Epidemiology Commons^™

Comparison Of Sars-Cov-2 Detection From Nasopharyngeal Swab Samples By The Roche Cobas 6800 Sars-Cov-2 Test And A Laboratory-Developed Real-Time Rt-Pcr Test, Elisabet Pujadas, Nnaemeka Ibeh, Matthew M Hernandez, Aneta Waluszko, Tatyana Sidorenko, Vanessa Flores, Biana Shiffrin, Numthip Chiu, Alicia Young-Francois, Michael D Nowak, Alberto E Paniz-Mondolfi, Emilia M Sordillo, Carlos Cordon-Cardo, Jane Houldsworth, Melissa R Gitman

Faculty, Staff and Student Publications

The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS-CoV-2 test and a laboratory-developed test (LDT) real-time reverse transcription-polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS-CoV-2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under …

Effect Of The Covid-19 Pandemic On Eating Habits And Food Purchasing Behaviors Of University Students, Hacı Ömer Yilmaz, Ramazan Aslan, Cihan Unal

Kesmas

COVID-19 disease, which spread rapidly all over the world after the first case was detected, became the primary agenda of the countries. Radical measures have been taken by governments to prevent the spread of the disease. Precautions and warnings to prevent disease caused some changes on daily life activities of people. University students who have to stop education are among the groups most affected by this disease sociologically, psychologically and physiologically. The aim of this study was planned and conducted to determine the effect of COVID-19 on university students' eating habits and food purchasing behavior. The study was completed with …

A Novel Methodology To Identify The Primary Topics Contained Within The Covid-19 Research Corpus, Allen Crane, Brock Freidrich, William Fehlman, Igor Frolow, Daniel W. Engels

SMU Data Science Review

In this paper, we present a novel framework and system for the identification of primary research topics from within a corpus of related publications, the classification of individual publications according to these topics, and the results of the application of our framework and system to the COVID-19 Open Research Dataset (CORD-19). CORD-19 is a corpus of published peer reviewed and pre-peer reviewed articles related to the coronavirus that causes COVID-19. Using machine learning techniques, such as Non-negative Matrix Factorization for Natural Language Processing and a Bayesian classifier, we developed a novel framework and system that automatically extracts sparse and meaningful …

The Incidence Of Common Respiratory Viruses During The Covid-19 Pandemic: Results From The Louisville Covid-19 Epidemiology Study, Brian C. Bohn Pharmd, Bcidp, Ashley M. Wilde Pharmd, Bcps-Aq Id, Sarah E. Moore Pharmd, Matthew Song Pharmd, Bcidp, Clayton J. Patross Pharmd, Bcps, Alan D. Junkins Phd, D(Abmm), Paul Schulz Md, Julio A. Ramirez Md Facp

The University of Louisville Journal of Respiratory Infections

Introduction: Social distancing has been utilized during the COVID-19 pandemic to reduce the spread of SARS-CoV-2; it is also expected to reduce the spread of common respiratory viruses.

Methods: This retrospective, descriptive study assessed the rate of positivity of common respiratory viruses from a commercially available respiratory pathogen panel across a five-hospital health system during four-week periods within March to April of 2019 and 2020.

Results: During the four-week period in 2019, the percent positivity of common respiratory viruses from week 1 to week 4 decreased from 6 to 32% among the four included viruses. In the comparator period in …

Understanding Covid-19: From Origin To Potential Therapeutics, Muhammad Moazzam, Muhammad Imran Sajid, Hamza Shahid, Jahanzaib Butt, Irfan Bashir, Muhammad Jamshaid, Amir Nasrolahi Shirazi, Rakesh Kumar Tiwari

Pharmacy Faculty Articles and Research

Currently, a global pandemic era of public health concerns is going on with the Coronavirus Disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The first case of COVID-19 was reported from Wuhan’s Huanan seafood market in China late December 2019. Bats, pangolins, and snakes have been nominated as salient carriers of the virus. Thanks to its high pathogenicity, it can cause severe respiratory infections. Fever, dry cough, sore throat, pneumonia, septic shock, and ground-glass opacities are the foremost clinical manifestations of COVID-19. Immunocompromised patients are at high risk for COVID-19 infection and may lead to …

Particulate Matter Pollution And Its Effect On Covid-19, Aída Fica Conejeros

International Programs

Growing research supports the significant effects of particulate matter on COVID-19. This air pollutant has been identified before as responsible for serious respiratory diseases. Studies on the differences in high and low polluted cities confirmed that COVID-19 not only correlates to the number of infections but also, increases of 1 ��g/m3 can cause a mortality rate to rise by 8% and the hospital admissions by 4.4%. However, laboratory studies are still needed to support these findings.

Anesthesia Services In The Time Of Covid, James Chen, Daisy Sangroula, Katelyn Williams, Sydney Pham, Ozan Akca, Jiapeng Huang, Sean Clifford

The University of Louisville Journal of Respiratory Infections

Our hospital is a 400-bed, Level-1 trauma center with 78 intensive care unit (ICU) beds serving the greater Louisville metropolitan area. The COVID-19 pandemic forced our hospital to re-evaluate our core business operations and to develop a coherent response to a fluid situation. Between March 15 and May 15, 2020, the University of Louisville Hospital admitted more than 100 COVID-19 inpatients; approximately 30 were admitted to the ICU, and most required endotracheal intubation. The following review describes our Department of Anesthesiology \& Perioperative Medicine foci, actions, and rationale during the COVID-19 pandemic. While we hope not to experience another pandemic …

Pre-Testing Of The Who’S Educational Video: “How To Protect Yourself Against Covid-19”, Hilyatul Fadliyah, Manendra Muhtar, Munih Munih, Sylviasari Risgiantini, Weny Wulandary, Hadi Pratomo

Kesmas

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared a public health emergency in many countries, including Indonesia. The World Health Organization (WHO) released an educational video, entitled "How to Protect Yourself Against COVID-19", which explained how to prevent the spread of COVID-19. This study is a qualitative study that aims to pre-test this video, based on the Information, Education, Communication (IEC) theory, by analyzing teenagers’ perceptions of the video. The design used was a Rapid Assessment Procedure (RAP), and the data were collected by conducting in-depth interviews with participants, through …

Impact Of Lockdown In India: A Case Study Comparing Kanataka With International Model, Stelvin Sebastian, Aby Paul, Jeeva Joseph, Joel Joby, Sanjo Saijan, Jobin Kunjumon Vilapurathu

Kesmas

The COVID-19 was declared a pandemic and a global health emergency by WHO, prompting various countries to implement early and stringent social distancing protocols through lockdown, to flatten the epidemic curve. The objective of the present study was to assess the impacts and effectiveness of the lockdown protocol in Karnataka and Punjab, compared with the implementation of this method in Australia and the UK. This study involved the collection of data from different authorized databases, in two phases. The first phase included the time starting with the first-reported index case through the 14th day after the declaration of lockdown, for …

Review Of Trial Therapies And Treatment For Covid-19: Lessons For Indonesia, Halma Zahro Mukhlida, Hilma Hasro Maulida, Gunanti Khairunnisa, Margaretha Josephine Mantrono, Risky Kusuma Hartono, Rindu Rindu, Eka R W Purnamasari, Rizky Fajar Meirawan

Kesmas

The infectious disease from Coronavirus Disease 2019, or COVID-19, has quickly spread world-wide since 2019. Therapies for managing COVID-19 have yet to be confirmed as medication for the severe sickness that the disease may cause. This study aimed to review the previous research of the efficacy of trial therapy and treatment to the patients in the hospital with COVID-19. Using PRISMA guidelines as a method for conducting a systematic literature review, a total of 67 articles were collected from several online journal databases. Various therapies were found that are effective in the treatment and management of COVID-19. In accordance with …

Prospects For Rnai Therapy Of Covid-19, Hasan Uludağ, Kylie Parent, Hamidreza Montazeri Aliabadi, Azita Haddadi

Pharmacy Faculty Articles and Research

COVID-19 caused by the SARS-CoV-2 virus is a fast emerging disease with deadly consequences. The pulmonary system and lungs in particular are most prone to damage caused by the SARS-CoV-2 infection, which leaves a destructive footprint in the lung tissue, making it incapable of conducting its respiratory functions and resulting in severe acute respiratory disease and loss of life. There were no drug treatments or vaccines approved for SARS-CoV-2 at the onset of pandemic, necessitating an urgent need to develop effective therapeutics. To this end, the innate RNA interference (RNAi) mechanism can be employed to develop front line therapies against …

Severe Covid-19, Arpan H. Chawala, Shivam Gulati, Bettina Sinanova, Jose Bordon

The University of Louisville Journal of Respiratory Infections

Introduction: There is substantial variation in the clinical characteristics and outcomes of severe coronavirus disease (COVID-19), making it difficult to do an optimal assessment of this condition. We reviewed the current English literature to identify the findings concerning the baseline characteristics and health outcomes of patients with severe COVID-19, primarily those with acute respiratory distress syndrome (ARDS).

Methods: We examined only studies that assessed patients with confirmed COVID-19 by reverse transcription-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with at least one of the following severity criteria: treated in the intensive care unit (ICU), ARDS, and/or invasive …

Is Sars-Cov-2 A Neurotropic Virus And A Potential Facilitator Of Cns Infection For Other Pathogens?, Jose Bordon

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Face Mask Effects Of Co2, Heart Rate, Respiration Rate, And Oxygen Saturation On Instructor Pilots, Andrew R. Dattel, Nicola M. O'Toole, Guillermina Lopez, Kenneth P. Byrnes

Publications

The COVID-19 pandemic has required people to take new measures to mitigate the spread of the communicable virus. Guidelines from health organizations, government offices, and universities have been disseminated. Adherence to these guidelines cannot be more critical for flight training. This study explored the effects face masks had on CO2, heart rate, respiration rate, and oxygen saturation while wearing a face mask at an oxygen level simulated to 5,000 feet. Thirty-two instructor pilots (IP) volunteered to participate in the study. IPs spent 90 minutes in a normobaric chamber while wearing a cloth face mask or a paper face mask. Participants …

The Importance Of Cycle Threshold Values In The Evaluation Of Patients With Persistent Positive Pcr For Sars-Cov-2: Case Study And Brief Review, Jose Bordon, Donghoon Chung, Priya Krishnan, Ruth Carrico, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Some patients recover from COVID-19, but their reverse transcription-polymerase chain reaction (RT-PCR) for SARS-CoV-2 remains persistently positive. In the evaluation of these patients, it is important to define the cycle threshold (Ct) value of the RT-PCR test. This article will present a case study, address relevant findings and interpretation of the RT-PCR test, and explain the use of Ct values in defining when a healthcare worker may return to work. Our current approach is to allow health care workers with persistently positive RT-PCR to return to work if the Ct value is greater than 35.

Covid-19 Surveillance Testing Of Healthcare Personnel Drives Universal Masking Practice, Paul S. Schulz, Ashley M. Wilde, Steve T. Hester, Jim Frazier, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Health care professionals (HCP) are at increased risk of COVID-19 infection due to the unpredictable clinical presentation of COVID-19 disease, limited SARS-CoV-2 testing, personal protective equipment (PPE) shortages, and the inherent inability to distance from patients. Infected HCP may infect others, including coworkers, leading to a simultaneous increase in the number of infections and decrease in the availability of HCP in a community. Due to PPE shortages, many healthcare systems have faced difficult decisions regarding utilization of PPE to protect HCP, patients, and the communities they serve. We describe Norton Healthcare’s success utilizing surveillance COVID-19 testing of HCP to inform …

Why Every Hospital Needs A Covid-19 Clinical Case Review Team, Ashley M. Wilde, Paul Schulz, Brian C. Bohn, Sarah E. Moore, Matthew Song, Clayton J. Patross, Bryan Denham, Jim Frazier, Steve T. Hester, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

A hospital’s response to a global pandemic requires a coordinated effort to provide consistent guidance as information rapidly changes. In the early months of the COVID-19 pandemic, diagnosis and subsequent containment was challenging due to unfamiliarity with disease presentation, unknown reverse transcription-polymerase chain reaction sensitivity, and inconsistent access to testing supplies. A centralized COVID-19 clinical case review team can provide guidance on test interpretation, isolation, resource coordination and more.

The Nurse Practitioner In The Time Of Covid, Julie Marfell, Lynn Kelso

The University of Louisville Journal of Respiratory Infections

No abstract provided.

An Overview Of Current Clinical Trials Of Agents For The Treatment And Prevention Of Covid-19 In The United States, Kenneth Schot Hannan, William P. Mckinney

The University of Louisville Journal of Respiratory Infections

Introduction: Given the rapid worldwide spread of SARS-CoV-2 and the attendant risks for severe complications and mortality, numerous clinical trials for its treatment and prevention have been generated in a short period. This report focuses on the categories of the wide spectrum of agents being studied in the United States and the intensity of effort involved with each so that clinicians may consider whether suggesting enrollment may be appropriate for their patients.

Methods: A search was completed of the ClinicalTrials.gov database on May 28, 2020, for all such trials underway as of that date in the US. A total 190 …

Rna-Gps Predicts Sars-Cov-2 Rna Residency To Host Mitochondria And Nucleolus, Kevin E Wu, Furqan M Fazal, Kevin R Parker, James Zou, Howard Y Chang

Faculty, Staff and Students Publications

SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral RNA could, thus, play important roles in viral replication and host antiviral immune response. We perform computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes with the human transcriptome and other coronaviruses. We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched toward the host mitochondrial matrix and nucleolus, and that the 5' and 3' viral untranslated regions contain the strongest, most distinct localization signals. We interpret the mitochondrial residency signal as an …

Vaccine-Preventable Diseases In The Time Of Covid, Thaddeus Zajdowicz, Margan Zajdowicz

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Covid-19 Spread In Europe: The Soccer Connection, Bibodh J. Karki, Raghava S. Ambadapoodi, Zahid Imran, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Introduction: Mass gatherings, such as sports events, are potential causes of the rapid spread of COVID-19 infection. Millions of soccer fans travel across Europe every week. With the world’s most popular leagues continuing play until the second week of March 2020, we hypothesize that a correlation exists between the number of people attending the soccer league games in Spain, Italy, France, Germany, and the UK and the increasing number of cases of COVID-19 in these countries during the ongoing epidemic.

Methods: We calculated the total number of attendees in the five major soccer leagues from the popular sports websites and …

A Study Of Covid-19 Mortality Under Varying Patient Frailty, Alison N. Sifuentes

Theses and Dissertations

Modeled the spread and mortality of COVID-19 throughout the city of Chicago. By incorporating group frailty into a classic SEIR infectious disease model, we were able to differentiate the population of Chicago by their response to COVID-19. Three age groups with different COVID-19-induced death rates were examined, and the model sought to showcase the multiplicative deviation of each age group death rate from the average disease-induced death rate. This adjustment for different death rates among age groups accounted for heterogeneity within the population, and sought to introduce a more accurate manner for modeling the spread of infectious diseases.

Cardiac Surgery During The Coronavirus Disease 2019 Pandemic: Perioperative Considerations And Triage Recommendations, Vivek Patel, Ernesto Jimenez, Lorraine Cornwell, Trung Tran, David Paniagua, Ali E Denktas, Andrew Chou, Samuel J Hankins, Biykem Bozkurt, Todd K Rosengart, Hani Jneid

Faculty, Staff and Students Publications

The coronavirus disease 2019 pandemic, caused by severe acute respiratory syndrome coronavirus-2, represents the third human affliction attributed to the highly pathogenic coronavirus in the current century. Because of its highly contagious nature and unprecedented global spread, its aggressive clinical presentation, and the lack of effective treatment, severe acute respiratory syndrome coronavirus-2 infection is causing the loss of thousands of lives and imparting unparalleled strain on healthcare systems around the world. In the current report, we discuss perioperative considerations for patients undergoing cardiac surgery and provide clinicians with recommendations to effectively triage and plan these procedures during the coronavirus disease …

False-Negative Sars-Cov-2 Reverse Transcriptase Polymerase Chain Reaction (Rt-Pcr) Is An Important Consideration For Patient Management And Infection Prevention: A Case Report From The Louisville Covid-19 Epidemiology Study, Matthew Song Pharmd, Bcidp, Ashley M. Wilde, Sarah E. Moore Pharmd, Brian C. Bohn Pharmd, Clayton J. Patross, Bryan Denham, Paul Schulz, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

We report a case of false-negative SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) on a nasopharyngeal swab. Treating clinicians and infection preventionists should maintain a high suspicion for COVID-19 in the appropriate clinical setting despite negative test results. Utilization of chest computed tomography (CT) should be strongly considered in the diagnostic work-up for suspected COVID-19, particularly in areas with limited RT-PCR availability.

Concomitant Invasive Pneumococcal Disease In A Patient With Covid-19 – A Case Report From The Louisville Epidemiology Study, Clayton J. Patross, Brian C. Bohn Pharmd, Sarah E. Moore Pharmd, Paul Schulz, Matthew Song Pharmd, Bcidp, Ashley M. Wilde, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

A 60-year-old male presented to the emergency department (ED) with a 1–2 day history of confusion, headache, and subjective fever. Because he had met with a contact two days prior to admission who had recently traveled from the Bahamas, a COVID-19 nasopharyngeal (NP) and oropharyngeal (OP) polymerase chain reaction (PCR) test was ordered. He was diagnosed with bacterial meningitis based on presenting neurologic symptoms and the identification of Streptococcus pneumoniae from blood cultures. The COVID-19 NP and OP test returned positive, although he never developed shortness of breath, cough, other respiratory symptoms, diarrhea, abdominal pain, nausea, vomiting, or any change …

Foundational Research And Nih Funding Enabling Emergency Use Authorization Of Remdesivir For Covid-19, Ekaterina Galkina Cleary, Matthew J. Jackson, Zoë Folchman-Wagner, Fred D. Ledley

Natural & Applied Sciences Faculty Publications

Emergency Use Authorization for remdesivir months after discovery of COVID-19 is unprecedented. Typically, decades of research and public-sector funding are required to establish the mature body of foundational research requisite for efficient, targeted drug discovery and development. This work quantifies the body of research related to remdesivir’s biological target, RNA-dependent RNA polymerase (RdRp), or parent chemical structure, nucleoside analogs (NcAn), through 2019, as well as NIH funding for this research 2000–2019. There were 6,567 RdRp-related publications in PubMed, including 1,263 with NIH support, and 11,073 NcAn-related publications, including 2,319 with NIH support. NIH support for RdRp research comprised 2,203 Project …

Stroke Management In The Time Of Covid, Marwa Elnazeir, Siddharth Narayanan, Kerri Remmel

The University of Louisville Journal of Respiratory Infections

No abstract provided.

We Are Not Alone In Trying To Be Alone, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Certain diseases, like colds, tend not to stop us. A paracetamol here, an ibuprofen there, and we are on the go. That is, until we, as a species, are faced with a virus that not only spreads through social contact, but has an estimated reproductive number of 2 to 2.5 and potentially kills 3–4% of those infected (WHO, 2020). To reduce transmission probability of COVID-19, governmental agencies around the world have recommended or enforced measures to decrease social contact; early evidence suggests these measures produce the intended effect (Kucharski et al., 2020).

A Patient With Escherichia Coli Bacteremia And Covid-19 Co-Infection: A Case Report For The Louisville Covid-19 Epidemiology Study, Sarah E. Moore Pharmd, Ashley M. Wilde Pharmd, Bcps-Aqid, Matthew Song Pharmd, Bcidp, Brian C. Bohn Pharmd, Clayton J. Patross Pharmd, Bcps, Bryan Denham Md, Paul Schulz, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Patients with COVID-19 may have co-infections with other microorganisms. Here we report a case of a patient with an Escheria coli bacteremia secondary to a urinary tract infection, who experienced fevers while on active antimicrobial therapy. The patient was eventually tested for COVID-19 and found to be positive. This case emphasizes the need to suspect COVID-19 even in patients with documented bacterial infection.