Competitive Epidemic Spreading Over Networks

In this letter, we consider an epidemic model for two competitive viruses spreading over a metapopulation network, termed the 'bivirus model' for convenience. The dynamics are described by a networked continuous-time dynamical system, with each node representing a population and edges representing infection pathways for the viruses. We survey existing results on the bivirus model beginning with the nature of the equilibria, including whether they are isolated, and where they exist within the state space with the corresponding interpretation in the context of epidemics. We identify key convergence results, including the conclusion that for generic system parameters, global convergence occurs for almost all initial conditions. Conditions relating to the stability properties of various equilibria are also presented. In presenting these results, we also recall some of the key tools and theories used to secure them. We conclude by discussing the various open problems, ranging from control and network optimization, to further characterization of equilibria, and finally extensions such as modeling three or more viruses.

Myanmar's path to democracy from 2016-2021: Progress, limitations and disruptions

While the NLD's landslide election victory in November 2020 had strengthened the hopes of the people of Myanmar and the international community that the process of democratization would continue, yet another majority bagged by the NLD was a threat to the military institution and its affiliates. On February 1, 2021, the Myanmar military staged a coup: the promising chapter of Myanmar's democratic and economic transition, albeit limited in duration and reach, has come to an end, as has the Union's ongoing reintegration into the international order after roughly sixty years of isolation. Despite the coup, this chapter argues that the democratic transition much lauded in 2015 had yet to fully occur;the future of it happening remains distant, although not impossible. This chapter also highlights reflections from the periphery and the challenges faced in 2020, namely, the general election and the Covid-19 pandemic. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.

Students Experience Testing in the Implementation of the 'Gather Town' Meeting Platform as an Alternative Learning Media other than Zoom Cloud Meeting Application

The COVID-19 pandemic has limited the mobility of everyone in the world. Education is one of the most affected sectors because education systems have been done face to face. Most educational institutions switch to online learning by using online meeting platforms. We discovered an online meeting platform called 'Gather town' which looks more attractive in increasing learning motivation and may be an alternative solution for online education. This paper aims to test student experience using 'Gather Town' as a new learning medium and compare the effectiveness with Zoom Meeting Application. We compare the User Experience of both applications by letting respondents try the application and ask for feedback from our questionnaire. The result from the questionnaire shows that Gather Town has excellent potential as an alternative new learning media. © 2022 IEEE.

The uneven distribution of futurity: slow emergencies and the event of COVID-19

The ongoing COVID-19 pandemic strains conventional temporal imaginaries through which emergencies are typically understood and governed. Rather than a transparent and linear temporality, a smooth transition across the series event/disruption-response-post-event recovery, the pandemic moves in fits and starts, blurring the boundary between normalcy and emergency. This distended temporality brings into sharp relief other slow emergencies such as racism, poverty, biodiversity loss, and climate change, which inflect how the pandemic is known and governed as an emergency. In this article, we reflect on COVID-19 responses in two settler colonial societies-Australia and the United States-to consider how distinct styles of pandemic responses in each context resonate and dissonate across the racially uneven distribution of futurity that structures liberal order. In each case, the event of COVID-19 has indeed opened a window that reveals multiple slow emergencies;yet in these and other responses this revelation is not leading to meaningful changes to address underlying forms of structural violence. In Australia and the United States, we see how specific slow emergencies-human-induced climate change and anti-Black violence in White supremacist societies, respectively-become intensified as liberal order recalibrates itself in response to the event of COVID-19.

P158 A nurse-led model for tuberculosis services delivers safe and effective care

P158 Table 1 2018–2019 2020–2021 No: of patients 33 38 Disease site Pulmonary Extra-pulmonary Pulmonary Extra-pulmonary 45.5% 55.5% 23.6% 76.4% Single site Multi-Site Single Site Multi-Site 87.9% 12.1% 78.9% 21.1% Sensitivity Sensitive Drug Resistant Sensitive Drug Resistant 62.5% 37.5% 81.2% 18.8% Treatment started by: Doctor Nurse Doctor Nurse Inpatient Outpatient Inpatient Outpatient 24.1% 75.9% 0% 7.9% 71.1% 21% Days from symptom onset to treatment(median) 73 65 Total clinic appointments Face to face Virtual Face to face Virtual 503 1 339 11 Clinic appointments per patient (median) 13 13 Follow-up appointments led by Doctor Nurse Doctor Nurse 52% 48% 28% 72% Patients lost to follow-up 3 1 Hospital admissions 7 1 Patient deaths 0 1 ConclusionA nurse-led model for TB services provides safe, effective, and timely care.An expanded TBSN role with the support of a proactive, easily-accessible consultant may present a good model for TB service provision going forward.Further research is needed to test this model outside of the pandemic context.ReferencesBritish Thoracic society. Tuberculosis services during the Covid-19 pandemic. Available at https://www.brit-thoracic.org.uk/covid-19/covid-19-information-for-the-respiratory-community/

Impact of a multifaceted, outpatient antimicrobial stewardship intervention bundle on unnecessary antimicrobial prescribing in upper respiratory tract infections (URI)

Background. URIs are the most common indication for outpatient antibiotic prescribing. Given high rates of unnecessary prescribing, these indications have been identified as a high-priority target for outpatient antimicrobial stewardship programs (ASP). Our primary objective was to evaluate the impact of a system-wide, multifaceted, outpatient ASP intervention bundle on unnecessary antibiotic prescribing for URI. Methods. This quasi-experimental study was conducted from 2019 to 2021. ICD-10 codes for URIs were grouped into 3 tiers (i.e., tier I = antibiotics always indicated, tier II = sometimes, tier III = never). Encounters from 5 care specialties (i.e., family medicine, community internal medicine, express care, pediatrics, and emergency department) with a tier III URI primary ICD-10 code but without a secondary tier I or tier II code were included. COVID-19 ICD-10 codes were excluded. Interventions included construction of a prescribing data model, dissemination of clinician prescribing data and education, promotion of symptom management strategies, a patient-facing commitment poster, and a pre-populated URI order panel. Tools were designed at a system level and implemented by regional champions beginning in the 3rd quarter of 2020. The primary outcome was the rate of antibiotic prescribing, and the secondary outcome and counterbalance measure was the rate of repeat URI-related healthcare contact within 14 days. Outcomes were analyzed with chi-square with an alpha level of 0.05. Results. A total of 147403 encounters were included. The overall antibiotic prescribing rate decreased from 24.1% to 12.3% between 2019 and 2021 (p< 0.01). Significant reductions in tier III antibiotic prescribing were demonstrated for each region, care specialty, and syndrome evaluated (Table 1). A reduction in repeat healthcare contact was seen across the total cohort (9.5% in 2019 vs. 8.3% in 2021, p< 0.01);decreases in repeat contact rates were observed in those not initially receiving an antibiotic (10.3% vs. 8.6%, p< 0.01), but not in those who initially received an antibiotic (6.8% vs. 6.8%, p = 0.94). Tier III URI encounter level antimicrobial prescribing rates by region, care specialty, and syndrome Conclusion. A multifaceted, outpatient ASP intervention bundle decreased rates of unnecessary antimicrobial prescribing without increasing rates of 14-day repeat URI-related healthcare contact.

COVID-19-Associated Collapsing Glomerulopathy: A Report of Three Patients With African Ancestry

Introduction: Collapsing glomerulopathy has become an important cause of acute kidney injury (AKI) in COVID-19 patients. Reports on presentation & outcomes of COVID-19-associated collapsing glomerulopathy (COVAN) have been published. We report 3 patients who presented with COVID-19, AKI & nephrotic range proteinuria. Case Description: Patient 1: 58 year-old African American (AA) male with hypertension presented with dyspnea, was diagnosed with COVID-19 & found to have serum creatinine (SCr) of 21.5 mg/dL (baseline 0.8 mg/dL) & urine protein of 9.3 g/ day. Renal biopsy showed collapsing glomerulopathy, acute tubular injury (ATI) & severe podocyte foot process effacement. APOL1 genotyping revealed high-risk genotype (G1/ G1). Patient required 4 sessions of hemodialysis (HD) & recovered enough kidney function to discontinue HD. At 6 months follow-up, SCr was 1.6 mg/dL. Patient 2: 29 year-old AA female with sickle cell disease & previous history of collapsing glomerulopathy in remission presented with dyspnea & was diagnosed with COVID-19. SCr was 3.6 mg/ dL (baseline 0.9 mg/dL) & urine protein of 28 g/day. Renal biopsy showed focal collapse of capillary loops, severe podocyte foot process effacement, & moderate interstitial fibrosis/tubular atrophy. APOL1 genotyping revealed high-risk genotype (G1/G1). Patient was started on prednisone. SCr stabilized between 2-2.5mg/dL on discharge. At 6-month follow-up, Scr was 2.6mg/dL. Patient 3: 53 year-old AA male with hypertension presented with cough and was diagnosed with COVID-19. SCr was 3.2 mg/dL (baseline 1.1 mg/dL), with nephrotic range proteinuria (5.6 g/day). Work up revealed new diagnosis of HIV & syphilis. Renal Biopsy showed collapsing glomerulopathy. APOL-1 genotyping showed high risk genotype (G1/G1). Patient was started on treatment for COVID- 19 pneumonia & penicillin G for syphilis. Renal function & proteinuria improved within a few days, prior to initiation of HIV therapy. At 1 month follow-up, SCr was 3.0 mg/dL & at 2 years, SCr was 1.6 mg/dL. Discussion(s): Our report supports the published findings that COVAN manifests as AKI, heavy proteinuria, can occur even in the absence of severe respiratory symptoms, & is strongly associated with high-risk APOL1 genotype. Although AKI & proteinuria improved all 3 patients, all are left with some degree of chronic kidney disease.

Using natural language processing on free-Text clinical notes to identify patients with long-Term COVID effects

As of May 15th, 2022, the novel coronavirus SARS-COV-2 has infected 517 million people and resulted in more than 6.2 million deaths around the world. About 40% to 87% of patients suffer from persistent symptoms weeks or months after their original infection. Despite remarkable progress in preventing and treating acute COVID-19 conditions, the clinical diagnosis of long-Term COVID remains difficult. In this work, we use free-Text clinical notes and natural language processing (NLP) techniques to explore long-Term COVID effects. We first obtain free-Text clinical notes from 719 outpatient encounters representing patients treated by physicians at Emory Clinic to detect patterns in patients with long-Term COVID symptoms. We apply state-of-The-Art NLP frameworks to automatically identify patients with long-Term COVID effects, achieving 0.881 recall (sensitivity) score for note-level prediction. We further interpret the prediction outcomes and discuss potential phenotypes. Our work aims to provide a data-driven solution to identify patients who have developed persistent symptoms after acute COVID infection. With this work, clinicians may be able to identify patients who have long-Term COVID symptoms to optimize treatment. © 2022 Owner/Author.

Competitive epidemic spreading over networks

In this letter, we consider an epidemic model for two competitive viruses spreading over a metapopulation network, termed the ‘bivirus model’for convenience. The dynamics are described by a networked continuous-time dynamical system, with each node representing a population and edges representing infection pathways for the viruses. We survey existing results on the bivirus model beginning with the nature of the equilibria, including whether they are isolated, and where they exist within the state space with the corresponding interpretation in the context of epidemics. We identify key convergence results, including the conclusion that for generic system parameters, global convergence occurs for almost all initial conditions. Conditions relating to the stability properties of various equilibria are also presented. In presenting these results, we also recall some of the key tools and theories used to secure them. We conclude by discussing the various open problems, ranging from control and network optimization, to further characterization of equilibria, and finally extensions such as modeling three or more viruses. IEEE

Increasing Underrepresented Minority Undergraduate Student Exposure to Pediatrics via a Longitudinal Mentorship Program

Background: The United States is increasingly diverse, but representation of minorities (specifically Black/African-American) in medicine has not followed this trend. Lack of mentorship is identified as a barrier at multiple levels. We developed and piloted a mentorship program between pediatric emergency medicine (PEM) physicians and underrepresented minority (URM) undergraduate students in the Porter Scholars program (the largest African American student organization at the University of Louisville), known as the Porter Scholars in Medicine Program (PSMP). By providing robust mentorship and educational activities, our goal is to encourage students in this program to matriculate to medical school. Methods: The pilot program included clinical experiences (simulation and ultrasound), direct mentorship, connections with medical school admissions agents, and personal development programming including a book club. Students selected for the PSMP completed a survey upon entry into the program including demographic questions, as well as 5-point Likert scale questions regarding familiarity with the medical school application process, comfort with being a physician, and barriers to becoming a physician. Additionally, they received a survey after specific experiences and at the end of the year. A final survey will be sent following graduation. Data were analyzed using descriptive statistics, and Wilcoxon-Signed Rank tests were used to compare entry to end of year results. Results: Twenty-three PEM faculty, fellows and clinicians volunteered as mentors or led clinical programs in the PSMP program. Twenty-five undergraduate students were accepted into the program in fall of 2020;22(88%) completed the initial survey. Mean age was 18.6 (+/- 0.8) years, 19 (86.4%) were female. On initial surveys, the median Likert scores were: awareness of available resources to assist with medical school application 2, understanding of the medical school application process 2.5, confidence in acceptance to medical school 3, and mentor support 4. Eight (36.3%) students completed the end of year survey. For these 8 students, significant increases in median Likert scores were noted for the following categories: awareness of available resources to assist with medical school application median 3.5 (p = 0.03) and understanding of the medical school application process median 4 (p = 0.03). While not statistically significant, increases were also noted in confidence in acceptance to medical school median 4 (p = 0.10), and mentor support median 5 (p = 0.06). Student comments were generally positive though experiences were limited by the COVID 19 pandemic, see table 2. Conclusion: This pilot program demonstrates feasibility of a longitudinal mentorship program for URM premedical students which was generally well-received by students and physicians. The pandemic was a limitation, with few opportunities for in-person activities, but we look forward to more robust programing this year.

Licensed Acupuncturists' Response to the Covid-19 Pandemic in the Us: Sources and Use of Evidence to Guide Treatment With Chinese Herbal Medicine

Methods: Following IRB approval LAcs who had been prescribing CHM for COVID-related patients were recruited to complete an anonymous survey consisting of 28 questions soliciting information about demographics, modes of practice, sources of information, and treatment success. The survey was undertaken between 4/1/21 and 7/20/21. Results: Our survey was undertaken by 125 LAcs from all regions of the US. Average years in practice was 17 and 68% had received formal research training. The majority did not get infected, and of those that did most took CHM. Over 2/3 reported they had received or intended to receive the vaccine. Most treated less than 30 patients and mainly in the acute initial infectious stage. Appointments were predominantly undertaken remotely with 18% being in-person. 14% of respondents never closed their office, and 18% closed and reopened. The predominant form of CHM was granules and the duration of treatment was usually less than 20 days. A variety of information sources informed their practice. These were mainly from East Asian medical sources, but 61% reported also using biomedical sources. LAcs reported few patient deaths and little development of long-COVID. Background: Licensed acupuncturists (LAcs) in the US started using Chinese herbal medicine (CHM) to treat patients with COVID-19 related symptoms soon after the pandemic began despite little information about the use of CHM to treat COVID-19. Throughout 2020 information about the use of CHM in China was disseminated in the US, and scientific studies were published. Our study examined the critical thinking process and information sources that US LAcs used to prescribe CHM for COVID-related patients. Conclusion: LAcs in the US used CHM to treat COVID-related patients throughout the pandemic. They predominantly interacted remotely with patients, used granulated herbs, accessed information disseminated from China through collegial networks, and reported effective treatment outcomes.

A Single Center Experience with Early Initiation of ECMO Prior to Mechanical Ventilation in COVID-19 Patients with Severe ARDS

Background: Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic that results in a viral pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Prognosis is poor among those that develop acute respiratory distress syndrome and progress to mechanical ventilation. Due to the high mortality associated with mechanical ventilation and the unique physiology associated with COVID-19, we compared outcomes in COVID-19 patients placed on ECMO prior to initiation of mechanical ventilation (early group) to patients treated with ECMO after mechanical ventilation (conventional group). Methods: This is a single center retrospective analysis of COVID-19 patients placed on veno-venous (VV) ECMO between 04/06/2020 and 01/15/2021 in a tertiary high-volume ECMO center. Patients between 18 - 70 years of age with a diagnosis of SARS-CoV-2 and diagnosed with ARDS. Patients were considered for ECMO if they had a P/F ratio of less than 50 mmHg for at least three hours, a P/F ratio of less than 80 mmHg for at least 6 hours or an arterial blood pH of less than 7.25 with a pCO2 greater than or equal to 60 mmHg for at least six hours despite optimized ventilator settings (RR> 35 breaths/minute, plateau pressure ≤ 32, tidal volume of 6ml/kg of predicted body weight, FiO2 ≥ 80% and PEEP ≥ 10 cm water). A subset of patients with a rapid deterioration (rapid escalation of O2 requirements, tachypnea RR > 30, tachycardia HR >100) or with clinical signs consistent with poor tolerance to positive pressure ventilation such as a pneumothorax or pneumomediastinum were considered for ECMO prior to mechanical ventilation if they had a P/F <80 despite selfproning with either HFNC 40L/100% in addition to a nonrebreather mask with 15L/100% or non-invasive positive pressure ventilation (NIPPV) with an FiO2 100%. The primary outcome was survival to discharge assessed as a binary outcome of survived or non-survived. Secondary outcomes evaluated included discharge location, length of stay, and incidence of adverse events such as bleeding events, infection, CVA, and pneumothorax requiring chest tube placement. Results: A total of 100 patients were reviewed, including 24 early ECMO patients and 76 conventional ECMO patients. The mean age of the cohort was 48.9 + 11.5 years, 28% were female, and 74% were Hispanic. At baseline, the mean BMI was 31.6 + 5.8, 55% had a history of hypertension, 36% were diabetic and 9% had a history of asthma. Overall, 57% of patients survived to discharge with a median of 23.3 (7.8-40.6) days on ECMO. There were no significant differences in age, gender, BMI, comorbidities, or APACHE scores between the two groups. Prior to ECMO, the early group had lower P/F ratios (52.7 + 11.5 vs. 71.1 + 20.7, p <0.0001), higher pH (7.4 + 0.0 vs. 7.3 + 0.1, p <0.0001), and lower CO2 (36.1 + 6.8 vs 50.9 + 19.1, p <0.0001) than the conventional cohort. Though not significant, there was a trend towards survival in the early ECMO group compared to the conventional group (71% survival vs. 53%, p= .12). Of the early cohort, 15 patients required intubation at some point after cannulation for a median time of 2.5 days (0- 27.0 days). Of the nine patients never intubated, two patients expired, two received a lung transplant, three were discharged home, one discharged to rehab and one to an LTAC facility. There was no difference in adverse events between the two groups. Conclusions: Certain patients with severe ARDS due to COVID-19 may benefit from VV-ECMO cannulation prior to mechanical ventilation with similar outcomes and a trend towards improved mortality.

Subclavian Cannulation Strategy

Background: For patients with acute respiratory distress requiring veno-venous (VV) extracorporeal membrane oxygenation (ECMO), there are several cannulation strategies that may be used. The typical cannulation strategy for VV ECMO is either femoral-femoral or a femoral-internal jugular due to the advantage of using larger vessels to access and can typically be done at the bedside under ultrasound and x-ray guidance. However, there is concern for limited mobility and an increased risk of infection due to the location of the cannulas. VV ECMO with a dual-lumen cannula placed via the subclavian approach is an effective cannulation strategy. Case Review: 38-year-old male with a past medical history of childhood asthma and depression. He was hospitalized for respiratory failure due to COVID-19 and intubated on hospital day 2. Despite heavy sedation, paralytics, and prone positioning, his P/F ratio remained less than 50 with peak pressures in the 40s. The multidisciplinary team decided to proceed with cannulation for VV ECMO on day four of intubation. He was cannulated using a 25 French multistage cannula via the left common femoral vein and a 21 French single-stage return cannula via the right common femoral vein. He underwent a tracheostomy on ECMO day four and was able to tolerate weaning of the ventilator over the next few days. Despite only requiring a sweep gas flow of 0.5L/min on ECMO day six, the patient had worsening oxygenation and was unable to achieve a blood flow of more than 3L/min due to chatter. The chest x-ray (CXR) revealed the drainage cannula was now too high and his PaO2 decreased from 101 to 50 despite the same ventilator settings. The drainage cannula was pulled back 6cm at the bedside and flows were increased from 3L/min to 4 L/min with an increase in the PaO2 to 83. On ECMO day seven, oxygenation remained suboptimal and the CXR demonstrated a worsening pneumomediastinum, so the decision was made to transition the patient to a dual-lumen cannula in order to optimize ECMO flow and allow for more aggressive weaning of the ventilator. By ECMO day 12, he was weaned off sedation, out of bed with physical therapy, tolerating CPAP and able to Facetime with his family. ECMO support was utilized to allow for more aggressive ventilator weaning given the pneumomediastinum and increase rehab and nutrition. On ECMO day 16, he was weaned off sweep while on a T-piece with 20L 60%. He remained off sweep for 24 hours and tolerated physical therapy without requiring additional support. By day 17, he was decannulated at bedside. Discussion: By transitioning the ECMO cannulation strategy to optimize oxygenation, facilitate weaning of mechanical ventilation and allow for increased mobility, patients may be decannulated at a higher functional status than if they continued with the original cannulation strategy. Since 2020, our institution has performed 137 dual-lumen subclavian cannulations for patients on VV ECMO with a survival rate of 63%.

ECMO Specialist to Primer: Redefining the role of the RN and RT

Background: Since 2018, Methodist Hospital's ECMO program has rapidly expanded and now cares for almost 200 ECMO patients per year. In order to support this growth, an ECMO specialist pathway was created for RNs and RTs. At the inception of the ECMO specialist program, the training took an average of 6 months to complete. As the program expanded, and the COVID-19 pandemic ensued, we redefined the training and increased the frequency of courses offered to facilitate a large volume of specialists. The ECMO training has been effectively condensed and is now often completed in less than a month. In anticipation of further growth and the need for cost-efficient ECMO management, an ECMO primer role was created to operate in tandem with the ECMO team. This position redefines the role of the RN and RT, allowing them to offload perfusion services by assisting in initial cannulations, responding to ECMO related emergencies, overseeing the specialists, and building and priming circuits for future use. Methods: ECMO specialist: The specialists' role encompasses the 24-hour management of the circuit. This includes hourly circuit maintenance checks, accessing the circuit, moving an ECMO patient, and responding to circuit complications. The specialist is charged with knowing when to clamp, when to initiate the emergency back-up drive, when to emergently change the circuit, and how to respond to an acute decannulation. The training encompasses a 10-hour didactic training course and 2-day wet lab training. Didactic curriculum includes physiology, ECMO fundamentals, ECMO physiology, and ECMO management. 2-day wet lab training integrates live instruction with hands on training integrating the themes and concepts from the 10-hour course. The specialist candidates are asked to showcase their new skills on the second day in fully immersive, high-fidelity, case-based simulations. Upon completion, the specialist candidates are required to complete four shadow shifts with an ECMO specialist/primer. On the final shift, the specialist candidate will complete a skills validation before earning their ECMO specialist badge. ECMO primers: The primer role encompasses the oversight and management of all the ECMO patients and specialist, up to 24 patients. This includes collaborating in patient care and multidisciplinary rounds, management of equipment and rolling stock, educating and mentoring specialist, responding to emergencies, and advanced troubleshooting. The training encompasses baseline mastery of specialist skills, a 3-day wet lab, plus a minimum of 4 weeks of shadow shifts. The 3-day wet lab includes circuit building and priming, bedside initiation, cath lab conversions, advanced configurations, advanced troubleshooting, and circuit changes. Primers will utilize the highfidelity case-based simulations as well as cannulation simulations. Most of the primer training occurs at the bedside. Shadow shifts are scheduled with a chief primer and candidates are evaluated on bedside management, building and priming circuits, intra-hospital transport, ECMO initiation, circuit change, sterile back table set up, maximum barrier prep and drape, bedside cannulation, decannulation, and cannula reconfigurations. Candidates are formally evaluated biweekly and action plans are written to facilitate candidate success. Results: Since the launch of the program in July 2021, 280 specialists and 8 primers have completed training. By January 1st of 2022, the primer will fully offload the perfusionists in 24-hour coverage for non-CVOR ECMO management for up to 24 pumps at a time. Conclusion: By implementing both the ECMO specialist and ECMO primer roles, our ECMO program has continued to grow without compromising patient outcomes despite the pandemic. In addition to being more cost-efficient, creating an alternative growth pathway for RNs and RTs at the bedside has led to improved morale and increased staff retention.

Case Report of a COVID-19 patient treated with Seraph® 100 on Extracorporeal Life Support

Background: The Seraph® 100 Microbind ® Affinity Blood Filter (Seraph ®100) is an extracorporeal broad-spectrum sorbent hemoperfusion filter that removes pathogens and cytokines from the blood and has Emergency Use Authorization (EUA) for the treatment of severe COVID-19. Seraph® 100 can be adapted and primed to a NxStage continuous renal replacement therapy (CRRT) machine and connected to the patient's ECMO circuit. This form of hemofiltration provided a safe and effective approach to decreasing pathogen response within the blood and was tested in our center. Case Review: A 42-year-old male with a past medical history of obesity, hypertension and hypothyroidism was admitted for acute hypoxemic respiratory failure secondary to COVID-19. His 65 day ECMO course was complicated by encephalopathy, right heart dysfunction, severe epistaxis, esophageal ulcers and enterococcus faecalis bacteremia. On ECMO day 16, the patient became febrile, C-reactive protein increased to 215 mg/L and he became hypotensive. In addition to appropriate antibiotics, the multidisciplinary team decided to initiate Seraph® 100 for the E.faecalis bacteremia. The filter was adapted and primed into the NxStage machine by the nurse caring for the patient. The NxStage lines were then connected to the ECMO circuit via pigtail connections. The blood was cycled from the post-oxygenator pigtail to the NxStage and returned to the pre-oxygenator pigtail on the ECMO circuit. The target time for continuous Seraph® 100 therapy is between 24-48 hours. Cultures were collected from the NxStage line pre-filter and again, six hours later, from a port post-filter. The pre-filter cultures came back positive for E.faecalis and the post-filter cultures were negative. Additional blood cultures collected the following day remained negative. The patient's condition improved rapidly and allowed him to begin physical therapy and reduce ventilator support over the next 48 days on ECMO. He was discharged from the hospital to rehab for two weeks before going home. Discussion: Introduction of hemofiltration by Exthera provided an additional therapy that has proven to be effective in the reduction of sepsis causing pathogens when used in conjunction with conventional care for patients with COVID-19 suffering from bacteremia. In this case, incorporating hemofiltration via the ECMO circuit showed no increase in undue risk to the patient with an efficacy in decreasing bacteremia, contributing to the survival of the patient.

DEVELOPMENT of A HIGH-THROUGHPUT NGS WORKFLOW for SARS-CoV-2 WHOLE-GENOME SEQUENCING

Background: Monitoring new mutations in SARS-CoV-2 is crucial for identifying diagnostic and therapeutic targets and important insights to achieve a more effective COVID-19 control strategy. Next-generation sequencing (NGS) has been widely used for whole-genome sequencing of SARS-CoV-2. However, NGS methods may be limited by the complexity of workflow, which limits scalability. Here, we address this limitation by designing a workflow optimized for high-throughput studies. Methods: We utilized modified ARTIC network v3 primers for SARS-CoV-2 whole-genome amplification. Similar to a previously reported tailed PCR approach, libraries were prepared by a 2-step PCR method but optimized to improve amplicon balance, integrate robotic liquid handlers, and minimize amplicon dropout for viral genomes harboring primer-binding site mutation(s). Sequencing was performed on the Illumina NovaSeq 6000 and the Illumina MiSeq. An in-house analysis pipeline utilized the BWA aligner and iVar software. Assay precision was assessed with unique clinical samples. Assay sensitivity was assessed with serial dilutions of clinical samples. Robustness was assessed by sequencing samples and controls on the NovaSeq from multiple prior ARTIC v3 runs. Results: Intra-assay (n=188) and inter-assay (n=168) precision at the amino acid substitution level was 99.8% and 99.5%, respectively. Over 98.2% (111/113) of samples with a cycle threshold (Ct) <28 yielded a near-complete (≥97%) consensus sequence, and 98.7% (147/149) of samples with a Ct <30 yielded ≥90% consensus coverage. 2,688 samples and controls were sequenced in a single NovaSeq run yielding a 94.3% (2,416/2,562) sample pass rate. The optimized workflow gave more complete SARS-CoV-2 genome consensus sequences for most viral clades than the original ARTIC v3 workflow (Table). From over 65,000 clinical samples sequenced in 2021, we observed clade and lineage prevalence in-line with those documented by the CDC in 2021, including the Alpha clade that peaked at 65.3% in May, and the Delta clade that attained near-100% prevalence in September. Conclusion: We present an optimized workflow to process up to 2,688 samples in a single NovaSeq 6000 run without compromising sensitivity or robustness and with fewer amplicon dropout events compared to the standard ARTIC protocol. We additionally report results for over 65,000 SARS-CoV-2 clinical specimens collected in the United States between January and September of 2021, as part of an ongoing national genomics surveillance effort.

Automated risk assessment of covid-19 patients at diagnosis using electronic healthcare records

COVID-19 causes significant morbidity and mortality and early intervention is key to minimizing deadly complications. Available treatments, such as monoclonal antibody therapy, may limit complications, but only when given soon after symptom onset. Unfortunately, these treatments are often expensive, in limited supply, require administration within a hospital setting, and should be given before the onset of severe symptoms. These challenges have created the need for early triage of patients likely to develop life-threatening complications. To meet this need, we developed an automated patient risk assessment model using a real-world hospital system dataset with over 17,000 COVID-positive patients. Specifically, for each COVID-positive patient, we generate a separate risk score for each of four clinical outcomes including death within 30 days, mechanical ventilator use, ICU admission, and any catastrophic event (a superset of dangerous outcomes). We hypothesized that a deep learning binary classification approach can generate these four risk scores from electronic healthcare records data at the time of diagnosis. Our approach achieves significant performance on the four tasks with an area under receiver operating curve (AUROC) for any catastrophic outcome, death within 30 days, ventilator use, and ICU admission of 86.7%, 88.2%, 86.2%, and 87.8%, respectively. In addition, we visualize the sensitivity and specificity of these risk scores to allow clinicians to customize their usage within different clinical outcomes. We believe this work fulfills a clear clinical need for early detection of objective clinical outcomes and can be used for early screening for treatment intervention. © 2021 IEEE

Ruggedizing CS1 robotics: Tools and approaches for online teaching

First-year students benefit from robotics-based programming exercises by learning how to use sensors to gain information on the (changing) world surrounding the robot, how to model this information using data structures, and how to design algorithms for performing meaningful activities. Robotics-based exercises are naturally experiential and team-based and provide among the most memorable teachable moments of first-year programming courses. We summarize the pedagogical challenges that robotics-based exercises face, even under ideal circumstances, and how a university responded to these challenges. We report on the additional challenges faced in late 2020 at the same university as a result of the COVID pandemic, and how the course staff addressed these challenges using programming language implementation and network tools. The crucial components were (1) a custom-built web-based development environment with collaborative features including a built-in compiler, (2) a portable virtual machine, (3) collaborative editing, (4) open source protocols, and (5) peer-to-peer teleconferencing software. We report on the lessons learnt and how to further improve the resilience of robotics-based programming exercises. © 2021 Owner/Author.

Otolaryngology consultations for COVID-19: Determining occupational exposure and inpatient interventions

Introduction: The novel coronavirus SARS-CoV-2 has ravaged the United States and transformed the way medical care is delivered. As specialists in upper airway anatomy, otolaryngology (ENT) services may be called upon to manage various head-and-neck complaints for patients with COVID-19. While ear, nose, and throat (ENT) consults may benefit critically ill patients, they also expose physicians to the transmission of COVID-19. We sought to identify the reasons for ENT intervention and examine trends in testing through the pandemic. Method: Records for all ENT consults from May 1 to September 29, 2020, were retrospectively reviewed. Demographic information, admission diagnoses, length of stay, COVID status, and ENT interventions were recorded. Univariate analysis was performed. Results: Of 1343 distinct consults, 965 (72%) were tested for COVID-19, with 62 (4.6%) positive. In May 200 (70%) of 287 consults were tested with 2 (0.7%) positive, while in September, 251 (78.5%) of 320 consults were tested with 22 (6.9%) positive. The most common ENT consultation for COVID-positive patients was nasal and oropharyngeal bleeding (n = 19, 30.6%), followed by facial trauma (n = 15, 24.2%). Other reasons included respiratory distress, tracheostomy, and foreign body (retained COVID swab). Of 96 interventions for patients with COVID-19, 49 (51%) were for management of bleeding, 24 (25%) were for upper airway evaluation (UAE), and 8 (8.3%) were for tracheostomy or trach management. Conclusion: Although patients with COVID-19 necessitated various otolaryngologic interventions, management of bleeding was the most common complaint, which may be associated with therapeutic anticoagulation as well as coagulopathy from the disease process. Bleeding control was followed by UAE and trach management, 2 aerosol-generating procedures that may increase the risk of COVID transmission. The proportion of consults tested and confirmed positive for COVID- 19 at our institution increased from May to September, possibly assisting otolaryngologists to take appropriate preventive precautions.