Browsing by Subject "Coronavirus"
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Item A Comparative Experimental and Computational Study on the Nature of the Pangolin-CoV and COVID-19 Omicron(MDPI, 2024-07-09) Wei, Lai; Song, Lihua; Dunker, A. Keith; Foster, James A.; Uversky, Vladimir N.; Goh, Gerard Kian-Meng; Biochemistry and Molecular Biology, School of MedicineThe relationship between pangolin-CoV and SARS-CoV-2 has been a subject of debate. Further evidence of a special relationship between the two viruses can be found by the fact that all known COVID-19 viruses have an abnormally hard outer shell (low M disorder, i.e., low content of intrinsically disordered residues in the membrane (M) protein) that so far has been found in CoVs associated with burrowing animals, such as rabbits and pangolins, in which transmission involves virus remaining in buried feces for a long time. While a hard outer shell is necessary for viral survival, a harder inner shell could also help. For this reason, the N disorder range of pangolin-CoVs, not bat-CoVs, more closely matches that of SARS-CoV-2, especially when Omicron is included. The low N disorder (i.e., low content of intrinsically disordered residues in the nucleocapsid (N) protein), first observed in pangolin-CoV-2017 and later in Omicron, is associated with attenuation according to the Shell-Disorder Model. Our experimental study revealed that pangolin-CoV-2017 and SARS-CoV-2 Omicron (XBB.1.16 subvariant) show similar attenuations with respect to viral growth and plaque formation. Subtle differences have been observed that are consistent with disorder-centric computational analysis.Item A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation(MDPI, 2022-09-23) Goh, Gerard Kian-Meng; Dunker, A. Keith; Foster, James A.; Uversky, Vladimir N.; Biochemistry and Molecular Biology, School of MedicineThe basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID-percentage of intrinsic disorder-of the membrane protein M, PIDM) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles in the lungs and bronchial tissues, respectively, as there is a greater level of mucus in the bronchi. The other observation revealed that there are lower viral loads in 2017-pangolin-CoV, which is predicted to have similarly low PIDN as Omicron. The abnormally hard M, which is very rarely seen in coronaviruses, arose from the fecal-oral behaviors of pangolins via exposure to buried feces. Pangolins provide an environment for coronavirus (CoV) attenuation, which is seen in Omicron. Phylogenetic study using M shows that COVID-19-related bat-CoVs from Laos and Omicron are clustered in close proximity to pangolin-CoVs, which suggests the recurrence of interspecies transmissions. Hard M may have implications for long COVID-19, with immune systems having difficulty degrading viral proteins/particles.Item An ethics framework for consolidating and prioritizing COVID-19 clinical trials(Sage, 2021) Meyer, Michelle N.; Gelinas, Luke; Bierer, Barbara E.; Chandros Hull, Sara; Joffe, Steven; Magnus, David; Mohapatra, Seema; Sharp, Richard R.; Spector-Bagdady, Kayte; Sugarman, Jeremy; Wilfond, Benjamin S.; Fernandez Lynch, Holly; Robert H. McKinney School of LawGiven the dearth of established safe and effective interventions to respond to COVID-19, there is an urgent ethical imperative to conduct meaningful clinical research. The good news is that interventions to be tested are not in short supply. Unfortunately, the human and material resources needed to conduct these trials are finite. It is essential that trials be robust and meet enrollment targets and that lower-quality studies not be permitted to displace higher-quality studies, delaying answers to critical questions. Yet, with few exceptions, existing research review bodies and processes are not designed to ensure these conditions are satisfied. To meet this challenge, we offer guidance for research institutions about how to ethically consolidate and prioritize COVID-19 clinical trials, while recognizing that consolidation and prioritization should also take place upstream (among manufacturers and funders) and at a higher level (e.g., nationally). In our proposed three-stage process, trials must first meet threshold criteria. Those that do are evaluated in a second stage to determine whether the institution has sufficient capacity to support all proposed trials. If it does not, the third stage entails evaluating studies against two additional sets of comparative prioritization criteria: those specific to the study and those that aim to advance diversification of an institution’s research portfolio. To implement these criteria fairly, we propose that research institutions form COVID-19 research prioritization committees. We briefly discuss some important attributes of these committees, drawing on the authors’ experiences at our respective institutions. Although we focus on clinical trials of COVID-19 therapeutics, our guidance should prove useful for other kinds of COVID-19 research, as well as non-pandemic research, which can raise similar challenges due to the scarcity of research resources.Item Associations between COVID-19 perceptions, anxiety, and depressive symptoms among adults living in the United States(2021-09) Wierenga, Kelly L.; Moore, Scott E.; Pressler, Susan; Hacker, Eileen; Perkins, SusanBackground: Associations among illness perceptions of viruses, anxiety and depression symptoms, and self-management decisions, such as mask-wearing, are critical to informing public health practices to mitigate the short- and long-term consequences of the SARS-CoV-2 viral pandemic. Purpose: Guided by the common-sense model of self-regulation, this observational study examined associations among illness perceptions of COVID-19, anxiety, and depression symptoms among community-dwelling adults. Method: Data were collected from 1380 adults living in the United States early in the pandemic (03-23-2020 to 06-02-2020). Participants completed online surveys. Analyses were conducted using descriptive statistics and correlations. Findings: While increased anxiety symptoms were associated with less perceived personal control, greater concern, and higher emotional responsiveness, increased depression symptoms were related to lower concern as well as greater emotional responsiveness and perceived consequences of the pandemic. Discussion: Associations among illness perceptions, anxiety, and depression symptoms may impact viral spread mitigation behavior adoption.Item Consequences of coronavirus infections for primitive and mature hematopoietic cells: new insights and why it matters(Wolters Kluwer, 2021) Ropa, James; Trinh, Thao; Aljoufi, Arafat; Broxmeyer, Hal E.; Microbiology and Immunology, School of MedicinePurpose of review: In recent history there have been three outbreaks of betacoronavirus infections in humans, with the most recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; causing Coronavirus disease 2019 [COVID-19]) outbreak leading to over two million deaths, with a rapidly rising death toll. Much remains unknown about host cells and tissues affected by coronavirus infections, including the hematopoietic system. Here, we discuss the recent findings examining effects that coronavirus infection or exposure has on hematopoietic cells and the clinical implications for these effects. Recent findings: Recent studies have centered on SARS-CoV-2, demonstrating that hematopoietic stem and progenitor cells and mature immune cells may be susceptible to infection and are impacted functionally by exposure to SARS-CoV-2 Spike protein. These findings have important implications regarding hematologic complications arising from COVID-19 and other coronavirus-induced disease, which we discuss here. Summary: Infection with coronaviruses sometimes leads to hematologic complications in patients, and these hematologic complications are associated with poorer prognosis. These hematologic complications may be caused by coronavirus direct infection or impact on primitive hematopoietic cells or mature immune cells, by indirect effects on these cells, or by a combination thereof. It is important to understand how hematologic complications arise in order to seek new treatments to improve patient outcomes.Item COVID-19 Associated leukoencephalopathy in a term neonate: imaging findings and clinical presentation(Elsevier, 2022) Murphy, Daniel A.; Wynia, Brian; Ho, Chang Y.; Radiology and Imaging Sciences, School of MedicineA 5-day old neonate presented with several episodes of seizure-like activity associated with hypoxia. The episodes were responsive to anti-epileptic medications and the infant was given empiric antibiotics and antiviral coverage. Cerebrospinal fluid polymerase chain reaction (PCR), culture, and gram stain were negative for viral or bacterial etiology. However, a nasopharyngeal PCR of the infant was positive for SARS-COV-2. While head computed tomography (CT) was negative, magnetic resonance imaging (MRI) showed evidence of white matter injury in the subcortical and periventricular regions and corpus callosum. With supportive therapies, the infant made a full neurologic recovery and was discharged following a 5-day admission. This case highlights the growing evidence of SARS-COV-2 associated leukoencephalopathy in neonates, and physicians should consider this diagnosis in neonates with similar presentation.Item COVID-19 Diagnosis and Risk of Death Among Adults With Cancer in Indiana: Retrospective Cohort Study(JMIR Publications, 2022-10-06) Valvi, Nimish; Patel, Hetvee; Bakoyannis, Giorgos; Haggstrom, David A.; Mohanty, Sanjay; Dixon, Brian E.; Surgery, School of MedicineBackground: Prior studies, generally conducted at single centers with small sample sizes, found that individuals with cancer experience more severe outcomes due to COVID-19, caused by SARS-CoV-2 infection. Although early examinations revealed greater risk of severe outcomes for patients with cancer, the magnitude of the increased risk remains unclear. Furthermore, prior studies were not typically performed using population-level data, especially those in the United States. Given robust prevention measures (eg, vaccines) are available for populations, examining the increased risk of patients with cancer due to SARS-CoV-2 infection using robust population-level analyses of electronic medical records is warranted. Objective: The aim of this paper is to evaluate the association between SARS-CoV-2 infection and all-cause mortality among recently diagnosed adults with cancer. Methods: We conducted a retrospective cohort study of newly diagnosed adults with cancer between January 1, 2019, and December 31, 2020, using electronic health records linked to a statewide SARS-CoV-2 testing database. The primary outcome was all-cause mortality. We used the Kaplan-Meier estimator to estimate survival during the COVID-19 period (January 15, 2020, to December 31, 2020). We further modeled SARS-CoV-2 infection as a time-dependent exposure (immortal time bias) in a multivariable Cox proportional hazards model adjusting for clinical and demographic variables to estimate the hazard ratios (HRs) among newly diagnosed adults with cancer. Sensitivity analyses were conducted using the above methods among individuals with cancer-staging information. Results: During the study period, 41,924 adults were identified with newly diagnosed cancer, of which 2894 (6.9%) tested positive for SARS-CoV-2. The population consisted of White (n=32,867, 78.4%), Black (n=2671, 6.4%), Hispanic (n=832, 2.0%), and other (n=5554, 13.2%) racial backgrounds, with both male (n=21,354, 50.9%) and female (n=20,570, 49.1%) individuals. In the COVID-19 period analysis, after adjusting for age, sex, race or ethnicity, comorbidities, cancer type, and region, the risk of death increased by 91% (adjusted HR 1.91; 95% CI 1.76-2.09) compared to the pre-COVID-19 period (January 1, 2019, to January 14, 2020) after adjusting for other covariates. In the adjusted time-dependent analysis, SARS-CoV-2 infection was associated with an increase in all-cause mortality (adjusted HR 6.91; 95% CI 6.06-7.89). Mortality increased 2.5 times among adults aged 65 years and older (adjusted HR 2.74; 95% CI 2.26-3.31) compared to adults 18-44 years old, among male (adjusted HR 1.23; 95% CI 1.14-1.32) compared to female individuals, and those with ≥2 chronic conditions (adjusted HR 2.12; 95% CI 1.94-2.31) compared to those with no comorbidities. Risk of mortality was 9% higher in the rural population (adjusted HR 1.09; 95% CI 1.01-1.18) compared to adult urban residents. Conclusions: The findings highlight increased risk of death is associated with SARS-CoV-2 infection among patients with a recent diagnosis of cancer. Elevated risk underscores the importance of adhering to social distancing, mask adherence, vaccination, and regular testing among the adult cancer population.Item COVID-19: Implications for Physical Activity, Health Disparities, and Health Equity(Sage, 2021-07-27) Hasson, Rebecca; Sallis, James F.; Coleman, Nailah; Kaushal, Navin; Nocera, Vincenzo G.; Keith, NiCole; Exercise & Kinesiology, School of Health and Human SciencesPhysical activity is one of the most efficacious pathways to promoting mental and physical health, preventing disease, and, most important during the COVID-19 pandemic, bolstering a stronger immune system. Efforts to “flatten the curve” have resulted in the temporary closure of exercise facilities and gyms, suspension of sport activities, and advisories to avoid public recreational spaces. All of these changes have made traditional opportunities to be physically active difficult to access. These changes have also exacerbated existing disparities in access to social and environmental supports for physical activity, potentially contributing to a widening gap in physical activity participation among those at greatest risk for COVID-19. Physical activity can play a special role in reducing the inequitable consequences of COVID-19; however, expansion and better targeting of evidence-informed interventions are needed that address the unique barriers present in communities that have been economically and socially marginalized to achieve health equity in COVID-19 outcomes. This review highlights effective and feasible strategies that provide more equitable access to physical activity programs and spaces across the United States. With a renewed investment in physical activity, this behavior can play a crucial role in improving population health and reducing disparities during the COVID-19 pandemic and beyond.Item Determination of the cycle threshold value of the Xpert Xpress SARS-CoV-2/Flu/RSV test that corresponds to the presence of infectious SARS-CoV-2 in anterior nasal swabs(American Society for Microbiology, 2024) Relich, Ryan F.; Van Benten, Kayla; Lei, Guang-Sheng; Robinson, Christopher M.; Carozza, Mariel; Sahoo, Malaya K.; Huang, ChunHong; Solis, Daniel; Sibai, Mamdouh; Myers, Christopher A.; Sikorski, Cynthia; Balagot, Caroline; Yang, David; Pinsky, Benjamin A.; Loeffelholz, Michael J.; Pathology and Laboratory Medicine, School of MedicineDespite having high analytical sensitivities and specificities, qualitative SARS-CoV-2 nucleic acid amplification tests (NAATs) cannot distinguish infectious from non-infectious virus in clinical samples. In this study, we determined the highest cycle threshold (Ct) value of the SARS-CoV-2 targets in the Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4plex) test that corresponded to the presence of detectable infectious SARS-CoV-2 in anterior nasal swab samples. A total of 111 individuals with nasopharyngeal swab specimens that were initially tested by the Xpert Xpress SARS-CoV-2 test were enrolled. A healthcare worker subsequently collected anterior nasal swabs from all SARS-CoV-2-positive individuals, and those specimens were tested by the Xpert 4plex test, viral culture, and laboratory-developed assays for SARS-CoV-2 replication intermediates. SARS-CoV-2 Ct values from the Xpert 4plex test were correlated with data from culture and replication intermediate testing to determine the Xpert 4plex assay Ct value that corresponded to the presence of infectious virus. Ninety-eight of the 111 (88.3%) individuals initially tested positive by the Xpert Xpress SARS-CoV-2 test. An anterior nasal swab specimen collected from positive individuals a median of 2 days later (range, 0–9 days) tested positive for SARS-CoV-2 by the Xpert 4plex test in 39.8% (39/98) of cases. Of these samples, 13 (33.3%) were considered to contain infectious virus based on the presence of cultivable virus and replication intermediates, and the highest Ct value observed for the Xpert 4plex test in these instances was 26.3. Specimens that yielded Ct values of ≤26.3 when tested by the Xpert 4plex test had a likelihood of containing infectious SARS-CoV-2; however, no infectious virus was detected in specimens with higher Ct values. IMPORTANCE: Understanding the correlation between real-time PCR test results and the presence of infectious SARS-CoV-2 may be useful for informing patient management and workforce return-to-work or -duty. Further studies in different patient populations are needed to correlate Ct values or other biomarkers of viral replication along with the presence of infectious virus in clinical samples.Item Early solicited adverse events following the BNT162b2 mRNA vaccination, a population survey from Saudi Arabia(Elsevier, 2021-10-11) Almohaya, Abdulellah M.; Qari, Farah; Zubaidi, Ghuzlan A.; Alnajim, Noura; Moustafa, Khadeeja; Alshabi, Malak M.; Alsubaie, Faleh M.; Almutairi, Ibrahim; Alwazna, Qusai; Al-Tawfiq, Jaffar A.; Barry, Mazin; Medicine, School of MedicinePost rollout safety for the coronavirus disease vaccines is crucial and recommended. To explore the early solicited adverse events (AE) following BNT162b2 mRNA vaccination in Saudi Arabia, we distributed an online survey to adults vaccinated with BNT162b2 over the first week of June 2021, to collect data on first (V1), second doses (V2), symptoms, severity, and outcome after an informed consent was obtained. We recruited 3639 BNT162b2 vaccinated individuals, of which one-third had received two doses, 63.3% were female, 77% were healthy, and 89% had 18–55 years of age, while only 9.8% had a history of allergy. Overall, 50.3% had any AEs after any dose, especially those younger than 55 years of age, female, history of comorbidity, and when adjusted for age and gender, lung or cardiovascular diseases. Overall, the most common AE were pain at the injection site (44%), tiredness (39%), or body ache (31%). Compared to V1, a higher rate of post-V2 systemic AE (36% vs. 51%). Most AEs started very early (within 3 days), and rarely delayed in recovery (>2 weeks). Anti-pyretic was the most commonly used (51.7%), a third of which was unnecessary. Only 1.7% required hospital admission. By multivariate analysis, predictors for admission were the presence of lung or immunocompromising diseases. In conclusion, common AEs after BNT162b2 in the real world were generally mild, self-limiting, higher after the second dose, and largely mimicking that reported in clinical trials. The causality of these AE and the persistence of post-vaccination symptoms needs to be investigated further.