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  • The ethical impact of mandating childhood vaccination: The importance of the clinical encounter

    Williamson, Laura; Institute of Public & Preventive Health (SAGE Publications, 2021-04-23)
    Health ethics can justify the use of vaccination mandates. However, policies that pressurize parents to vaccinate their children can undermine traditional clinical ethics standards (e.g. autonomy and informed consent). The aim of this paper is to argue that the ethical impact of vaccination mandates can only be determined in the context of the clinical encounter. Public debate on the topic tends to be general in nature and, as a result, issues that require clarification to help sustain the trust of service users are underexamined. In addition, ethical debates are hampered by a toxic dichotomy in the public sphere between those (anti-vaccinators) who claim a move away from parental choice is necessarily a serious ethical violation; and others (often health scientists) who neglect serious consideration of ethical issues. This predicament permits flawed ethical claims to be made, and to remain unchallenged. Despite this, ethical concerns – including those relating to trust and individual freedom – are fundamental to sustaining confidence in vaccination. This has recently been highlighted by the Covid-19 pandemic which made accessing childhood vaccinations harder, leading to a further decline in uptake. The pandemic has also revealed the strength of public feeling towards infection control measures that restrict peoples’ freedoms. In this paper I argue that to minimize the ethical disruption associated with the use of vaccination mandates, it is essential to focus more attention on their impact in the clinic and to accurately identify the drivers of such tensions.
  • A Narrative Review of Factors Historically Influencing Telehealth Use across Six Medical Specialties in the United States

    Rangachari, Pavani; Mushiana, Swapandeep S.; Herbert, Krista; Department of Interdisciplinary Health Sciences; Department of Family Medicine (MDPI, 2021-05-08)
    Prior to the COVID-19 pandemic, studies in the US have identified wide variations in telehealth use across medical specialties. This is an intriguing problem, because the US has historically lacked a standardized set of telehealth coverage and reimbursement policies, which has posed a barrier to telehealth use across all specialties. Although all medical specialties in the US have been affected by these macro (policy-level) barriers, some specialties have been able to integrate telehealth use into mainstream practice, while others are just gaining momentum with telehealth during COVID-19. Although the temporary removal of policy (coverage) restrictions during the pandemic has accelerated telehealth use, uncertainties remain regarding future telehealth sustainability. Since macro (policy-level) factors by themselves do not serve to explain the variation in telehealth use across specialties, it would be important to examine meso (organizational-level) and micro (individual-level) factors historically influencing telehealth use across specialties, to understand underlying reasons for variation and identify implications for widespread sustainability. This paper draws upon the existing literature to develop a conceptual framework on macro-meso-micro factors influencing telehealth use within a medical specialty. The framework is then used to guide a narrative review of the telehealth literature across six medical specialties, including three specialties with lower telehealth use (allergy-immunology, family medicine, gastroenterology) and three with higher telehealth use (psychiatry, cardiology, radiology) in the US, in order to synthesize themes and gain insights into barriers and facilitators to telehealth use. In doing so, this review addresses a gap in the literature and provides a foundation for future research. Importantly, it helps to identify implications for ensuring widespread sustainability of telehealth use in the post-pandemic future.
  • Implementation of a Vaccination Program Based on Epidemic Geospatial Attributes: COVID-19 Pandemic in Ohio as a Case Study and Proof of Concept

    Awad, Susanne F.; Musuka, Godfrey; Mukandavire, Zindoga; Froass, Dillon; MacKinnon, Neil J.; Cuadros, Diego F.; Department of Population Health Sciences (MDPI AG, 2021-10-25)
    Geospatial vaccine uptake is a critical factor in designing strategies that maximize the population-level impact of a vaccination program. This study uses an innovative spatiotemporal model to assess the impact of vaccination distribution strategies based on disease geospatial attributes and population-level risk assessment. For proof of concept, we adapted a spatially explicit COVID-19 model to investigate a hypothetical geospatial targeting of COVID-19 vaccine rollout in Ohio, United States, at the early phase of COVID-19 pandemic. The population-level deterministic compartmental model, incorporating spatial-geographic components at the county level, was formulated using a set of differential equations stratifying the population according to vaccination status and disease epidemiological characteristics. Three different hypothetical scenarios focusing on geographical subpopulation targeting (areas with high versus low infection intensity) were investigated. Our results suggest that a vaccine program that distributes vaccines equally across the entire state effectively averts infections and hospitalizations (2954 and 165 cases, respectively). However, in a context with equitable vaccine allocation, the number of COVID-19 cases in high infection intensity areas will remain high; the cumulative number of cases remained >30,000 cases. A vaccine program that initially targets high infection intensity areas has the most significant impact in reducing new COVID-19 cases and infection-related hospitalizations (3756 and 213 infections, respectively). Our approach demonstrates the importance of factoring geospatial attributes to the design and implementation of vaccination programs in a context with limited resources during the early stage of the vaccine rollout.
  • Global effect of COVID-19 pandemic on physical activity, sedentary behaviour and sleep among 3- to 5-year-old children: a longitudinal study of 14 countries

    Okely, Anthony D.; Kariippanon, Katharina E.; Guan, Hongyan; Taylor, Ellie K.; Suesse, Thomas; Cross, Penny L.; Chong, Kar Hau; Suherman, Adang; Turab, Ali; Staiano, Amanda E.; et al. (Springer Science and Business Media LLC, 2021-05-17)
    Background The restrictions associated with the 2020 COVID-19 pandemic has resulted in changes to young children’s daily routines and habits. The impact on their participation in movement behaviours (physical activity, sedentary screen time and sleep) is unknown. This international longitudinal study compared young children’s movement behaviours before and during the COVID-19 pandemic. Methods Parents of children aged 3–5 years, from 14 countries (8 low- and middle-income countries, LMICs) completed surveys to assess changes in movement behaviours and how these changes were associated with the COVID-19 pandemic. Surveys were completed in the 12 months up to March 2020 and again between May and June 2020 (at the height of restrictions). Physical activity (PA), sedentary screen time (SST) and sleep were assessed via parent survey. At Time 2, COVID-19 factors including level of restriction, environmental conditions, and parental stress were measured. Compliance with the World Health Organizations (WHO) Global guidelines for PA (180 min/day [≥60 min moderate- vigorous PA]), SST (≤1 h/day) and sleep (10-13 h/day) for children under 5 years of age, was determined. Results Nine hundred- forty-eight parents completed the survey at both time points. Children from LMICs were more likely to meet the PA (Adjusted Odds Ratio [AdjOR] = 2.0, 95%Confidence Interval [CI] 1.0,3.8) and SST (AdjOR = 2.2, 95%CI 1.2,3.9) guidelines than their high-income country (HIC) counterparts. Children who could go outside during COVID-19 were more likely to meet all WHO Global guidelines (AdjOR = 3.3, 95%CI 1.1,9.8) than those who were not. Children of parents with higher compared to lower stress were less likely to meet all three guidelines (AdjOR = 0.5, 95%CI 0.3,0.9). Conclusion PA and SST levels of children from LMICs have been less impacted by COVID-19 than in HICs. Ensuring children can access an outdoor space, and supporting parents’ mental health are important prerequisites for enabling pre-schoolers to practice healthy movement behaviours and meet the Global guidelines.
  • Correlates of COVID-19 Vaccine Hesitancy among a Community Sample of African Americans Living in the Southern United States

    Moore, Justin Xavier; Gilbert, Keon L.; Lively, Katie L.; Laurent, Christian; Chawla, Rishab; Li, Cynthia; Johnson, Ryan; Petcu, Robert; Mehra, Mehul; Spooner, Antron; et al. (MDPI, 2021-08-08)
    In the United States, African Americans (AAs) have been disproportionately affected by COVID-19 mortality. However, AAs are more likely to be hesitant in receiving COVID-19 vaccinations when compared to non-Hispanic Whites. We examined factors associated with vaccine hesitancy among a predominant AA community sample. We performed a cross-sectional analysis on data collected from a convenience sample of 257 community-dwelling participants in the Central Savannah River Area from 5 December 2020, through 17 April 2021. Vaccine hesitancy was categorized as resistant, hesitant, and acceptant. We estimated relative odds of vaccine resistance and vaccine hesitancy using polytomous logistic regression models. Nearly one-third of the participants were either hesitant (n = 40, 15.6%) or resistant (n = 42, 16.3%) to receiving a COVID-19 vaccination. Vaccine-resistant participants were more likely to be younger and were more likely to have experienced housing insecurity due to COVID-19 when compared to both acceptant and hesitant participants, respectively. Age accounted for nearly 25% of the variation in vaccine resistance, with 21-fold increased odds (OR: 21.93, 95% CI: 8.97–5.26–91.43) of vaccine resistance in participants aged 18 to 29 compared to 50 and older adults. Housing insecurity accounted for 8% of the variation in vaccine resistance and was associated with 7-fold increased odds of vaccine resistance (AOR: 7.35, 95% CI: 1.99–27.10). In this sample, AAs under the age of 30 and those experiencing housing insecurity because of the COVID-19 pandemic were more likely to be resistant to receiving a free COVID-19 vaccination.
  • The Effects of the COVID-19 Pandemic on Trauma Presentations in a Level One Trauma Center

    Devarakonda, Aditya K.; Wehrle, Chase J.; Chibane, Fairouz L.; Drevets, Peter D.; Fox, Elizabeth D.; Lawson, Andrew G. (SAGE Publications, 2020-11-24)
    Background: Over 28 million confirmed cases of COVID-19 have been reported to date, resulting in over 900 000 deaths. With an increase in awareness regarding the virus, the behavior of general population has changed dramatically. As activities such as driving and hospital presentation patterns have changed, our study aimed to assess the differences in trauma case variables before and during the COVID-19 pandemic. Methods: Trauma data for the period of March 1st-June 15th were compared for the years 2015-2019 (pre-COVID) and 2020 (COVID). The data were analyzed across the following categories: injury severity score, injury mechanism, motor vehicle crashes (MVCs) vs. other blunt injuries, alcohol involvement, and length of hospital stay. Results: The median injury severity score pre-COVID and during COVID was 9, representing no change. There was no difference in overall distribution of mechanism of injury; however, there was a significant decrease in the percentage of MVCs pre-COVID (36.39%) vs. COVID (29.6%, P < .05). Alcohol was significantly more likely to be involved in trauma during COVID-19 (P < .05). The mean hospital stay increased from 3.87-5.4 days during COVID-19 (P < .05). Discussion: We saw similar results to prior studies in terms of there being no change in trauma severity. Our observation that motor vehicle collisions have decreased is consistent with current data showing decreased use of motor vehicles during the pandemic. We also observed an increase in alcohol-related cases which are consistent with the reported changes in alcohol consumption since the pandemic began.
  • Estimation of epidemiological parameters for COVID-19 cases using a stochastic SEIRS epidemic model with vital dynamics

    Otunuga, Olusegun M.; Department of Mathematics (Elsevier BV, 2021-09)
    We estimate and analyze the time-dependent parameters: transmission rate, symptomatic recovery rate, immunity rate, infection noise intensities, and the effective reproduction number for the United States COVID-19 cases for the period 01/22/2020-02/25/2021 using an innovative generalized method of moments estimation scheme. We assume the disease-dynamic is described by a stochastic susceptible–exposed–infected– recovered–susceptible (SEIRS) epidemic model, where the infected class is divided into the asymptomatic infected, and symptomatic infectious classes. Stochasticity appears in the model due to fluctuations in the disease’s transmission and recovery rates. The disease eradication threshold is derived from the reproduction number. The estimated parameters are used to model the disease outbreak’s possible trajectories. Our analysis reveals that current interventions are having positive effects on the transmission and recovery rates. The analysis is demonstrated using the daily United States COVID-19 infection and recovered cases for the period: 01/22/2020-02/25/2021.
  • Human security as biosecurity

    Albert, Craig; Baez, Amado; Rutland, Joshua; Department of Social Sciences (Cambridge University Press (CUP), 2021-01-19)
    Research within security studies has struggled to determine whether infectious disease (ID) represents an existential threat to national and international security. With the emergence of SARS-CoV-2 (COVID-19), it is imperative to reexamine the relationship between ID and global security. This article addresses the specific threat to security from COVID-19, asking, “Is COVID-19 a threat to national and international security?” To investigate this question, this article uses two theoretical approaches: human security and biosecurity. It argues that COVID-19 is a threat to global security by the ontological crisis posed to individuals through human security theory and through high politics, as evidenced by biosecurity. By viewing security threats through the lens of the individual and the state, it becomes clear that ID should be considered an international security threat. This article examines the relevant literature and applies the theoretical framework to a case study analysis focused on the United States.
  • Low utilisation of bronchoscopy to assess COVID-19 respiratory infection: a multicenter experience

    Mahmood, Kamran; Abbott, Matt; Van Nostrand, Keriann; Bechara, Rabih; Gonzalez, Anne V; Brucker, Amanda; Green, Cynthia L; Polage, Christopher R; Department of Medicine (BMJ, 2021-07-23)
    Objective For the diagnosis of COVID-19, the yield of nasopharyngeal (NP) swabs is unclear, and bronchoalveolar lavage (BAL) is obtained to confirm the diagnosis. We assessed the utilisation of bronchoscopy for COVID-19 diagnosis in a multicenter study and compared the diagnostic yield of BAL versus NP swabs. Methods This retrospective study included all patients who were admitted with clinical presentation concerning for COVID-19 and underwent BAL from 1 March to 31 July 2020 at four tertiary care centres in North America. We also compared concordance of BAL with NP swabs for diagnosis of COVID-19 infection. Results Fifty-three patients, with clinical suspicion for COVID-19 and admitted for respiratory failure, underwent bronchoscopy to collect BAL for SARS-CoV-2 testing. During the same period, 2039 bronchoscopies were performed on patients not infected with COVID-19. Of 42 patients with NP swabs and BAL collected within ≤7 days, 1 was NP swab negative but positive by BAL for SARSCoV-2 (n=1/42 (2.4%)). Across a wide array of testing platforms, the overall agreement between NP swabs and BAL results was 97.6% (95% CI: 93.0% to 100%) with Cohen’s k of 0.90 (95% CI: 0.69 to 1.00). The sensitivity, specificity, positive and negative predictive values of NP swabs compared with BAL were 83.3% (95% CI: 53.5% to 100%), 100%, 100% and 97.3% (95% CI: 92.1% to 100%), respectively. Conclusions BAL was used infrequently to assess COVID-19 in busy institutions. NP swabs have a high concordance with BAL for COVID-19 testing, but negative NP swabs should be confirmed with BAL when clinical suspicion is high.
  • Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic

    Sahajpal, Nikhil S.; Mondal, Ashis K.; Ananth, Sudha; Njau, Allan; Fulzele, Sadanand; Ahaluwalia, Pankaj; Chaubey, Alka; Hegde, Madhuri; Rojiani, Amyn M.; Kolhe, Ravindra; et al. (Sage, 2021-06-29)
    The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, led to unprecedented demands assigned to clinical diagnostic laboratories worldwide, forcing them to make significant changes to their regular workflow as they adapted to new diagnostic tests and sample volumes. Herein, we summarize the modifications/adaptation the laboratory had to exercise to cope with rapidly evolving situations in the current pandemic. In the first phase of the pandemic, the laboratory validated 2 reverse transcription polymerase chain reaction–based assays to test ∼1000 samples/day and rapidly modified procedures and validated various preanalytical and analytical steps to overcome the supply chain constraints that would have otherwise derailed testing efforts. Further, the pooling strategy was validated for wide-scale population screening using nasopharyngeal swab samples and saliva samples. The translational research arm of the laboratory pursued several initiatives to understand the variable clinical manifestations that this virus presented in the population. The phylogenetic evolution of the virus was investigated using next-generation sequencing technology. The laboratory has initiated the formation of a consortium that includes groups investigating genomes at the level of large structural variants, using genome optical mapping via this collaborative global effort. This article summarizes our journey as the laboratory has sought to adapt and continue to positively contribute to the unprecedented demands and challenges of this rapidly evolving pandemic.
  • Nanobased Platforms for Diagnosis and Treatment of COVID-19: From Benchtop to Bedside

    Bidram, Elham; Esmaeili, Yasaman; Amini, Abbas; Sartorius, Rossella; Tay, Franklin R.; Shariati, Laleh; Makvandi, Pooyan; The Graduate School (American Chemical Society (ACS), 2021-05-12)
    Human respiratory viral infections are the leading cause of morbidity and mortality around the world. Among the various respiratory viruses, coronaviruses (e.g., SARSCoV-2) have created the greatest challenge and most frightening health threat worldwide. Human coronaviruses typically infect the upper respiratory tract, causing illnesses that range from common cold-like symptoms to severe acute respiratory infections. Several promising vaccine formulations have become available since the beginning of 2021. Nevertheless, achievement of herd immunity is still far from being realized. Social distancing remains the only effective measure against SARS-CoV-2 infection. Nanobiotechnology enables the design of nanobiosensors. These nanomedical diagnostic devices have opened new vistas for early detection of viral infections. The present review outlines recent research on the effectiveness of nanoplatforms as diagnostic and antiviral tools against coronaviruses. The biological properties of coronavirus and infected host organs are discussed. The challenges and limitations encountered in combating SARS-CoV-2 are highlighted. Potential nanodevices such as nanosensors, nanobased vaccines, and smart nanomedicines are subsequently presented for combating current and future mutated versions of coronaviruses.
  • High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses

    Sahajpal, Nikhil S.; Mondal, Ashis K.; Njau, Allan; Petty, Zachary; Chen, Jiani; Ananth, Sudha; Ahluwalia, Pankaj; Williams, Colin; Ross, Ted M.; Chaubey, Alka; et al. (MDPI, 2021-10-14)
    Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.
  • Infection and Immune Memory: Variables in Robust Protection by Vaccines Against SARS-CoV-2

    Ahluwalia, Pankaj; Vaibhav, Kumar; Ahluwalia, Meenakshi; Mondal, Ashis K.; Sahajpal, Nikhil; Rojiani, Amyn M.; Kolhe, Ravindra; Department of Pathology; Department of Neurosurgery (Frontiers Media, 2021-05-11)
    SARS-CoV-2 is the cause of a recent pandemic that has led to more than 3 million deaths worldwide. Most individuals are asymptomatic or display mild symptoms, which raises an inherent question as to how does the immune response differs from patients manifesting severe disease? During the initial phase of infection, dysregulated effector immune cells such as neutrophils, macrophages, monocytes, megakaryocytes, basophils, eosinophils, erythroid progenitor cells, and Th17 cells can alter the trajectory of an infected patient to severe disease. On the other hand, properly functioning CD4+, CD8+ cells, NK cells, and DCs reduce the disease severity. Detailed understanding of the immune response of convalescent individuals transitioning from the effector phase to the immunogenic memory phase can provide vital clues to understanding essential variables to assess vaccine-induced protection. Although neutralizing antibodies can wane over time, longlasting B and T memory cells can persist in recovered individuals. The natural immunological memory captures the diverse repertoire of SARS-CoV-2 epitopes after natural infection whereas, currently approved vaccines are based on a single epitope, spike protein. It is essential to understand the nature of the immune response to natural infection to better identify ‘correlates of protection’ against this disease. This article discusses recent findings regarding immune response against natural infection to SARS-CoV-2 and the nature of immunogenic memory. More precise knowledge of the acute phase of immune response and its transition to immunological memory will contribute to the future design of vaccines and the identification of variables essential to maintain immune protection across diverse populations.
  • Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

    John, Goldin; Sahajpal, Nikhil Shri; Mondal, Ashis K.; Ananth, Sudha; Williams, Colin; Chaubey, Alka; Rojiani, Amyn M.; Kolhe, Ravindra; Department of Pathology (MDPI, 2021-07-30)
    This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.
  • SalivaSTAT: Direct-PCR and Pooling of Saliva Samples Collected in Healthcare and Community Setting for SARS-CoV-2 Mass Surveillance

    Sahajpal, Nikhil S.; Mondal, Ashis K.; Ananth, Sudha; Njau, Allan; Ahluwalia, Pankaj; Newnam, Gary; Lozoya-Colinas, Adriana; Hud, Nicholas V.; Kota, Vamsi; Ross, Ted M.; et al. (MDPI, 2021-05-19)
    Objectives: Limitations of widespread current COVID-19 diagnostic testing exist in both the pre-analytical and analytical stages. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction-free RT-PCR test using commercially available RT-PCR kits. Methods: We optimized saliva collection devices, heat-shock treatment, and homogenization. Saliva samples (879) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. A five-sample pooling strategy was evaluated as per FDA guidelines. Results: Saliva collection (done without any media) showed performance comparable to that of the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95 ◦C for 30-min and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreements (NPAs) of 95.0% and 100%, respectively. The LoD was established as ~60–180 copies/mL by absolute quantification. Furthermore, a five-samplepooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively. Conclusion: We have optimized an extraction-free RT-PCR assay for saliva samples that demonstrates comparable performance to FDA-EUA assay (Extraction and RT-PCR).
  • COVID-19 RT-PCR diagnostic assay sensitivity and SARS-CoV-2 transmission: A missing link?

    Sahahjpal, Nikhil Shri; Hon, Ephrem Chin Lip; Dallaire, Stephanie; Williams, Colin; Ananth, Sudha; Mondal, Ashis K; Rojiani, Amyn M; Hegde, Madhuri; Kolhe, Ravindra; Department of Pathology (medRxiv, 2021-03-26)
    Background The sensitivity of commercially available RT-PCR assays varies over 10,000 fold, ranging from 10 to 20,000 viral copies/ml. The reporting of high Ct value results has been under scrutiny, as the clinical significance of these values is not yet completely understood. The early detection of infected individuals (high Ct results) in the pre-symptomatic phase of the disease using highly sensitive RT-PCR methods has been argued as a strategy to prevent transmission, while on the contrary, the reporting of high Ct has been criticized as false-positive results causing unnecessary testing and having several negative implications. The purpose of this study was to verify the presence of SARS-CoV-2 genomes in samples with a wide range of RT-PCR Ct values including samples with high Ct (37 to 42) using next-generation sequencing (NGS). Methods The study evaluated a total of 547 previously positive samples tested with the PerkinElmer® New Coronavirus Nucleic Acid Detection RT-PCR kit. The samples included in this study ranged from Ct values of 17-42, with 44 samples having a Ct > 37. Of the 547 samples, 149 were sequenced using PerkinElmer NEXTFLEX Variant-Seq SARS-CoV2 assay on NovaSeq 6000, and 398 samples were sequenced using Illumina SARS-CoV-2 respiratory viral panel kits using the NextSeq 500/550 system. Results Between the two clinical laboratories, a total of ~1.95 million samples were tested using the FDAEUA PerkinElmer® New Coronavirus RT-PCR assay. Of the 1.95 million samples, ~1.72 million were negative, ~250,000 positive, and ~16,500 in the range of 37-42. Of the 547 samples sequenced, the percentage of sequencing reads that aligned to the SARS-CoV-2 Wuhan-hu-1 reference genome (NC_045512.2) ranged from 25.5% to 99.69%. All samples sequenced showed high sequence specificity to the SARS-CoV-2 virus. Low Ct samples showed complete uniform coverage across the entire 29kb SAR-CoV-2 genome. The average coverage in samples with high Ct (>37) was found to be 55.5% (range 16.1-99.2%). However, as sample Ct increased, a gradual decrease in coverage uniformity was observed for few samples. Conclusion This study demonstrates for the first time that the viral RNA is present in the high Ct value range of 37- 42 and the sequence is unique to SARS-CoV-2 confirmed using two separate sequencing assays. This confirms that the detected Ct values are reflective of the presence of the SARS-CoV2 virus and they are not an artifact or contamination. In light of the recent work highlighting the majority of transmission being pre-symptomatic/ asymptomatic, and high Ct results being observed at both the early and late phases of infection warrants further investigation into the clinical utility of high Ct results to curtail the spread of the virus.
  • Isothermal amplification and fluorescent detection of SARS-CoV-2 and SARS-CoV-2 variant virus in nasopharyngeal swabs

    Jones, Les; Bakre, Abhijeet; Naikare, Hemant; Kolhe, Ravindra; Sanchez, Susan; Mosley, Yung-Yi C.; Tripp, Ralph A.; Department of Pathology (Public Library of Science (PLoS), 2021-09-17)
    The COVID-19 pandemic caused by the SARS-CoV-2 is a serious health threat causing worldwide morbidity and mortality. Real-time reverse transcription PCR (RT-qPCR) is currently the standard for SARS-CoV-2 detection. Although various nucleic acid-based assays have been developed to aid the detection of SARS-CoV-2 from COVID-19 patient samples, the objective of this study was to develop a diagnostic test that can be completed in 30 minutes without having to isolate RNA from the samples. Here, we present an RNA amplification detection method performed using reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions to achieve specific, rapid (30 min), and sensitive (<100 copies) fluorescent detection in real-time of SARS-CoV-2 directly from patient nasopharyngeal swab (NP) samples. When compared to RT-qPCR, positive NP swab samples assayed by fluorescent RT-LAMP had 98% (n = 41/42) concordance and negative NP swab samples assayed by fluorescent RT-LAMP had 87% (n = 59/68) concordance for the same samples. Importantly, the fluorescent RT-LAMP results were obtained without purification of RNA from the NP swab samples in contrast to RT-qPCR. We also show that the fluorescent RTLAMP assay can specifically detect live virus directly from cultures of both SARS-CoV-2 wild type (WA1/2020), and a SARS-CoV-2 B.1.1.7 (alpha) variant strain with equal sensitivity to RT-qPCR. RT-LAMP has several advantages over RT-qPCR including isothermal amplification, speed (<30 min), reduced costs, and similar sensitivity and specificity.
  • Acute Kidney Injury and Advanced Kidney Disease in the COVID-19 Pandemic: Proceedings From a National Kidney Foundation Symposium

    . Hirsch, Jamie S; Ikizler, Talat Alp; Sharma, Shuchita; Mohammed, Azeem; Department of Radiology and Imaging (Elsevier, 2021-04-17)
    The coronavirus disease 2019 (COVID-19) pandemic is an unprecedented and historic public health crisis that continues to expand and evolve. The National Kidney Foundation held a 2-part continuing medical education live virtual symposium on July 16 and July 24, 2020, to address the multiple challenges of COVID-19 in the context of advanced chronic kidney disease. Faculty addressed the pathophysiology, impact, risks, and management of COVID-19 as it relates to advanced kidney disease. Testing, risk mitigation, and inpatient and outpatient management were also addressed. This concise review addresses major findings of the symposium along with certain updates regarding vaccinations since then. These findings include: (1) severe COVID-19 infection has been associated with acute kidney injury, (2) it is essential to prevent and actively manage acute kidney injury to decrease mortality in these critically ill patients, (3) management of patients with advanced kidney disease should be geared toward minimizing their risk for exposure while making sure they are receiving adequate treatments, and (4) patients with kidney disease, especially ones in advanced stages, should be prioritized for vaccination.
  • Understanding the cycles of COVID-19 incidence: Principal Component Analysis and interaction of biological and socio-economic factors

    Duarte, Pablo; Riveros-Perez, Efrain; Department of Anesthesiology and Perioperative Medicine (Elsevier, 2021-06-01)
    The incidence curve of coronavirus disease 19 (COVID-19) shows cyclical patterns over time. We examine the cyclical properties of the incidence curves in various countries and use principal components analysis to shed light on the underlying dynamics that are common to all countries. We find that the cyclical series of 37 countries can be summarized in four principal components which explain over 90% of the variation. We also discuss the influence of complex interactions between biological viral natural history and socio-political reactions and measures adopted by different countries on the cyclical patterns exhibited by COVID-19 around the globe.
  • Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19

    Kolhe, Ravindra; Sahajpal, Nikhil Shri; Vyavahare, Sagar; Dhanani, Akhilesh S.; Adusumilli, Satish; Ananth, Sudha; Mondal, Ashis K.; Patterson, G. Taylor; Kumar, Sandeep; Rojiani, Amyn M.; et al. (MDPI, 2021-09-05)
    Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) is an infectious virus that causes coronavirus disease 2019 (COVID-19) transmitted mainly through droplets and aerosol affecting the respiratory tract and lungs. Little is known regarding why some individuals are more susceptible than others and develop severe symptoms. In this study, we analyzed the nasopharyngeal microbiota profile of aged patients with COVID-19 (asymptomatic vs. symptomatic) vs. healthy individuals. We examined the nasopharynx swab of 84 aged-matched patients, out of which 27 were negative asymptomatic (NegA), 30 were positive asymptomatic (PA), and 27 patients were positive symptomatic (PSY). Our analysis revealed the presence of abundant Cyanobacterial taxa at phylum level in PA (p-value = 0.0016) and PSY (p-value = 0.00038) patients along with an upward trend in the population of Litoricola, Amylibacter, Balneola, and Aeromonas at the genus level. Furthermore, to know the relationship between the nasal microbiota composition and severity of COVID-19, we compared PA and PSY groups. Our data show that the nasal microbiota of PSY patients was significantly enriched with the signatures of two bacterial taxa: Cutibacterium (p-value = 0.045) and Lentimonas (p-value = 0.007). Furthermore, we also found a significantly lower abundance of five bacterial taxa, namely: Prevotellaceae (p-value = 7 × 10−6 ), Luminiphilus (p-value = 0.027), Flectobacillus (p-value = 0.027), Comamonas (p-value = 0.048), and Jannaschia (p-value = 0.012) in PSY patients. The dysbiosis of the nasal microbiota in COVID-19 positive patients might have a role in contributing to the severity of COVID-19. The findings of our study show that there is a strong correlation between the composition of the nasal microbiota and COVID-19 severity. Further studies are needed to validate our finding in large-scale samples and to correlate immune response (cytokine Strome) and nasal microbiota to identify underlying mechanisms and develop therapeutic strategies against COVID-19.

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