing robust surveillance and management strategies. Here, …

Epidemiology Of Invasive Candidiasis, Derek J Bays, Emily N Jenkins, Meghan Lyman, Tom Chiller, Nora Strong, Luis Ostrosky-Zeichner, Martin Hoenigl, Peter G Pappas, George R Thompson Iii

Faculty, Staff and Student Publications

Invasive candidiasis (IC) is an increasingly prevalent, costly, and potentially fatal infection brought on by the opportunistic yeast, Candida. Previously, IC has predominantly been caused by C. albicans which is often drug susceptible. There has been a global trend towards decreasing rates of infection secondary to C. albicans and a rise in non-albicans species with a corresponding increase in drug resistance creating treatment challenges. With advances in management of malignancies, there has also been an increase in the population at risk from IC along with a corresponding increase in incidence of breakthrough IC infections. Additionally, the emergence of …