Structural Insights of the SARS-CoV-2 Nucleocapsid Protein: Implications for the Inner-workings of Rapid Antigen Tests

The nucleocapsid (N) protein is an abundant component of SARS-CoV-2 and a key analyte for lateral-flow rapid antigen tests. Here, we present new structural insights for the SARS-CoV-2 N protein using cryo-electron microscopy (EM) and molecular modeling tools. Epitope mapping based on structural data supported host-immune interactions in the C-terminal portion of the protein, while other regions revealed protein-protein interaction sites. Complementary modeling results suggested that N protein structures from known variants of concern (VOC) are nearly 100% conserved at specific antibody-binding sites. Collectively, these results suggest that rapid tests that target the nucleocapsid C-terminal domain should have similar accuracy across all VOCs. In addition, our combined structural modeling workflow may guide the design of immune therapies to counter viral processes as we plan for future variants and pandemics.

SURFACE TENSION-MEDIATED PROCESSING OF WASTEWATER SAMPLES FOR SARS-CoV-2

Wastewater testing for SARS-CoV-2 has emerged as a promising tool for disease surveillance in aggregate populations. We present a novel method to rapidly extract, concentrate, and amplify viral RNA from wastewater using Exclusion-based Sample Preparation (ESP) and RT-PCR. This technology identified potential outbreaks of SARS-CoV-2 at University of Kentucky dormitories, resulting in targeted clinical testing and quarantine procedures. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

Development and Validation of a Simplified Method for Analysis of SARS-CoV-2 RNA in University Dormitories

Over the course of the COVID-19 pandemic, wastewater surveillance has become a useful tool for describing SARS-CoV-2 prevalence in populations of varying size, from individual facilities (e.g., university residence halls, nursing homes, prisons) to entire municipalities. Wastewater analysis for SARS-CoV-2 RNA requires specialized equipment, expensive consumables, and expert staff, limiting its feasibility and scalability. Further, the extremely labile nature of viral RNA complicates sample transportation, especially in regions with limited access to reliable cold chains. Here, we present a new method for wastewater analysis, termed exclusion-based sample preparation (ESP), that substantially simplifies workflow (at least 70% decrease in time;40% decrease in consumable usage compared with traditional techniques) by targeting the labor-intensive processing steps of RNA purification and concentration. To optimize and validate this method, we analyzed wastewater samples from residence halls at the University of Kentucky, of which 34% (44/129) contained detectible SARS-CoV-2 RNA. Although concurrent clinical testing was not comprehensive, student infections were identified in the 7 days following a positive wastewater detection in 68% of samples. This pilot study among university residence halls validated the performance and utility of the ESP method, laying the foundation for future studies in regions of the world where wastewater testing is not currently feasible.

County-level COVID-19 Case Fatality Rate in Medicaid Expansion States Compared to Non-Expansion States

Background. Medicaid expansion has been adopted by 38 states and the District of Columbia,1,2 contributing to lower rates of uninsured individuals in the US.3 During the COVID-19 pandemic, Medicaid enrollment offset employer-based insurance losses precipitated by the recession.4 The aim of this study was to evaluate whether Medicaid expansion may have impacted COVID-19 mortality. Methods. We conducted an ecologic study that included all US counties in the 50 states and District of Columbia. County-specific Medicaid expansion status was based on whether expansion was adopted within the state. COVID-19 cases and deaths for each county were obtained from the Centers of Disease Control (CDC). Unadjusted and multivariable negative binomial regression with robust standard errors to account for clustering of counties within each state were used to evaluate the association of COVID-19 case fatality rate and Medicaid expansion status. Adjusted models included the addition of four sets of county-level covariates thought to influence the association of Medicaid status and COVID-19 fatality rate: demographics, comorbidities, economic indicators, and physician density. These analyses were then performed in subgroups of counties defined by urbanicity (metro, suburban or rural) and quartiles of poverty rates. Incidence Rate Ratios (IRR) and 95% confidence intervals (CI) are reported. Results. A total of 1,814 Medicaid expansion and 1,328 non-expansion counties were included in the analysis. Crude case fatality rates were 2.1% (non-expansion) and 1.8% (expansion). Medicaid expansion was not associated with a significantly lower COVID-19 case fatality rate in either the unadjusted (IRR: 0.86;95% CI: 0.74, 1.01) or fully adjusted (IRR: 1.02;95% CI: 0.90, 1.16) models. In adjusted models, Medicaid expansion status was also not associated with differences in COVID-19 case fatality rate when counties were stratified by either urbanicity or percent of individuals living below the poverty line. Conclusion. In this county-level analysis, Medicaid expansion status was not associated with a significant difference in county-level COVID-19-related case fatality rates among people of all ages. Future individual-level studies are needed to better characterize the effect of Medicaid on COVID-19 mortality.

Single use nasal endoscopes - a review of the cost and organisational implications based on department size

Aim: Single use nasal endoscopes have become increasingly popular since the COVID-19 pandemic. By avoiding the risk of cross contamination and reducing exposure by eliminating the need for re-processing, the disposable scopes have clear safety benefits. Despite ENT UK guidelines recommending that disposable nasal endoscopes be available in every department for use in emergencies, they have often been considered prohibitively expensive. The aim of this study was to analyse the costs associated with traditional nasal endoscopes and compare them to the single use scopes. Method: A micro costing exercise was undertaken in three ENT departments: 2 university hospitals, and 1 district general hospital. The outcomes were compared and discussed with relation to the logistics of the departments, as well as organizational considerations. Results: Cost per procedure varied according to the reprocessing methods used in the different departments. The cost of the disposable nasal endoscopes appears high, however there are many hidden costs associated with the traditional scopes, which can be difficult to quantify accurately. Conclusions: Although disposable endoscopes appear costly, reprocessing and frequent repairs required for re-usable scopes account for the comparable cost per procedure. The high risk of COVID-19 transmission from examining the upper aerodigestive tract means that the safety benefits bear more weight in the current climate. However, concerns regarding environmental impact, image quality and storage of examinations also need to be considered.

Feasibility of a telephone-based frailty and functional assessment during COVID-19 pandemic

Background: Frailty and functional status assessment is seldom done due to time constraints and increased reliance on telehealth during COVID-19 pandemic. With the goal of increasing its clinical use, this quality improvement project aimed to determine feasibility of telephone-based frailty and functional status measurement. Methods: In 9/2020-1/2021, we identified 85 patients with serious illness in an academic geriatrics clinic. A geriatric fellow assessed functional status and conducted the Mini Nutritional Assessment, telephone-MoCA and Geriatric Depression Scale by telephone. A deficit-accumulation frailty index (FI) was calculated using an electronic medical record (EMR)-based calculator (robust <0.15, pre-frail 0.15-0.24, mildly frail 0.25-0.34, moderately frail 0.35-0.44, and severely frail ≥0.45) and a standardized documentation was generated for providers. Primary outcome was feasibility defined as the proportion of assessments completed. Secondary outcomes included administration time and providers' perception of the assessment. Results: Seventy-one (83.5%) patients were successfully assessed. There were 7 (9.9%) robust, 17 (23.9%) pre-frail, 22 (40.0%) mildly frail, 12 (16.9%) moderately frail, and 13 (18.3%) severely frail patients. Assessments of functional and nutritional domains were completed by all patients. Cognitive and mood domains were obtained from 37 patients (52.1%). Top 3 patient-level barriers to cognitive and mood assessments included advanced dementia (n=10), perception that the assessment was lengthy (n=9), and hearing impairment (n=4). Average administration time was 28 minutes (SD 7) for the complete assessment and 18 minutes (SD 8) when cognition and mood were not assessed. All five providers found the information from the assessment easy to understand, useful in understanding patient's current health status and prognosis, and useful in making clinical decisions. Conclusion: Telephone-based frailty and functional status assessment is feasible in older adults with serious illness during COVID-19 pandemic. Use of templates and an FI calculator in EMR can improve its usability. Future research should investigate more feasible cognitive and mood assessment and the impact of the assessment on health outcomes, costs and resource utilization.

Opiate Use in Hospitalized Patients with IBD Can Be Significantly Reduced Using a Proactive Pain Protocol: Results of a Randomized Controlled Trial

INTRODUCTION: Hospitalized patients with inflammatory bowel disease (IBD) are often treated with high doses of opioids, which can lead to opioid dependence, decreased quality of life, and increased mortality. We developed an evidence-based inpatient pain protocol for adults with inflammatory bowel disease (IBD) comprised of scheduled acetaminophen, celecoxib, gabapentin, and as-needed lorazepam (Table 1). In this study, we compared this proactive pain protocol to usual care in a randomized control trial. METHODS: Hospitalized, nonpregnant adults with IBD with abdominal pain and without recent surgery were randomized to the proactive pain protocol or to a standard-of-care reactive pain regimen (as-needed acetaminophen and opioids). Outcomes included daily pain (assessed by numeric rating scores, 0-10), average daily morphine milligram equivalents (MME), length of stay (LOS), need for surgery during admission, and 30-day readmission rates. Intended sample size was 166 subjects, but enrollment was halted early due to lower than expected recruitment and COVID-19 research restrictions. Subjects were analyzed per-protocol. RESULTS: Thirty-three subjects were enrolled;1 withdrew consent and was excluded from analysis. Seventeen were randomized to the proactive protocol and 15 to the reactive regimen (control group). One subject in the control group received the proactive protocol. Baseline demographics, race, type of IBD, CRP, and reason for admission were similar between the two groups. There was a significant decrease in pain over time in both groups (22.8 ± 2.8 points, P < 0.0001). Overall, those receiving the proactive protocol had numerically lower pain scores over the course of hospitalization (3.02 ± 0.90 vs 4.29 ± 0.81, P = 0.059) (Figure 1) and consumed fewer daily MME than controls (13.94 ± 5.96 vs 37.26 ± 10.51, P = 0.02) (Figure 2). There were no differences in LOS (7.3 ± 6.6 vs 7.1 ± 3.5, P = 0.66), surgery during admission (11.1% vs 21.4%, P = 0.63), and readmission (11.1% vs 14.3%, P . 0.99) between the two groups. One subject had emesis after taking celecoxib which stopped after discontinuation;no other adverse events were noted. CONCLUSION: A proactive pain protocol reduces the use of opioids and may also improve overall pain control compared with a standard, reactive pain regimen in hospitalized patients with IBD. Proactive pain control with scheduled non-opioid pain medications should be considered for patients hospitalized with IBD to reduce reliance on opioids.

Peri-operative COVID-19 infection in urgent elective surgery during a pandemic surge period: a retrospective observational cohort study.

Maintaining safe elective surgical activity during the global coronavirus disease 2019 (COVID-19) pandemic is challenging and it is not clear how COVID-19 may impact peri-operative morbidity and mortality in this population. Therefore, adaptations to normal care pathways are required. Here, we establish if implementation of a bespoke peri-operative care bundle for urgent elective surgery during a pandemic surge period can deliver a low COVID-19-associated complication profile. We present a single-centre retrospective cohort study from a tertiary care hospital of patients planned for urgent elective surgery during the initial COVID-19 surge in the UK between 29 March and 12 June 2020. Patients asymptomatic for COVID-19 were screened by oronasal swab and chest imaging (chest X-ray or computed tomography if aged ≥ 18 years), proceeding to surgery if negative. COVID-19 positive patients at screening were delayed. Postoperatively, patients transitioning to COVID-19 positive status by reverse transcriptase polymerase chain reaction testing were identified by an in-house tracking system and monitored for complications and death within 30 days of surgery. Out of 557 patients referred for surgery (230 (41.3%) women; median (IQR [range]) age 61 (48-72 [1-89])), 535 patients (96%) had COVID-19 screening, of which 13 were positive (2.4%, 95%CI 1.4-4.1%). Out of 512 patients subsequently undergoing surgery, 7 (1.4%) developed COVID-19 positive status (1.4%, 95%CI 0.7-2.8%) with one COVID-19-related death (0.2%, 95%CI 0.0-1.1%) within 30 days. Out of these seven patients, four developed pneumonia, of which two required invasive ventilation including one patient with acute respiratory distress syndrome. Low rates of COVID-19 infection and mortality in the elective surgical population can be achieved within a targeted care bundle. This should provide reassurance that elective surgery can continue, where possible, despite high community rates of COVID-19.