MODELING OF ANTIBODY RESPONSE TO COVID-19 VACCINATIONS IN PATIENTS WITH RHEUMATOID ARTHRITIS

BackgroundUnderstanding the dynamics of humoral immunity after COVID-19 vaccination is crucial in developing vaccination strategies. Antibody response patterns are more complex in patients with rheumatoid arthritis (RA) because of their underlying autoimmunity and immunosuppressive medications. The kinetics of vaccine response in RA patients are not well understood.ObjectivesTo construct a model of antibody response to COVID-19 vaccination in patients with RA.MethodsTwo patient groups were included for the study. The first group was composed of RA patients who were enrolled for influenza vaccination study between Oct 6, 2021 and November 3, 2021, in whom serial serum samples were obtained 0, 4, 16 weeks after vaccination. The second group was consecutively enrolled from outpatient clinic between October 6, 2021 and June 3, 2022, in whom serum sample was obtained once. After collecting data on demographics, vaccination and infection history of COVID-19 were obtained by self-report via questionnaire and data from Korean center for disease control. We then measured antibody titers against receptor binding domain of spike protein (anti-RBD) and nucleocapsid (anti-N), using Chemiluminescence microparticle immunosaasy (Abbott, USA) and Electrochemiluminescence immunoassay (Roche, Germany) respectively. The anti-RBD titer was log-transformed to improve normality. Time from vaccination and log of anti-RBD titer was modeled using fractional polynomial. Covariates including age, sex, BMI, underlying disease and immunosuppressive drugs were analyzed using Generalized Estimating Equations to account for repeated measured from a subject.ResultsA total of 736 patients (1042 samples) were enrolled. After excluding patients who experienced COVID-19 infection before sampling (n=84), those unvaccinated (n=44) and uncertain COVID-19 infection history (n=59), the data on 778 samples from 549 patients were analyzed (Group 1: 125, Group 2: 424). Antibody titer reached peak at 12 days after vaccination and decreased exponentially (Figure 1) which fell to 36.5% from peak after 2 months. Compared to the first vaccination, the 3rd and 4th vaccination significantly shifted anti-RBD antibody response curve (28 times, 95% CI 4~195;32 times 95% CI 4~234, respectively). However, there was no significant shift after the 4th vaccination from the 3rd vaccination (p=0.6405). Multivariable analysis showed that number of vaccinations and sulfasalazine (coefficient: 0.40, 95% CI 0.12~0.68) increased vaccine response but age (coefficient: -0.03, 95% CI -0.04~-0.02), abatacept (coefficient: -2.07, 95% CI -3.30~-0.84) and, JAK inhibitor (coefficient: -0.82, 95% CI -1.34~-0.31) decreased vaccine response.ConclusionAnti-RBD response to COVID-19 vaccination showed a peak at 12 days after vaccination and then exponentially decreased in patient with RA. The antibody response is affected by age and medications used for the treatment of RA.Table 1.ln[RBD (U/ml)]coefficient (univariable)95% CIp-valuecoefficient (multivariable)95% CIp-valuesex (female)0.17-0.22, 0.550.393---age-0.02-0.03, -0.01<.001**-0.03-0.04, -0.02<.001**DM0.11-0.27, 0.500.568---HTN-0.38-0.69, -0.070.018*---CKD0.680.07, 1.290.030*---RA duration (yr)-0.04-0.06, -0.010.001**---Pd (mg/d)-0.06-0.11, 0.000.035*---MTX use-0.23-0.52, 0.050.105---HCQ use0.01-0.28, 0.290.965---SSZ use0.450.07, 0.840.022*0.400.12,0.680.005**LEF use0.00-0.37, 0.370.988---TNF inhibitors use0.29-0.16, 0.730.208---Abatacept use-2.07-3.14, -0.99<.001**-2.07-3.30, -0.840.001**JAK inhibitors use-0.88-1.52, -0.240.007**-0.82-1.34, -0.310.002**Time (months)log(t)-1.96-2.37, -1.54<.001**-1.90-2.29, -1.50<.001**t

Do plexiglass barriers reduce the risk for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?

Barriers are commonly installed in workplace situations where physical distancing cannot be maintained, but their effectiveness in decreasing viral transmission is unknown. In simulations, physical barriers with no openings were effective in reducing contamination with an aerosolized benign virus or fluorescent microspheres, but barriers with openings were not.

Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data generated. The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet. While challenges remain for public health genomic surveillance worldwide, California COVIDNet serves as a framework for a scaled and successful bioinformatics infrastructure that has expanded beyond SARS-CoV-2 to other pathogens of public health importance.

Development of an amplicon-based sequencing approach in response to the global emergence of mpox.

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.

Examinations of the relationships between self-efficacy, self-regulation, teaching, cognitive presences, and learning engagement during COVID-19.

This study investigated the relationships between self-efficacy, self-regulation, and teaching presence, cognitive presence, and learning engagement during the pandemic. A total of 1435 undergraduate students in Korea completed an online survey on their learning experiences during COVID-19. The findings indicate that self-efficacy had a positive relationship with teaching presence and cognitive presence as well as self-regulation. No direct relationship between self-efficacy on learning engagement was found; however, the relationship between self-efficacy and learning engagement was fully mediated by self-regulation, teaching presence, and cognitive presence. Self-regulation had a positive relationship with both cognitive presence and learning engagement. Teaching presence had a positive impact on cognitive presence, but not on learning engagement. However, cognitive presence fully mediated the relationship between teaching presence and learning engagement. In effect, this study lends support to the significance of the role of cognitive presence in online learning.

Effectiveness of a novel 1-step cleaner and disinfectant against Candida auris.

A novel 1-step anionic surfactant disinfectant was effective against Candida auris isolates from the 4 major phylogenetic clades as well as methicillin-resistant Staphylococcus aureus (MRSA) and the enveloped virus bacteriophage Phi6. This anionic surfactant disinfectant may be a useful addition to the disinfectant products available for use against C. auris.

One Year Later: Family Members of Patients with COVID-19 Experience Persistent Symptoms of Posttraumatic Stress Disorder.

Rationale: Family members of critically ill patients with coronavirus disease (COVID-19) have described increased symptoms of posttraumatic stress disorder (PTSD). Little is known about how these symptoms may change over time. Objectives: We studied changes in PTSD symptoms in family members of critically ill patients with COVID-19 over 12 months. Methods: This prospective, multisite observational cohort study recruited participants at 12 hospitals in five states. Calls were made to participants at 3-4 months, 6 months, and 12 months after patient admission to the intensive care unit. Results: There were 955 eligible family members, of whom 330 (53.3% of those reached) consented to participate. Complete longitudinal data was acquired for 115 individuals (34.8% consented). PTSD symptoms were measured by the IES-6 (Impact of Events Scale-6), with a score of at least 10 identifying significant symptoms. At 3 months, the mean IES-6 score was 11.9 ± 6.1, with 63.6% having significant symptoms, decreasing to 32.9% at 1 year (mean IES-6 score, 7.6 ± 5.0). Three clusters of symptom evolution emerged over time: persistent symptoms (34.8%, n = 40), recovered symptoms (33.0%, n = 38), and nondevelopment of symptoms (32.2%, n = 37). Although participants identifying as Hispanic demonstrated initially higher adjusted IES-6 scores (2.57 points higher [95% confidence interval (CI), 1.1-4.1; P < 0.001]), they also demonstrated a more dramatic improvement in adjusted scores over time (4.7 greater decrease at 12 months [95% CI, 3.2-6.3; P < 0.001]). Conclusions: One year later, some family members of patients with COVID-19 continue to experience significant symptoms of PTSD. Further studies are needed to better understand how various differences contribute to increased risk for these symptoms.

The 'omics of obesity in B-cell acute lymphoblastic leukemia.

The obesity pandemic currently affects more than 70 million Americans and more than 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (eg, SARS-CoV-2), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. We and others have demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multidrug chemoresistance. Furthermore, others have demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used a multi-omic RNA-sequencing (single-cell and bulk transcriptomic) and mass spectroscopy (metabolomic and proteomic) approaches to define adipocyte-induced changes in normal and malignant B cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells associated with metabolism, protection from oxidative stress, increased survival, B-cell development, and drivers of chemoresistance. Single-cell RNA sequencing analysis of mice on low- and high-fat diets revealed that obesity suppresses an immunologically active B-cell subpopulation and that the loss of this transcriptomic signature in patients with B-ALL is associated with poor survival outcomes. Analyses of sera and plasma samples from healthy donors and those with B-ALL revealed that obesity is associated with higher circulating levels of immunoglobulin-associated proteins, which support observations in obese mice of altered immunological homeostasis. In all, our multi-omics approach increases our understanding of pathways that may promote chemoresistance in human B-ALL and highlight a novel B-cell-specific signature in patients associated with survival outcomes.

Containment of COVID-19 outbreak at a veterans affairs community living center.

Asymptomatic and pre-symptomatic staff and residents likely contribute to widespread transmission of COVID-19 in long-term care settings. Here, we describe the successful containment of a COVID-19 outbreak on one floor of a 163-bed Veterans Affairs (VA) Community Living Center (CLC). Testing using nasopharyngeal swabs with a rapid turn-around-time identified 3 of 28 (11%) residents and 2 of 41 (5%) healthcare personnel (HCP) with COVID-19. Both HCP likely worked on the floor while pre-symptomatic. When one HCP reported a cough to the secondary (employee) screening clinic, she was erroneously advised to work. Protocols to limit the risk for HCP to import COVID-19 were reinforced with Community Living Center staff as well as with personnel in secondary screening. Further, the CLC implemented an expanded screening tool that assessed residents for typical and atypical symptoms of COVID-19. No further cases of COVID-19 were detected on the CLC floor in the subsequent 6 weeks. Swift recognition and response helped contain the outbreak and prevent further COVID-19 infections among other residents and staff.

An approach to rapid distributed manufacturing of broad spectrum anti-viral griffithsin using cell-free systems to mitigate pandemics.

This study describes the cell-free biomanufacturing of a broad-spectrum antiviral protein, griffithsin (GRFT) such that it can be produced in microgram quantities with consistent purity and potency in less than 24 h. We demonstrate GRFT production using two independent cell-free systems, one plant and one microbial. Griffithsin purity and quality were verified using standard regulatory metrics. Efficacy was demonstrated in vitro against SARS-CoV-2 and HIV-1 and was nearly identical to that of GRFT expressed in vivo. The proposed production process is efficient and can be readily scaled up and deployed wherever a viral pathogen might emerge. The current emergence of viral variants of SARS-CoV-2 has resulted in frequent updating of existing vaccines and loss of efficacy for front-line monoclonal antibody therapies. Proteins such as GRFT with its efficacious and broad virus neutralizing capability provide a compelling pandemic mitigation strategy to promptly suppress viral emergence at the source of an outbreak.

Effectiveness of commercial portable air cleaners and a do-it-yourself minimum efficiency reporting value (MERV)-13 filter box fan air cleaner in reducing aerosolized bacteriophage MS2.

In an unventilated room, 2 commercial portable air cleaners with high efficiency particulate air (HEPA) filters and a do-it-yourself box fan air cleaner with minimum efficiency reporting value (MERV)-13 filters significantly reduced aerosolized bacteriophage MS2. Increasing airflow and addition of ultraviolet-C light plus titanium dioxide-generated photocatalytic oxidation enhanced viral clearance.

Planning, Prioritizing, and Conducting Clinical Research in the Va Learning Healthcare System during the Covid-19 Pandemic

The Veterans Affairs (VA) Cooperative Studies Program (CSP) and Clinical Science Research and Development (CSRD) are both divisions of the VA Office of Research and Development (ORD) that is responsible for the planning and conduct of clinical trials and epidemiological studies within the VA's learning healthcare system. Since the outbreak of the COVID-19 pandemic in the United States, the VA has been facing some new and evolving challenges in clinical research, especially in planning, prioritizing, and conducting new clinical research projects aimed at preventing and/or treating SARS CoV-2 infection/ COVID-19 disease. In considering clinical research projects, different stakeholders of the VA research enterprise assess needs using numerous parameters: (1) CSP and CSRD leadership: VAMC network infrastructure, financial support, available funding, and enterprise-wide impact. (2) Clinical researchers: clinical perspectives and needs, as they relate to study design and operations, in the context of an ever-evolving epidemiological picture and disease knowledgebase. (3) VA research Coordinating Center(s): the challenges that reside in aspects of trial design and planning, in an effort to account for frequent changes in the COVID-19 epidemiology, and its impact on project feasibility/participant recruitment, choice of study endpoints, safety of healthcare providers, research personnel, and study participants. Notwithstanding these evolving challenges, the VA ORD stood up the VA CoronavirUs Research and Efficacy Studies (VA CURES) network in a coordinated effort to develop a master protocol framework that could efficiently utilize the VA's clinical research infrastructure to address the COVID-19 pandemic. The VA CURES framework has been serving as the umbrella structure encompassing numerous COVID-19 clinical research activities. Both CSP and CSRD have an established clinical research infrastructure, including Coordinating Centers, a Network Of Enrollment Dedicated Sites (NODES) and over 150 VA Medical Centers across the United States, with a clear and streamlined process of submission and review of research proposals (Letters of Intent;LOI), subsequent trial planning leading up to scientific review and, once approved, conduct of research projects. In this session, we will present the VA clinical research infrastructure and share its mobilization in this pandemic. Furthermore, we will share lessons learned in conducting research in emergency situations and how the research infrastructure pivoted and adapted to fulfill its mission of providing the best healthcare to Veterans. The following four areas will be the focus of this session: the VA ORD leadership perspective: Infrastructure/support/funding/priorities;clinical research perspectives: Study design in the face of evolving epidemiological picture;trial design and planning: Protocol drafting/timelines/shifting priorities/feasibility/ VAMC networks;organizing and operationalizing the VA CURES umbrella/platform: CURES-1, and CURES-2.

Containment of COVID-19 outbreak at a veterans affairs community living center

Asymptomatic and pre-symptomatic staff and residents likely contribute to widespread transmission of COVID-19 in long-term care settings. Here, we describe the successful containment of a COVID-19 outbreak on one floor of a 163-bed Veterans Affairs (VA) Community Living Center (CLC). Testing using nasopharyngeal swabs with a rapid turn-around-time identified 3 of 28 (11%) residents and 2 of 41 (5%) healthcare personnel (HCP) with COVID-19. Both HCP likely worked on the floor while pre-symptomatic. When one HCP reported a cough to the secondary (employee) screening clinic, she was erroneously advised to work. Protocols to limit the risk for HCP to import COVID-19 were reinforced with Community Living Center staff as well as with personnel in secondary screening. Further, the CLC implemented an expanded screening tool that assessed residents for typical and atypical symptoms of COVID-19. No further cases of COVID-19 were detected on the CLC floor in the subsequent 6 weeks. Swift recognition and response helped contain the outbreak and prevent further COVID-19 infections among other residents and staff.

Continuously active disinfectant inactivates severe acute respiratory coronavirus virus 2 (SARS-CoV-2) and human coronavirus 229E two days after the disinfectant was applied and following wear exposures.

The surface environment in rooms of coronavirus disease 2019 (COVID-19) patients may be persistently contaminated despite disinfection. A continuously active disinfectant demonstrated excellent sustained antiviral activity following a 48-hour period of wear and abrasion exposures with reinoculations. Reductions of >4-log10 were achieved within a 1-minute contact time for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) and the human coronavirus, 229E.

Transfer of methicillin-resistant Staphylococcus aureus by fist bump versus elbow bump.

For 40 patients with methicillin-resistant Staphylococcus aureus (MRSA) colonization, fist bump and elbow bump greetings resulted in frequent transfer of MRSA (25% vs 15%, respectively), but significantly fewer colonies were transferred via the elbow bump. Noncontact greetings should be encouraged to reduce the risk of transfer of healthcare-associated pathogens.

Evaluation of Ultraviolet-C Light for Rapid Decontamination of Airport Security Bins in the Era of SARS-CoV-2.

BACKGROUND: Contaminated surfaces are a potential source for spread of respiratory viruses including SARS-CoV-2. Ultraviolet-C (UV-C) light is effective against RNA and DNA viruses and could be useful for decontamination of high-touch fomites that are shared by multiple users. METHODS: A modification of the American Society for Testing and Materials standard quantitative carrier disk test method (ASTM E-2197-11) was used to examine the effectiveness of UV-C light for rapid decontamination of plastic airport security bins inoculated at 3 sites with methicillin-resistant Staphylococcus aureus (MRSA) and bacteriophages MS2, PhiX174, and Phi6, an enveloped RNA virus used as a surrogate for coronaviruses. Reductions of 3 log10 on inoculated plastic bins were considered effective for decontamination. RESULTS: UV-C light administered as 10-, 20-, or 30-second cycles in proximity to a plastic bin reduced contamination on each of the test sites, including vertical and horizontal surfaces. The 30-second cycle met criteria for decontamination of all 3 test sites for all the test organisms except bacteriophage MS2 which was reduced by greater than 2 log10 PFU at each site. CONCLUSIONS: UV-C light is an attractive technology for rapid decontamination of airport security bins. Further work is needed to evaluate the utility of UV-C light in real-world settings and to develop methods to provide automated movement of bins through a UV-C decontamination process.

Cyanovirin-N binds to select SARS-CoV-2 spike oligosaccharides outside of the receptor binding domain and blocks infection by SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped positive stranded RNA virus which has caused the recent deadly pandemic called COVID-19. The SARS-CoV-2 virion is coated with a heavily glycosylated Spike glycoprotein which is responsible for attachment and entry into target cells. One, as yet unexploited strategy for preventing SARS-CoV-2 infections, is the targeting of the glycans on Spike. Lectins are carbohydrate-binding proteins produced by plants, algae, and cyanobacteria. Some lectins can neutralize enveloped viruses displaying external glycoproteins, offering an alternative therapeutic approach for the prevention of infection with virulent ß-coronaviruses, such as SARS-CoV-2. Here we show that the cyanobacterial lectin cyanovirin-N (CV-N) can selectively target SARS-CoV-2 Spike oligosaccharides and inhibit SARS-CoV-2 infection in vitro and in vivo. CV-N neutralizes Delta and Omicron variants in vitro better than earlier circulating viral variants. CV-N binds selectively to Spike with a Kd as low as 15 nM and a stoichiometry of 2 CV-N: 1 Spike but does not bind to the receptor binding domain (RBD). Further mapping of CV-N binding sites on Spike shows that select high-mannose oligosaccharides in the S1 domain of Spike are targeted by CV-N. CV-N also reduced viral loads in the nares and lungs in vivo to protect hamsters against a lethal viral challenge. In summary, we present an anti-coronavirus agent that works by an unexploited mechanism and prevents infection by a broad range of SARS-CoV-2 strains.