Characterizing SARS-CoV-2 transcription of subgenomic and genomic RNAs during early human infection using multiplexed droplet digital PCR.

BACKGROUND: Control of SARS-CoV-2 (SCV-2) transmission requires understanding SCV-2 replication dynamics. METHODS: We developed a multiplexed droplet digital PCR (ddPCR) assay to quantify SCV-2 subgenomic RNAs (sgRNAs), which are only produced during active viral replication, and discriminate them from genomic RNAs (gRNAs). We applied the assay to specimens from 144 people with single nasopharyngeal samples and 27 people with >1 sample. Results were compared to qPCR and viral culture. RESULTS: sgRNAs were quantifiable across a range of qPCR cycle threshold (Ct) values and correlated with Ct values. The ratio of sgRNA:gRNA was stable across a wide range of Ct values, whereas adjusted amounts of N sgRNA to a human housekeeping gene declined with higher Ct values. Adjusted sgRNA and gRNA amounts were quantifiable in culture-negative samples, although levels were significantly lower than in culture-positive samples. Daily testing of 6 persons revealed that sgRNA is concordant with culture results during the first week of infection but may be discordant with culture later in infection. Further, sgRNA:gRNA is constant during infection despite changes in viral culture. CONCLUSIONS: Ct values from qPCR correlate with active viral replication. More work is needed to understand why some cultures are negative despite presence of sgRNA.

Process Development of a SARS-CoV-2 Nanoparticle Vaccine

One of the outcomes from the global COVID-19 pandemic caused by SARS-CoV-2 has been an acceleration of development timelines to provide treatments in a timely manner. For example, it has recently been demonstrated that the development of monoclonal antibody therapeutics from vector construction to IND submission can be achieved in five to six months rather than the traditional ten-to-twelve-month timeline using CHO cells [1, 2]. This timeline is predicated on leveraging existing, robust platforms for upstream and downstream processes, analytical methods, and formulation. These platforms also reduce;the requirement for ancillary studies such as cell line stability, or long-term product stability studies. Timeline duration was further reduced by employing a transient cell line for early material supply and using a stable cell pool to manufacture toxicology study materials. The development of non-antibody biologics utilizing traditional biomanufacturing processes in CHO cells within a similar timeline presents additional challenges, such as the lack of platform processes and additional analytical assay development. In this manuscript, we describe the rapid development of a robust and reproducible process for a two-component self-assembling protein nanoparticle vaccine for SARS-CoV-2. Our work has demonstrated a successful academia-industry partnership model that responded to the COVID-19 global pandemic quickly and efficiently and could improve our preparedness for future pandemic threats. Graphical abstract

Design of a stabilized RBD enables potently neutralizing SARS-CoV-2 single-component nanoparticle vaccines

Waning immunity and emerging variants necessitate continued vaccination against SARS-CoV-2. Improvements in vaccine safety, tolerability, and ease of manufacturing would benefit these efforts. Here, we develop a potent and easily manufactured nanoparticle vaccine displaying the spike receptor-binding domain (RBD). Computational design to stabilize the RBD, eliminate glycosylation, and focus the immune response to neutralizing epitopes results in an RBD immunogen that resolves issues hindering the efficient nanoparticle display of the native RBD. This non-glycosylated RBD can be genetically fused to diverse single-component nanoparticle platforms maximizing manufacturing ease and flexibility. All engineered RBD-nanoparticles elicit potently neutralizing antibodies in mice that far exceed monomeric RBD. A 60-copy particle (noNAG-RBD-E2p) also elicits potently neutralizing antibodies in non-human primates. The neutralizing antibody titers elicited by noNAG-RBD-E2p are comparable to a benchmark stabilized spike antigen and reach levels against omicron BA.5 that suggest it would provide protection against emerging variants. Graphical SARS-CoV-2 RBD vaccines are cost-effective but require methods to increase their potency. Dickey et al. use a computational design method to create a stabilized non-glycosylated RBD that it can be fused to a nanoparticle carrier, boosting its potency to levels of a gold-standard spike antigen.

Design of a stabilized RBD enables potently neutralizing SARS-CoV-2 single-component nanoparticle vaccines.

Waning immunity and emerging variants necessitate continued vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Improvements in vaccine safety, tolerability, and ease of manufacturing would benefit these efforts. Here, we develop a potent and easily manufactured nanoparticle vaccine displaying the spike receptor-binding domain (RBD). Computational design to stabilize the RBD, eliminate glycosylation, and focus the immune response to neutralizing epitopes results in an RBD immunogen that resolves issues hindering the efficient nanoparticle display of the native RBD. This non-glycosylated RBD can be genetically fused to diverse single-component nanoparticle platforms, maximizing manufacturing ease and flexibility. All engineered RBD nanoparticles elicit potently neutralizing antibodies in mice that far exceed monomeric RBDs. A 60-copy particle (noNAG-RBD-E2p) also elicits potently neutralizing antibodies in non-human primates. The neutralizing antibody titers elicited by noNAG-RBD-E2p are comparable to a benchmark stabilized spike antigen and reach levels against Omicron BA.5 that suggest that it would provide protection against emerging variants.

Process development of a SARS-CoV-2 nanoparticle vaccine.

One of the outcomes from the global COVID-19 pandemic caused by SARS-CoV-2 has been an acceleration of development timelines to provide treatments in a timely manner. For example, it has recently been demonstrated that the development of monoclonal antibody therapeutics from vector construction to IND submission can be achieved in five to six months rather than the traditional ten-to-twelve-month timeline using CHO cells [1], [2]. This timeline is predicated on leveraging existing, robust platforms for upstream and downstream processes, analytical methods, and formulation. These platforms also reduce; the requirement for ancillary studies such as cell line stability, or long-term product stability studies. Timeline duration was further reduced by employing a transient cell line for early material supply and using a stable cell pool to manufacture toxicology study materials. The development of non-antibody biologics utilizing traditional biomanufacturing processes in CHO cells within a similar timeline presents additional challenges, such as the lack of platform processes and additional analytical assay development. In this manuscript, we describe the rapid development of a robust and reproducible process for a two-component self-assembling protein nanoparticle vaccine for SARS-CoV-2. Our work has demonstrated a successful academia-industry partnership model that responded to the COVID-19 global pandemic quickly and efficiently and could improve our preparedness for future pandemic threats.

Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses.

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

Can active learning be asynchronous? Implementing online peer review assignments in undergraduate political science and international relations courses

The phenomenon known as emergency eLearning saw many institutions of higher education switch from face-to-face learning to virtual or online course delivery in response to the COVID-19 pandemic. The transition posed a unique suite of challenges to instructors and students alike, especially in the case of active learning pedagogy. This article reflects on the experiences of a multi-institutional, multi-term pedagogical project that implemented peer review assignments as opportunities for asynchronous but nevertheless active learning. We shared instructor experiences through the course design and application stages of courses in International Relations and political economy, discuss the ability of peer review assignments to create active learning opportunities in online courses, and reflect on our own pedagogical development benefited from the community of practice.

Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants.

The recent emergence of multiple SARS-CoV-2 variants has caused considerable concern due to both reduced vaccine efficacy and escape from neutralizing antibody therapeutics. It is, therefore, paramount to develop therapeutic strategies that inhibit all known and future SARS-CoV-2 variants. Here, we report that all SARS-CoV-2 variants analyzed, including variants of concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron, exhibit enhanced binding affinity to clinical grade and phase 2 tested recombinant human soluble ACE2 (APN01). Importantly, soluble ACE2 neutralized infection of VeroE6 cells and human lung epithelial cells by all current VOC strains with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. Effective inhibition of infections with SARS-CoV-2 variants was validated and confirmed in two independent laboratories. These data show that SARS-CoV-2 variants that have emerged around the world, including current VOC and several variants of interest, can be inhibited by soluble ACE2, providing proof of principle of a pan-SARS-CoV-2 therapeutic.

Adjuvanting a subunit SARS-CoV-2 vaccine with clinically relevant adjuvants induces durable protection in mice.

Adjuvants enhance the magnitude and the durability of the immune response to vaccines. However, there is a paucity of comparative studies on the nature of the immune responses stimulated by leading adjuvant candidates. In this study, we compared five clinically relevant adjuvants in mice-alum, AS03 (a squalene-based adjuvant supplemented with α-tocopherol), AS37 (a TLR7 ligand emulsified in alum), CpG1018 (a TLR9 ligand emulsified in alum), O/W 1849101 (a squalene-based adjuvant)-for their capacity to stimulate immune responses when combined with a subunit vaccine under clinical development. We found that all four of the adjuvant candidates surpassed alum with respect to their capacity to induce enhanced and durable antigen-specific antibody responses. The TLR-agonist-based adjuvants CpG1018 (TLR9) and AS37 (TLR7) induced Th1-skewed CD4+ T cell responses, while alum, O/W, and AS03 induced a balanced Th1/Th2 response. Consistent with this, adjuvants induced distinct patterns of early innate responses. Finally, vaccines adjuvanted with AS03, AS37, and CpG1018/alum-induced durable neutralizing-antibody responses and significant protection against the B.1.351 variant 7 months following immunization. These results, together with our recent results from an identical study in non-human primates (NHPs), provide a comparative benchmarking of five clinically relevant vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV-2 subunit vaccines to provide durable protection against the B.1.351 variant. Furthermore, these results reveal differences between the widely-used C57BL/6 mouse strain and NHP animal models, highlighting the importance of species selection for future vaccine and adjuvant studies.

COVID-19 aerosol transmission modeling in support of company HVAC guideline.

A company COVID-19 Heating, Ventilation, and Air Conditioning Guideline was implemented globally, as part of a larger control measure toolset, to minimize the potential for SARS-CoV-2 aerosol transmission. The COVID-19 Heating, Ventilation, and Air Conditioning Guideline informed and provided the process to optimize existing ventilation systems, set occupancy duration limits, and set clearance periods for a given space. Aerosol transmission modeling was used extensively to determine space limitations to reduce the potential for aerosol transmission in various manufacturing, lab, warehouse, aircraft, and administrative workspaces. This paper focuses on the modeling completed for administrative spaces (e.g., offices, conference rooms, restrooms, elevators) due to their lower ventilation rates, higher occupant densities, and greater vocalization levels. A detailed description of how the Guideline was implemented, with examples showing the evaluation and determinations made for specific spaces, is provided. World-wide implementation of this Guideline, as one of the layers of protection, was a key component in the overall strategy to reduce aerosol transmission of the SARS-CoV-2 virus.

Use of portable air purifiers as local exhaust ventilation during COVID-19.

The purpose of this study was to determine if strategic placement of portable air purifiers would improve effectiveness of aerosol reduction in a space as compared to use as a general room air purifier. Two sizes of portable air purifiers were placed in two different positions intended to function similar to either a local exhaust ventilation hood or an air curtain to determine if strategic placement would lead to a reduction of particles in a worker's position at a desk in an office environment. Particle generators were used to introduce particulate into the air and personal aerosol monitors measured particles during each test condition. Results showed that when the medium room portable air purifiers used in this study were set to high, corresponding to 98 CFM, and placed near the breathing zone of each office worker with the unit's filter cover removed, the particle concentration was reduced 35% beyond the reduction that would be expected if the same units were placed on the floor behind the occupant's workstation. Results also indicated that the larger portable air purifier tested, positioned as close as reasonable to each occupant's breathing zone with the largest capture area possible (i.e., removing the unit's filter cover), delivers the best aerosol reduction performance. The authors concluded that as a layer of protection against transmission of airborne infectious organisms for office occupants, installing a portable air purifier, sized and operated similar to the units tested in this study on the desk 12 inches from the breathing zone of the worker, has the potential to reduce airborne particulate to a greater degree than if the same units were placed outside of the breathing zone, in the general cubicle area.

Schools that Breathe: Studio Education in the Pandemic

The COVID-19 pandemic dramatically exposed the vulnerabilities of the American public school system. The architecture of educational buildings themselves became the flashpoint in discussions about equity, support for teachers, and student health. In a recent graduate architecture studio at the Massachusetts Institute of Technology, students considered the proposition of the pandemic-resilient school by proposing retrofits to increase fresh air ventilation to existing school buildings and add outdoor classrooms. This seemingly straightforward exercise was a gateway to much larger issues, such as the intersections between air ventilation and educational inequality, as the studio responded to unfolding evidence and a global emergency in real time. [ FROM AUTHOR] Copyright of Journal of Architectural Education is the property of Routledge and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Exploring the Ethics of a Nurses' Strike During a Pandemic.

ABSTRACT: It's usually considered a violation of professional ethics for health care workers, including nurses, to refuse to work during mass medical emergencies, especially if their refusal is over concerns like compensation. Strikes and other forms of work stoppage may result in harm to patients and, therefore, violate professional obligations of beneficence. However, in rare circumstances a health care worker's choice to remain on the job despite risk or potential harm to themselves or even their family may be considered beyond their professional obligation. During a pandemic such as COVID-19, the ethical calculus (that is, finding the right balance between beneficence and harm before deciding on a course of action) must take account of a confluence of factors, including the risks to present patients, future patients, and health care workers; the severity and duration of the risks; and the availability of ameliorative or protective steps that reduce risk and harm. The principle of beneficence to both future patients and health care workers may be thwarted if the risk analysis is confined only to short-term concerns (that is, to concerns occurring within a narrow temporal window). If a significantly elevated risk has been demonstrated to affect nurses and other health care workers of color disproportionately, racial justice must also be considered. The purpose of this article is to assess the moral framework of a work stoppage by nurses during a pandemic.

WellSpace: Peer-led groups for first-episode psychosis before and during the COVID era.

AIM: Coordinated specialty care (CSC) is a collaborative-team based approach that has been shown to be helpful for patients with first-episode psychosis. Peer support is an important component of CSC. Here, we describe the development and implementation of peer-led group programming (McLean WellSpace) that was loosely affiliated with a CSC (McLean OnTrack). We discuss how we adapted this program to the challenges imposed by COVID-19. METHODS: WellSpace was developed to have minimal barriers to entry other than a self-reported history of recent onset of psychosis. It is free for participants with minimal restrictions about who may attend. WellSpace and WellSpace groups are largely administered by peer specialists who align with the recovery movement. WellSpace has been a virtual program since March 2020. RESULTS: McLean WellSpace participants include many people who are not patients of McLean OnTrack, suggesting that such programs may have greater reach than standard medical programs. We transitioned to virtual programming and saw average group attendance and unique participants increase during the pandemic. CONCLUSIONS: Our experience suggests that peer-led group programming for first-episode psychosis is well-accepted by patients, including many who are not engaged with a CSC. This may be related to our efforts to minimize barriers to entry and our peer-led, non-medical orientation.

SARS-CoV-2 Aptasensors Based on Electrochemical Impedance Spectroscopy and Low-Cost Gold Electrode Substrates.

SARS-CoV-2 diagnostic practices broadly involve either quantitative polymerase chain reaction (qPCR)-based nucleic amplification of viral sequences or antigen-based tests such as lateral flow assays (LFAs). Reverse transcriptase-qPCR can detect viral RNA and is the gold standard for sensitivity. However, the technique is time-consuming and requires expensive laboratory infrastructure and trained staff. LFAs are lower in cost and near real time, and because they are antigen-based, they have the potential to provide a more accurate indication of a disease state. However, LFAs are reported to have low real-world sensitivity and in most cases are only qualitative. Here, an antigen-based electrochemical aptamer sensor is presented, which has the potential to address some of these shortfalls. An aptamer, raised to the SARS-CoV-2 spike protein, was immobilized on a low-cost gold-coated polyester substrate adapted from the blood glucose testing industry. Clinically relevant detection levels for SARS-CoV-2 are achieved in a simple, label-free measurement format using sample incubation times as short as 15 min on nasopharyngeal swab samples. This assay can readily be optimized for mass manufacture and is compatible with a low-cost meter.

Short Form of the Pediatric Symptom Checklist-Youth Self-Report (PSC-17-Y): Spanish Validation Study.

BACKGROUND: The short form, 17-item version of the Pediatric Symptom Checklist-Youth Self-Report (PSC-17-Y) is a validated measure that assesses psychosocial problems overall (OVR) and in 3 major psychopathological domains (internalizing, externalizing, and attention-deficit/hyperactivity disorder), taking 5-10 min to complete. Prior research has established sound psychometric properties of the PSC-17-Y for English speakers. OBJECTIVE: This study extends psychometric evidence for the acceptability of the PSC-17-Y in a large sample of Spanish adolescents, providing proof of its reliability and structure, convergent and discriminant validity, and longitudinal and gender invariance. METHODS: Data were collected on 5430 adolescents, aged 12-18 years, who filled out the PSC-17-Y twice during 2018-2019 (7-month interval). We calculated the Cronbach alpha and the McDonald omega coefficients to test reliability, the Pearson correlation for convergent (distress) and criterion validity (well-being, quality of life, and socioemotional skills), confirmatory factor analysis (CFA) for structure validity, and multigroup and longitudinal measurement invariance analysis for longitudinal and gender stability. RESULTS: Within structural analysis for the PSC-17-Y, CFA supported a correlated 3-factor solution, which was also invariant longitudinally and across gender. All 3 subscales showed evidence of reliability, with coefficients near or above .70. Moreover, scores of PSC-17-Y subscales were positively related with convergent measures and negatively related with criterion measures. Normative data for the PSC-17-Y are presented in the form of percentiles (75th and 90th). CONCLUSIONS: This work provides the first evidence of the reliability and validity of the Spanish version of the PSC-17-Y administered over the internet to assess mental health problems among adolescents, maintaining the same domains as the long version.

Sangivamycin is highly effective against SARS-CoV-2 in vitro and has favorable drug properties.

Sangivamycin is a nucleoside analog that is well tolerated by humans and broadly active against phylogenetically distinct viruses, including arenaviruses, filoviruses, and orthopoxviruses. Here, we show that sangivamycin is a potent antiviral against multiple variants of replicative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with half-maximal inhibitory concentration in the nanomolar range in several cell types. Sangivamycin suppressed SARS-CoV-2 replication with greater efficacy than remdesivir (another broad-spectrum nucleoside analog). When we investigated sangivamycin's potential for clinical administration, pharmacokinetic; absorption, distribution, metabolism, and excretion (ADME); and toxicity properties were found to be favorable. When tested in combination with remdesivir, efficacy was additive rather than competitive against SARS-CoV-2. The proven safety in humans, long half-life, potent antiviral activity (compared to remdesivir), and combinatorial potential suggest that sangivamycin is likely to be efficacious alone or in combination therapy to suppress viremia in patients. Sangivamycin may also have the ability to help combat drug-resistant or vaccine-escaping SARS-CoV-2 variants since it is antivirally active against several tested variants. Our results support the pursuit of sangivamycin for further preclinical and clinical development as a potential coronavirus disease 2019 therapeutic.

Four shareworthy SEPR scenario ideas.

In this communication article, we share our scenario ideas at the request of the journal editor. These are (1) a scenario for building sustainable suburbs; (2) a counterfactual scenario for coping with the super wicked COVID problem; (3) envisioning alternative futures of cultural ecosystem services supplies in Southwestern Ghana; and (4) a path toward writing successful scenarios. The ideas will be fully developed in due course into scholarly articles for the journal.

Airway antibodies emerge according to COVID-19 severity and wane rapidly but reappear after SARS-CoV-2 vaccination.

Understanding the presence and durability of antibodies against SARS-CoV-2 in the airways is required to provide insights into the ability of individuals to neutralize the virus locally and prevent viral spread. Here, we longitudinally assessed both systemic and airway immune responses upon SARS-CoV-2 infection in a clinically well-characterized cohort of 147 infected individuals representing the full spectrum of COVID-19 severity, from asymptomatic infection to fatal disease. In addition, we evaluated how SARS-CoV-2 vaccination influenced the antibody responses in a subset of these individuals during convalescence as compared with naive individuals. Not only systemic but also airway antibody responses correlated with the degree of COVID-19 disease severity. However, although systemic IgG levels were durable for up to 8 months, airway IgG and IgA declined significantly within 3 months. After vaccination, there was an increase in both systemic and airway antibodies, in particular IgG, often exceeding the levels found during acute disease. In contrast, naive individuals showed low airway antibodies after vaccination. In the former COVID-19 patients, airway antibody levels were significantly elevated after the boost vaccination, highlighting the importance of prime and boost vaccinations for previously infected individuals to obtain optimal mucosal protection.