Dermatologists' perceptions of using teledermatology to manage hidradenitis suppurativa

The COVID-19 pandemic has led to rapid adoption of teledermatology. Hidradenitis Suppurativa (HS) is a chronic inflammatory condition that requires recurrent clinical evaluation and may be subjected to privacy concerns amongst patients when managed over teledermatology. We assessed dermatologists' perceptions of teledermatology in managing HS. Participants were invited to completed a survey electronically via a secure online platform. The survey was disseminated to members of the Asia Pacific Hidradenitis Suppurativa Foundation and through word of mouth, over February to June 2022. Demographics and survey responses were collated. Associations between demographics and attitudes towards teledermatology for HS were evaluated by multivariable ordered logistic regression. 100 responses were obtained comprising of 76 (81.7%) dermatologists and 17 dermatology trainees (18.3%). Older physicians tended to express sentiments that it was difficult to accurately assess disease severity for HS.There was increased tendency for physicians to perceive difficulty in managing HS compared to AD (assessed as a control cohort) - in terms of photography of sensitive areas (adjusted OR 4.71 (95% confidence interval: 2.44-9.07);p value < 0.001), accurate assessment (adjusted OR 2.66 (95% confidence interval: 1.48-4.79);p value 0.001), privacy issues from examination of private body areas (adjusted OR 2.75 (95% confidence interval 1.36-5.56);p value 0.005). This study, is the first, to our knowledge that assess physician attitudes towards the use of teledermatology in managing HS patients, and compares differential perspectives of its use on HS and AD patients. Physicians' efforts should be focused on streamlining patient selection and optimizing consult environments for patients with HS.Copyright © 2023

Routine Opt out Hepatitis C Testing Upon Intake in the Philadelphia Jail System

Background: Hepatitis C (HCV) infection disproportionately affects those in United States' correctional institutions with seroprevalence rates from 17.4-23.1%. Jails have represented a particularly challenging setting for HCV testing and treatment given the short duration of stay and uncertainty of the timing of prisoners' release. Despite recommendations that all incarcerated persons undergo HCV testing, screening is not universally performed. In the Philadelphia jails, 1463 (7.5%) of the 19395 prisoners in 2018 were screened at sentencing. Method(s): On September 3, 2019 the Philadelphia jail partnered with Philadelphia FIGHT Community Health Centers to implement routine opt out HCV testing upon intake. Protocols for testing, result delivery and provider follow up were developed in a collaborative manner between the jail and FIGHT and subsequently adapted to ensure success in response to the COVID-19 pandemic. Herein, we report the findings of the first thirty-two months of routine opt out screening at intake. Result(s): Between September 3, 2019 and April 30, 2022, 27633 individuals entered the jail. 25206 (91.22%) individuals were tested for HCV antibody (ab) upon entry. 2639 (95.72%) of 2757 ab+ individuals had reflexive RNA confirmatory testing and 1892 (68.63%) were chronically infected. Of those, 950 (50.21%) were seen by a linkage coordinator from FIGHT while incarcerated, 1338 (70.72%) were seen by a jail-based HCV provider, and 619 individuals were prescribed HCV treatment. Of the treated persons, 304 (65.84%) were released from jail before completing HCV treatment, but all left jail with a full course of treatment;linkage to care to determine treatment response and ongoing medical care is in progress. Conclusion(s): Establishment of routine opt out HCV screening in a jail setting resulted in more than 90% of individuals entering the jail being screened for HCV and 32% of those with chronic infection initiating treatment. Short duration of incarceration, the need for rapid result delivery, increased linkage coordinator visits, and coordination of treatment between the jail and the community are challenges that must be addressed for successful program implementation in a jail setting. Collaboration between health care providers in the correctional system and community is necessary to coordinate HCV services in a high volume, high turnover urban jail.

SOCIAL INNOVATION AS THE NEED OF THE HOUR IN HEALTH EMERGENCIES

This chapter addresses social innovation in the context of COVID-19 and its potential to resolve complex problems, particularly how innovation emerges through shared values and collaborative relationships. Different kinds of innovations are explored with particular attention to case studies from India and Kenya. The Indian case study presents socially and culturally relevant innovations to build health infrastructure and technologically intensive innovations. In Kenya, training innovations to strengthen the child protection workforce are explored in the context of the pandemic highlighting the creative use of technology to overcome barriers and the benefits of inclusive collaboration. © 2022 selection and editorial matter, Patricia Fronek and Karen Smith Rotabi-Casares;individual chapters, the contributors.

Epiglottic Abscess in a Healthy but Unvaccinated Patient With COVID: Predilection for the Upper Airway?

Introduction: With new SARS-CoV-2 variants emerging such as Delta and Omicron, it is important to reevaluate patterns of presentation and affected patient characteristics. SARS-CoV-2 infection may be shifting from a primary insult of the lower airway to one primarily affecting the upper airway. Method(s): This is a report of a novel case of SARS-CoV-2 infection causing an epiglottic abscess during the peak of the Omicron wave. A literature review showed no previous reports of this specific entity. Result(s): An otherwise healthy, unvaccinated 25-year-old man presented with 3 days of throat pain and mild cough. He had no subjective or objective fevers, malaise, voice changes, or difficulty breathing. White blood cell count was normal. A computed tomography neck with intravenous (IV) contrast revealed edema and gas formation of the epiglottis with a small developing abscess. Flexible fiber-optic laryngoscopy showed an edematous epiglottis with prolapse posteriorly to the pharyngeal wall and mild arytenoid edema without involvement of the vocal folds. He was intubated in the operating room, and incision and drainage of the epiglottic abscess was performed. He was given steroids and broad-spectrum IV antibiotics and extubated without difficulty on postoperative day 2. Intraoperative cultures unfortunately did not speciate to guide antibiotic therapy. He continued to improve clinically and was discharged home on postoperative day 3 with a course of amoxicillin/clavulanate. Conclusion(s): This case highlights a unique presentation of COVID in a young, unvaccinated patient that was successfully managed with operative drainage. He was without any medical comorbidities or immunodeficiency. It is possible that current COVID variants have a predilection for the upper airway as evidenced by this case.

Upper Airway Manifestations of SARS-CoV-2 Infection During New York City Omicron Wave: A Single-Institution Experience

Introduction: Studies have shown that COVID-19 viral glycoproteins bind to angiotensin-converting enzyme 2 (ACE2) receptors in the airway, causing downregulation of the ACE protein and leading to angioedema-like symptoms. Further, compared with previous variants, the Omicron variant of SARS-CoV-2 appears to replicate more readily in the upper airway than in the lungs. To our knowledge, this is the first case series to explore presentations involving the upper airway in patients with SARS-CoV-2 infection during the Omicron wave of the COVID-19 pandemic. Method(s): We reviewed a case series of adult patients who presented to a single New York City emergency department between December 2021 and January 2022 with acute upper airway symptoms that prompted otolaryngology consultation and who tested positive for SARS-CoV-2. Result(s): Between December 2021 and January 2022, there were at least 3 SARS-CoV-2-positive patients who presented to the New York-Presbyterian Hospital with upper airway conditions requiring evaluation by an otolaryngologist. Conditions included supraglottitis, tracheitis, and epiglottitis. Two patients had received the COVID vaccine;1 had not. One patient required intubation;2 were maintained on room air. One patient was admitted to the intensive care unit, 1 to the step-down unit, and 1 to the floor. Length of stay varied from 3 to 11 days, 1 for nonairway issues. All 3 had methicillinsusceptible/ methicillin-resistant Staphylococcus aureus nasal swabs;2 were positive. All had respiratory viral panels that were negative. One had a throat culture that was negative. All received antibiotics. Conclusion(s): To date, there have been no studies exploring the upper airway manifestations of SARS-CoV-2 infection in the Omicron wave. These data provide important clinical correlates that are highly relevant to otolaryngologists.

Comparing Course Outcomes of Hybrid Delivery with Classroom-based Instruction in an Introductory Engineering Management Course

An undergraduate engineering management course for engineers was strategically implemented to allow greater agility through a hybrid delivery approach given the disruption and uncertainty of the COVID-19 pandemic. The course reaches approximately 100 students per semester with the redesign focused on activity-based learning and increased flexibility. The goal was to provide a learning environment capable of agile delivery in the face of changing conditions while still meeting ABET learning outcomes. Results from sections from 2020 revealed strong student satisfaction, but no quantitative assessment was completed to determine how progress in learning outcomes compared to traditional classroom-based lectures. This research compares cross-sectional, preliminary performance in measured ABET outcomes between the hybrid section with a traditional classroom-based section. Sections from Spring 2020 through Fall 2021 are used in the comparison. End of course surveys and assessment data were also used to evaluate student satisfaction and inform future iterations for both courses. Hybrid delivery included expanded use of team case analyses, course pack activities covering concepts and terms, and increased summative assessments. The classroom-based section employed in-class clicker-based activities, formalized lectures presenting concepts and terms, and traditional exams. Mid-semester feedback mechanisms were used as part of the Hybrid course design and implemented as appropriate for the final half of the relevant semester. Results show that ABET thresholds were met for both hybrid and classroom-based delivery methods, with no notable differences. Student satisfaction as evidenced by end of course surveys was higher for the hybrid delivery section, with similar response rates. Enrollment in the hybrid section was higher when both formats were offered concurrently. Future work will consider longitudinal analysis of learning outcomes as well as student preferences in non-pandemic conditions. Lessons learned from hybrid delivery will also be considered for use in classroom-based environments. © American Society for Engineering Education, 2022.

<span contenteditable="false" data-cke-magic-line="1" style="width: 695px;height: 0px;padding: 0px;margin: 0px;display: block;z-index: 9999;color: rgb(255,255,255);font-size: 0px;line-height: 0px;position: absolute;border-top: 1px dashed rgb(255,0,0);user-select: none;left:-2px;top: 64.2px;"><span style="color:#ffffff"> </span><span style="color:#ffffff"> </span><span style="color:#ffffff">?</span></span>Estimating daily ground-level NO2 concentrations over China based on TROPOMI observations and machine learning approach

Nitrogen dioxide (NO2) is an important target for monitoring atmospheric quality. Deriving ground-level NO2 concentrations with much finer resolution, it requires high-resolution satellite tropospheric NO2 column as input and a reliable estimation algorithm. This paper aims to estimate the daily ground-level NO2 concentrations over China based on machine learning models and the TROPOMI NO2 data with high spatial resolution. In this study, four tree-based algorithm machine learning models, decision trees (DT), gradient boost decision tree (GBDT), random forest (RF) and extra-trees (ET), were used to estimate ground-level NO2 concentrations. In addition to considering many influencing factors of the ground-level NO2 concentrations, we especially introduced simplified temporal and spatial information into the estimation models. The results show that the extra-trees with spatial and temporal information (ST-ET) model has great performance in estimating ground-level NO2 concentrations with a cross-validation R-2 of 0.81 and RMSE of 3.45 mu g/m(3) in test datasets. The estimated results for 2019 based on the ST-ET model achieves a satisfactory accuracy with a cross-validation R-2 of 0.86 compared with the other models. Through time-space analysis and comparison, it was found that the estimated high-resolution results were consistent with the ground observed NO2 concentrations. Using data from January 2020 to test the prediction power of the models, the results indicate that the ST-ET model has a good performance in predicting ground-level NO2 concentrations. Taking four ground-level NO2 concentrations hotspots as examples, the estimated ground-level NO2 concentrations and ground-based observation data during the coronavirus disease (COVID-19) pandemic were lower compared with the same period in 2019. The findings offer a solid solution for accurately and efficiently estimating ground-level NO2 concentrations by using satellite observations, and provide useful information for improving our understanding of the regional atmospheric environment.

SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2 (SARSCoV- 2) VACCINE-INDUCED THYROID DYSFUNCTION: A TALE OF TWO PATIENTS

Introduction SARS-CoV-2 vaccine has been the main pillar in battling the coronavirus disease 2019 (COVID-19) pandemic. However, the current vast scale of SARS-CoV-2 vaccination programme has led to inevitable reports of various adverse reactions, one of which include thyroid dysfunction. CASES We describe two patients who manifested hyperthyroidism following BNT162b2 mRNA-based COVID-19 vaccine boosters. Patient 1, a previously euthyroid 46-year-old female, has an eight-year history of type 1 diabetes mellitus. She developed palpitations of increasing severity about two weeks after her COVID-19 booster vaccine on 20th January 2022. She had weight loss of 4 kg and experienced menstrual irregularities in the subsequent three months. Examination revealed tachycardia (112 beats per minute, regular) and bilateral fine tremors of the hands. There was no goitre or neck tenderness. Blood investigations showed overt hyperthyroidism with positive thyroid autoantibodies, consistent with Graves' disease. Treatment with carbimazole led to marked symptomatic improvement. Patient 2, a 38-year-old female with a six-year history of Hashimoto thyroiditis, was clinically and biochemically euthyroid while taking levothyroxine 100 mcg daily prior to her COVID-19 booster vaccine on 5th January 2022. Five weeks following the vaccine, her thyroid function test during her endocrine clinic appointment showed overt hyperthyroidism, which was confirmed by a second blood sample ten days later. There was neither a change in levothyroxine dose nor any additional supplement intake. She was otherwise asymptomatic. Levothyroxine was then withheld. She regained her baseline hypothyroid state two weeks later, during which levothyroxine was resumed. Conclusion SARS-CoV-2 vaccine-induced thyroid dysfunction can affect both euthyroid and hypothyroid patients. A history of recent COVID-19 vaccination should be included in the clinical evaluation of a newly diagnosed hyperthyroid patient or unexplained hyperthyroidism in a long-standing hypothyroid patient.

Chemokines, soluble PD-L1, and immune cell hyporesponsiveness are distinct features of SARS-CoV-2 critical illness.

Critically ill patients manifest many of the same immune features seen in coronavirus disease 2019 (COVID-19), including both "cytokine storm" and "immune suppression." However, direct comparisons of molecular and cellular profiles between contemporaneously enrolled critically ill patients with and without severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are limited. We sought to identify immune signatures specifically enriched in critically ill patients with COVID-19 compared with patients without COVID-19. We enrolled a multisite prospective cohort of patients admitted under suspicion for COVID-19, who were then determined to be SARS-CoV-2-positive (n = 204) or -negative (n = 122). SARS-CoV-2-positive patients had higher plasma levels of CXCL10, sPD-L1, IFN-γ, CCL26, C-reactive protein (CRP), and TNF-α relative to SARS-CoV-2-negative patients adjusting for demographics and severity of illness (Bonferroni P value < 0.05). In contrast, the levels of IL-6, IL-8, IL-10, and IL-17A were not significantly different between the two groups. In SARS-CoV-2-positive patients, higher plasma levels of sPD-L1 and TNF-α were associated with fewer ventilator-free days (VFDs) and higher mortality rates (Bonferroni P value < 0.05). Lymphocyte chemoattractants such as CCL17 were associated with more severe respiratory failure in SARS-CoV-2-positive patients, but less severe respiratory failure in SARS-CoV-2-negative patients (P value for interaction < 0.01). Circulating T cells and monocytes from SARS-CoV-2-positive subjects were hyporesponsive to in vitro stimulation compared with SARS-CoV-2-negative subjects. Critically ill SARS-CoV-2-positive patients exhibit an immune signature of high interferon-induced lymphocyte chemoattractants (e.g., CXCL10 and CCL17) and immune cell hyporesponsiveness when directly compared with SARS-CoV-2-negative patients. This suggests a specific role for T-cell migration coupled with an immune-checkpoint regulatory response in COVID-19-related critical illness.

COMMUNICATION CHALLENGES BETWEEN DOCTORS & RELATIVES DURING THE COVID-19 PANDEMIC: SIMPLE INTERVENTIONSWITH MEANINGFUL IMPACT

Background: & Aims Visiting restrictions during the COVID-19 pandemic resulted in reduced and inconsistent communication with the next-of-kin of elderly inpatients. This project aimed to improve communication between doctors and patients' relatives in accordance with the GMC Good Medical Practice guidelines which outline that doctors 'must be considerate to those close to the patient and be sensitive and responsive in giving them information and support'. Methods: We created a virtual whiteboard on an elderly care ward in an inner London hospital documenting patient demographics, details of named next-of-kin and when they had been contacted. We aimed to update next-of-kin within 48-hours of ward admission and subsequently twice weekly. The outcome was measured via identical 'pre- and postintervention' questionnaires recording the next-of-kin's satisfaction with communication from the doctors. Questionnaires included 11 questions utilising a 5-point Likert scale for satisfaction. Results: were anonymised and analysed using Microsoft Excel. Results: Satisfaction with communication improved in 10 of the 11 domains of the questionnaire following intervention. Cumulative satisfaction scores post-intervention (N = 13) in comparison to pre-intervention (N= 25) were closer to the total possible satisfaction score per question for these 10 domains. The mean cumulative satisfaction score across all domains was 60% post-intervention compared with 44% pre-intervention. Satisfaction following intervention was particularly improved in the domains of frequency of communication (60% post-intervention. 32.8% pre-intervention) and how adequately questions and concerns were addressed (69.2% post-intervention;45.6% pre-intervention). Conclusion: During the COVID-19 pandemic healthcare professionals have had to adapt in communicating with patients' next-of-kin. Our Introduction: of robust standards and a virtual whiteboard to track communication resulted in improved satisfaction and proved useful in adapting to remote communication. We propose that similar practice and standards are extended across additional wards to encourage widespread optimal and consistent communication between doctors and patients' relatives, an integral part of patient care.

Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas.

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.

Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma

Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, andSARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer 160 was 80% or greater with anti-RBD or anti-ECD titers of 1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers 160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of 1:1350, and evidence of VN1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of1:1350 may provide critical information about protection against COVID-19 disease.

Healthcare Personnel Perceived Benefit of Infection Prevention Strategies during COVID

Background. During the COVID-19 pandemic, many infection prevention policy and practice changes were introduced to mitigate hospital transmission. Although each change had evidence-based infection prevention rationale, healthcare personnel (HCP) may have variable perceptions of their relative values. Methods. Between October-December 2020, we conducted a voluntary, anonymous, IRB-approved survey of UNC Medical Center HCP regarding their views on personal protective equipment (PPE) and hospital policies designed to prevent COVID acquisition. The survey collected occupational and primary work location data (COVID unit or not) as well as their views on specific infection prevention practices during COVID. Chi squared tests (two tailed) were used to compare differences in the proportions. Results. The overall results are displayed (Figure). Among the 694 HCP who responded to the survey, we found HCP were largely (68%) satisfied that the organization was taking all the necessary measures to protect them from COVID-19. A significantly greater proportion (14% more) of HCP (81.7% compared to 67.6%;95% CI of difference 9.4-18.5%, P< 0.0001) agreed that all PPE was available to them compared to those who were confident that the organization was taking necessary steps for protection, highlighting that safety is more than simply availability of supplies. More than 90% felt that daily screening of patients/visitors and patient/visitor mask requirements were important for protecting them from acquiring COVID in the workplace and that wearing a mask themselves was a key intervention for protecting others. Fewer HCP (72-80%), although still a majority, perceived that eye protection and daily symptom screening for HCP were beneficial. Symptom screening for patients/visitors was perceived by 19% more HCP (90.9% compared to 72.2%;95% CI of difference 15-23%) to be beneficial than symptom screening of HCP (P< 0.0001). Conclusion. Although infection prevention strategies were implemented based on evidence and in alignment with CDC recommendations, it is important to acknowledge that the perception and acceptance of these recommendations varied among our HCP. Compliance can only be optimized with key interventions when we seek to understand the perceptions of our staff.

Resident travel path planning based on risk assessment of epidemic-related areas

Aiming at the problem of residents' need to travel during the epidemic, this paper designs a risk assessment method based on the spatial interaction of space-time objects in the epidemic-related area, and evaluates the epidemic risk in the associated area based on an improved gravity model and a one-dimensional steady-state water quality migration model. Based on the Floyd algorithm and according to the residents' choice preferences, an optimal path solution model that simultaneously considers the epidemic risk factor and travel distance is established and the algorithm is verified. An actual road network in Shenyang City was used for example verification, and the difference between the path guidance during the regular period and the epidemic period was compared. The results show that the improved Floyd algorithm can effectively avoid epidemic-related areas. As residents increase their preference for risk avoidance, the length of the guide path will gradually increase, but the risk of infection will gradually decrease. © 2021 SPIE.

Disaster planning in the age of pandemics

The COVID-19 pandemic impacts are deep and pervasive;the far-reaching consequences are only beginning to be understood. In addition to the tragic direct impacts such as deaths and hospitalizations, indirect impacts have devastated the global economy. Supply chain disruptions, quarantine restrictions, and travel bans, as well as other factors, have resulted in a projected 5-8% contraction of the global GDP for 2020 [1]. Disaster planning and risk management are mature fields with extensive literature, yet businesses across the globe were largely unprepared to respond to this crisis due to high levels of emergent conditions. This research examines pandemic-induced crises and argues that the unique nature of these crises makes existing theories and models insufficient to help business practitioners before or during such an event. A confirmatory approach was used to develop a model of key attributes of the more successful companies. This model is supported by empirical performance data that was collected and analyzed using structural equation modeling (SEM). The relatively new concept of “transiliency”, or “the ability to simultaneously restore some processes and change-often radically-others” [2] is also discussed as a characteristic possessed by companies exhibiting better performance during the COVID-19 crisis. This research can be harnessed by engineering managers to create actionable strategies for disaster response and recovery. © 2021 IISE Annual Conference and Expo 2021. All rights reserved.

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein.

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.

Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas.

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.