Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation (preprint)

The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.

The increase in medical admissions with anorexia nervosa during the COVID-19 pandemic in Western Australia.

OBJECTIVE: A comparative study to describe the increase in medical admissions of children and adolescents with anorexia nervosa (AN) in Western Australia in 2019 (pre-pandemic) and 2020 (peri-pandemic). METHOD: Patient demographics, physiological parameters, length of stay, time to assessment by the Eating Disorder Service (EDS), and commencement of specialist eating disorder (ED) outpatient treatment was collected for adolescents admitted with AN between 1st January 2019 and 31st December 2020. RESULTS: The number of admissions doubled from 126 in 2019 to 268 in 2020. The number of children admitted increased by 52%. The median length of hospital stay was shorter in 2020 (12 vs. 17 days; p < .001), but the 28-day readmission rate was greater (39.9% vs. 22.2%; p < .001). At the time of hospital discharge in 2020, only 60% of patients were able to step-down into specialist ED outpatient treatment, compared to 93% in 2019. The mean number of admissions per child before completing EDS assessment increased significantly in 2020 (2.75 vs. 0, p < .001). DISCUSSION: Shorter inpatient stays and delays in the commencement of specialist ED outpatient treatment may have contributed to the increased readmission rate seen in 2020. PUBLIC SIGNIFICANCE: This research is important as it explores the reasons for increased medical presentations and admissions of youth with AN during the COVID-19 pandemic in Western Australia. We hope that our lessons learned may be helpful to others trying to balance similar clinical workloads.

Myopericarditis following COVID-19 vaccination in adolescent triplets.

Multiple studies have reported myocarditis and pericarditis after the Pfizer-BioNTech coronavirus disease 2019 messenger ribonucleic acid vaccine. We describe male adolescent triplets who presented with myopericarditis within one week following vaccine administration.

BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children.

Currently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of variants of concerns (VOCs) has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine-induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of VOCs that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine-induced antibody titers in children 5-11 years receiving two doses of the age-recommended 10 µg dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12-15 years) or adults receiving the 30 µg dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-VOC responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to VOCs in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2-induced antibody response in children, vaccine-induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to the attenuation of disease.

Viral infectivity in pediatric SARS-CoV-2 clinical samples does not vary by age (preprint)

During the early months of the SARS-CoV-2 pandemic, notable uncertainty emerged regarding the role of children in transmission dynamics. With time, it became more clear that children were susceptible to infection with SARS-CoV-2, but that the vast majority of children experienced mild symptoms with lower incidence of severe disease. This pattern remained consistent despite the later emergence of SARS-CoV-2 variants, including Delta and Omicron, even among children <5 ineligible for vaccination. The relative lack of severe disease in the pediatric population raised questions regarding viral kinetics and infectivity in children versus adults. We hypothesized that unique virologic features in children could explain this apparent decrease in symptoms and transmissibility early in the pandemic.

Characteristics and outcome of COVID-19 patients admitted to the ICU: a nationwide cohort study on the comparison between the first and the consecutive upsurges of the second wave of the COVID-19 pandemic in the Netherlands

BackgroundTo assess trends in the quality of care for COVID-19 patients at the ICU over the course of time in the Netherlands.MethodsData from the National Intensive Care Evaluation (NICE)-registry of all COVID-19 patients admitted to an ICU in the Netherlands were used. Patient characteristics and indicators of quality of care during the first two upsurges (N = 4215: October 5, 2020–January 31, 2021) and the final upsurge of the second wave, called the ‘third wave’ (N = 4602: February 1, 2021–June 30, 2021) were compared with those during the first wave (N = 2733, February–May 24, 2020).ResultsDuring the second and third wave, there were less patients treated with mechanical ventilation (58.1 and 58.2%) and vasoactive drugs (48.0 and 44.7%) compared to the first wave (79.1% and 67.2%, respectively). The occupancy rates as fraction of occupancy in 2019 (1.68 and 1.55 vs. 1.83), the numbers of ICU relocations (23.8 and 27.6 vs. 32.3%) and the mean length of stay at the ICU (HRs of ICU discharge = 1.26 and 1.42) were lower during the second and third wave. No difference in adjusted hospital mortality between the second wave and the first wave was found, whereas the mortality during the third wave was considerably lower (OR = 0.80, 95% CI [0.71–0.90]).ConclusionsThese data show favorable shifts in the treatment of COVID-19 patients at the ICU over time. The adjusted mortality decreased in the third wave. The high ICU occupancy rate early in the pandemic does probably not explain the high mortality associated with COVID-19.

BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children (preprint)

Currently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of novel variants of concerns has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of variants of concern that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine induced antibody titers in children 5-11 years receiving two doses of the age recommended 10 g dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12-15 years) or adults receiving the 30 g dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-variants of concern responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to variants of concern (VOCs) in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2 induced antibody response in children, vaccine induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to attenuation of disease.

Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children.

Emergent SARS-CoV-2 variants and waning humoral immunity in vaccinated individuals have resulted in increased infections and hospitalizations. Children are not spared from infection nor complications of COVID-19, and the recent recommendation for boosters in individuals ages 12 years or older calls for broader understanding of the adolescent immune profile after mRNA vaccination. We tested the durability and cross-reactivity of anti-SARS-CoV-2 serologic responses over a six-month time course in vaccinated adolescents against the SARS-CoV-2 D614G ("wild type") and Omicron antigens. Serum from 77 adolescents showed that anti-Spike antibodies wane significantly over six months. After completion of a two-vaccine series, cross-reactivity against Omicron-specific receptor-binding domain (RBD) was seen. Functional humoral activation against wild type and Omicron SARS-CoV-2 also declines over time in vaccinated adolescent children. Evidence of waning mRNA-induced vaccine immunity underscores vulnerabilities in long-term pediatric protection against SARS-CoV-2 infection, while cross-reactivity highlights the additional benefits of vaccination. Characterization of adolescent immune signatures post-vaccination will inform guidance on vaccine platforms and timelines, and ultimately optimize immunoprotection of children.

An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples.

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.

Empowering Equitable Data Use Partnerships and Indigenous Data Sovereignties Amid Pandemic Genomics.

The COVID-19 pandemic has inequitably impacted Indigenous communities in the United States. In this emergency state that highlighted existing inadequacies in US government and tribal public health infrastructures, many tribal nations contracted with commercial entities and other organization types to conduct rapid diagnostic and antibody testing, often based on proprietary technologies specific to the novel pathogen. They also partnered with public-private enterprises on clinical trials to further the development of vaccines. Indigenous people contributed biological samples for assessment and, in many cases, broadly consented for indefinite use for future genomics research. A concern is that the need for crisis aid may have placed Indigenous communities in a position to forego critical review of data use agreements by tribal research governances. In effect, tribal nations were placed in the unenviable position of trading short-term public health assistance for long-term, unrestricted access to Indigenous genomes that may disempower future tribal sovereignties over community members' data. Diagnostic testing, specimen collection, and vaccine research is ongoing; thus, our aim is to outline pathways to trust that center current and future equitable relationship-building between tribal entities and public-private interests. These pathways can be utilized to increase Indigenous communities' trust of external partners and share understanding of expectations for and execution of data protections. We discuss how to navigate genomic-based data use agreements in the context of pathogen genomics. While we focus on US tribal nations, Indigenous genomic data sovereignties relate to global Indigenous nations regardless of colonial government recognition.

Tracheotomy in the SARS-CoV-2 pandemic.

The severe acute respiratory syndrome (SARS)-CoV-2 pandemic continues to produce a large number of patients with chronic respiratory failure and ventilator dependence. As such, surgeons will be called upon to perform tracheotomy for a subset of these chronically intubated patients. As seen during the SARS and the SARS-CoV-2 outbreaks, aerosol-generating procedures (AGP) have been associated with higher rates of infection of medical personnel and potential acceleration of viral dissemination throughout the medical center. Therefore, a thoughtful approach to tracheotomy (and other AGPs) is imperative and maintaining traditional management norms may be unsuitable or even potentially harmful. We sought to review the existing evidence informing best practices and then develop straightforward guidelines for tracheotomy during the SARS-CoV-2 pandemic. This communication is the product of those efforts and is based on national and international experience with the current SARS-CoV-2 pandemic and the SARS epidemic of 2002/2003.

Impact of the COVID-19 Pandemic on Breast Imaging Education.

OBJECTIVE: To determine the impact of the COVID-19 pandemic on breast imaging education. METHODS: A 22-item survey addressing four themes during the early pandemic (time on service, structured education, clinical training, future plans) was emailed to Society of Breast Imaging members and members-in-training in July 2020. Responses were compared using McNemar's and Mann-Whitney U tests; a general linear model was used for multivariate analysis. RESULTS: Of 136 responses (136/2824, 4.8%), 96 U.S. responses from radiologists with trainees, residents, and fellows were included. Clinical exposure declined during the early pandemic, with almost no medical students on service (66/67, 99%) and fewer clinical days for residents (78/89, 88%) and fellows (48/68, 71%). Conferences shifted to remote live format (57/78, 73%), with some canceled (15/78, 19%). Compared to pre-pandemic, resident diagnostic (75/78, 96% vs 26/78, 33%) (P < 0.001) and procedural (73/78, 94% vs 21/78, 27%) (P < 0.001) participation fell, as did fellow diagnostic (60/61, 98% vs 47/61, 77%) (P = 0.001) and procedural (60/61, 98% vs 43/61, 70%) (P < 0.001) participation. Most thought that the pandemic negatively influenced resident and fellow screening (64/77, 83% and 43/60, 72%, respectively), diagnostic (66/77, 86% and 37/60, 62%), and procedural (71/77, 92% and 37/61, 61%) education. However, a majority thought that decreased time on service (36/67, 54%) and patient contact (46/79, 58%) would not change residents' pursuit of a breast imaging fellowship. CONCLUSION: The pandemic has had a largely negative impact on breast imaging education, with reduction in exposure to all aspects of breast imaging. However, this may not affect career decisions.

Digital Solutions to Alleviate the Burden on Health Systems During a Public Health Care Crisis: COVID-19 as an Opportunity.

The COVID-19 pandemic has generated unprecedented and sustained health management challenges worldwide. Health care systems continue to struggle to support the needs of the majority of infected individuals that are either asymptomatic or have mild symptoms. In addition, long-term effects in the form of long-lasting COVID-19 symptoms or widespread mental health issues aggravated by the pandemic pose a burden on health care systems worldwide. This viewpoint article considers aspects of digital health care solutions and how they can play an ongoing role in safely addressing gaps in the health care support available from initially and repeatedly overwhelmed providers and systems. Digital solutions can be readily designed to address this need and can be flexible enough to adapt to the evolving management requirements of various stakeholders to reduce COVID-19 infection rates, acute hospitalizations, and mortality. Multiplatform solutions provide a hybrid model of care, which can include mobile and online platforms accompanied by direct clinician input and feedback. Desirable components to be included are discussed, including symptom tracking, patient education, well-being support, and bidirectional communication between patients and clinicians. Customizable and scalable digital health platforms not only can be readily adapted to further meet the needs of employers and public health stakeholders during the ongoing pandemic, but also hold relevance for flexibly meeting broader care management needs into the future.

All Hands-On Deck and All Decks on Hand: Surmounting Supply Chain Limitations During the COVID-19 Pandemic.

Testing during the COVID-19 pandemic has been crucial to public health surveillance and clinical care. Supply chain constraints-spanning limitations in testing kits, reagents, pipet tips, and swabs availability-have challenged the ability to scale COVID-19 testing. During the early months, sample collection kits shortages constrained planned testing expansions. In response, the University of Vermont Medical Center, University of Vermont College of Medicine, Vermont Department of Health Laboratory, Aspenti Health, and providers across Vermont including 16 area hospitals partnered to surmount these barriers. The primary objectives were to increase supply availability and manage utilization. Within the first month of Vermont's stay-at-home order, the University of Vermont Medical Center laboratory partnered with College of Medicine to create in-house collection kits, producing 5000 per week. University of Vermont Medical Center reassigned 4 phlebotomists, laboratory educators, and other laboratory staff, who had reduced workloads, to participate (requiring a total of 5.3-7.6 full-time equivalent (FTE) during the period of study). By August, automation at a local commercial laboratory produced 22,000 vials of media in one week (reducing the required personnel by 1.2 FTE). A multisite, cross-institutional approach was used to manage specimen collection kit utilization across Vermont. Hospital laboratory directors, managers, and providers agreed to order only as needed to avoid supply stockpiles and supported operational constraints through ongoing validations and kit assembly. Throughout this pandemic, Vermont has ranked highly in number of tests per million people, demonstrating the value of local collaboration to surmount obstacles during disease outbreaks and the importance of creative allocation of resources to address statewide needs.

An international, inter-laboratory ring trial confirms the feasibility of an open source, extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples (preprint)

RT-qPCR is used world-wide to test and trace the spread of SARS-CoV-2. Extraction-less or direct RT-PCR is an open-access qualitative method for SARS-CoV-2 detection from nasopharyngeal (NP) or oral pharyngeal (OP) samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged ten global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international inter-laboratory ring trial. Participating labs were provided a common protocol, common reagents, aliquots of identical pooled clinical samples and purified nucleic acids, and used their existing in-house equipment. We observed 100% concordance across labs in the correct identification of all positive and negative samples, with highly similar Ct values observed. The test also performed well when applied to locally collected patient NP samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that open access, direct RT-PCR assays are a feasible option for more efficient COVID-19 testing as demanded by the continuing pandemic.

Factors linked to severe outcomes in multisystem inflammatory syndrome in children (MIS-C) in the USA: a retrospective surveillance study.

BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C) is a newly identified and serious health condition associated with SARS-CoV-2 infection. Clinical manifestations vary widely among patients with MIS-C, and the aim of this study was to investigate factors associated with severe outcomes. METHODS: In this retrospective surveillance study, patients who met the US Centers for Disease Control and Prevention (CDC) case definition for MIS-C (younger than 21 years, fever, laboratory evidence of inflammation, admitted to hospital, multisystem [≥2] organ involvement [cardiac, renal, respiratory, haematological, gastrointestinal, dermatological, or neurological], no alternative plausible diagnosis, and either laboratory confirmation of SARS-CoV-2 infection by RT-PCR, serology, or antigen test, or known COVID-19 exposure within 4 weeks before symptom onset) were reported from state and local health departments to the CDC using standard case-report forms. Factors assessed for potential links to severe outcomes included pre-existing patient factors (sex, age, race or ethnicity, obesity, and MIS-C symptom onset date before June 1, 2020) and clinical findings (signs or symptoms and laboratory markers). Logistic regression models, adjusted for all pre-existing factors, were used to estimate odds ratios between potential explanatory factors and the following outcomes: intensive care unit (ICU) admission, shock, decreased cardiac function, myocarditis, and coronary artery abnormalities. FINDINGS: 1080 patients met the CDC case definition for MIS-C and had symptom onset between March 11 and Oct 10, 2020. ICU admission was more likely in patients aged 6-12 years (adjusted odds ratio 1·9 [95% CI 1·4-2·6) and patients aged 13-20 years (2·6 [1·8-3·8]), compared with patients aged 0-5 years, and more likely in non-Hispanic Black patients, compared with non-Hispanic White patients (1·6 [1·0-2·4]). ICU admission was more likely for patients with shortness of breath (1·9 [1·2-2·9]), abdominal pain (1·7 [1·2-2·7]), and patients with increased concentrations of C-reactive protein, troponin, ferritin, D-dimer, brain natriuretic peptide (BNP), N-terminal pro B-type BNP, or interleukin-6, or reduced platelet or lymphocyte counts. We found similar associations for decreased cardiac function, shock, and myocarditis. Coronary artery abnormalities were more common in male patients (1·5 [1·1-2·1]) than in female patients and patients with mucocutaneous lesions (2·2 [1·3-3·5]) or conjunctival injection (2·3 [1·4-3·7]). INTERPRETATION: Identification of important demographic and clinical characteristics could aid in early recognition and prompt management of severe outcomes for patients with MIS-C. FUNDING: None.

Early Data From Case Series of Tracheostomy in Patients With SARS-CoV-2.

Thirty-eight tracheostomies were performed on patients with respiratory failure secondary to SARS-CoV-2 infection over the month of April at North Shore University Hospital and Lenox Hill Hospital (members of Northwell Health System in Long Island and New York City). Follow-up by May 14 revealed that 21 (55.2%) had been weaned from ventilators and 7 (18.4%) underwent decannulation. Two patients (5.3%) expired in the weeks following tracheostomy. Between the 2 institutions, 10 attending surgeons performed all of the tracheostomies using appropriate personal protective equipment, and none demonstrated seroconversion within 1 to 2 weeks of this article.

#ENT: Otolaryngology Residency Programs Create Social Media Platforms to Connect With Applicants During COVID-19 Pandemic.

OBJECTIVE: To determine which otolaryngology residency programs have social media platforms and to review which programs are utilizing platforms to advertise virtual open houses and virtual subinternships for residency applicants. STUDY DESIGN: Cross-sectional study. SETTING: The study was conducted online by reviewing all accredited otolaryngology residency programs in the United States participating in the Electronic Residency Application Service. METHODS: Otolaryngology residency programs were reviewed for social media presence on Instagram, Twitter, and Facebook. Social media posts were evaluated for virtual open houses and virtual subinternships. Residency websites and the Visiting Student Application Service were evaluated for the presence of virtual subinternships. All data were collected between September 5, 2020, and September 9, 2020. This study did not require approval from the University of Alabama at Birmingham Institutional Review Board for Human Use. RESULTS: Among 118 otolaryngology residency programs, 74 (62.7%) participate on Instagram, 52 (44.1%) participate on Twitter, and 44 (37.3%) participate on Facebook. Fifty-one Instagram accounts, 20 Twitter accounts, and 4 Facebook accounts have been created during 2020. Forty-two (36%), 30 (25.4%), and 15 (13%) programs are promoting virtual open houses on Instagram, Twitter, and Facebook, respectively. Two programs on the Visiting Student Application Service offered virtual subinternships. Seven residency program websites offered virtual subinternships. Nine, 6, and 1 program offered virtual subinternships on Instagram, Twitter, and Facebook, respectively. CONCLUSION: This study demonstrates that social media presence on Instagram and Twitter among otolaryngology residency programs has substantially grown in 2020 at a higher rate compared to previous years. These data suggest that otolaryngology residency programs are finding new ways to reach out to applicants amid an unprecedented type of application cycle due to the challenges presented by COVID-19. Many programs are advertising virtual open houses via social media platforms to connect with applicants, and a few programs are offering virtual subinternships to replace traditional subinternships.