A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection.

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.

Development of Effective PEDV Vaccine Candidates Based on Viral Culture and Protease Activity.

Porcine epidemic diarrhea (PED) is a highly contagious disease that has been reported annually in several Asian countries, causing significant economic losses to the swine livestock industry. Although vaccines against the porcine epidemic diarrhea virus (PEDV) are available, their efficacy remains questionable due to limitations such as viral genome mutation and insufficient intestinal mucosal immunity. Therefore, the development of a safe and effective vaccine is necessary. In this study, a virulent Korean strain of PEDV, CKT-7, was isolated from a piglet with severe diarrhea, and six different conditions were employed for serial passage of the strain in a cell culture system to generate effective live attenuated vaccine (LAV) candidates. The characteristics of these strains were analyzed in vitro and in vivo, and the CKT-7 N strain was identified as the most effective vaccine candidate, with a viral titer peak of 8.67 ± 0.29 log10TCID50/mL, and no mortality or diarrhea symptoms were observed in five-day-old piglets. These results indicate that LAV candidates can be generated through serial passage with different culture conditions and provide valuable insights into the development of a highly effective LAV against PEDV.

Neutrophil Extracellular Traps in Airway Diseases: Pathological Roles and Therapeutic Implications.

Neutrophils are important effector cells of the innate immune response that fight pathogens by phagocytosis and degranulation. Neutrophil extracellular traps (NETs) are released into the extracellular space to defend against invading pathogens. Although NETs play a defensive role against pathogens, excessive NETs can contribute to the pathogenesis of airway diseases. NETs are known to be directly cytotoxic to the lung epithelium and endothelium, highly involved in acute lung injury, and implicated in disease severity and exacerbation. This review describes the role of NET formation in airway diseases, including chronic rhinosinusitis, and suggests that targeting NETs could be a therapeutic strategy for airway diseases.

The impact of COVID-19 on gun violence across census tracts in NYC

This study explores the impact of COVID-19 on gun violence in NYC and its interactive effects with neighborhood factors at the census tract level. Random effects negative binomial models are used to analyze monthly data from January 2017 to March 2021. There was a significant increase in gun violence during the pandemic. In addition, poverty, economic inequality, African Americans, Hispanics, residential mobility, and total population were significantly associated with increases in gun violence. However, there were no significant interaction effects between the pandemic and neighborhood characteristics. This study concludes with a discussion of study limitations and implications. (PsycInfo Database Record (c) 2023 APA, all rights reserved)

When COVID-19 and guns meet: A rise in shootings.

OBJECTIVE: The present study examines the impact of the COVID-19 stay-at-home order on gun violence in Buffalo, New York: fatal shootings, all non-fatal shootings, non-fatal shootings with injury, and non-fatal shootings without injury. It also estimated its impact on gang and non-gang related shootings. METHODS: Weekly crime data are analyzed at the city level using ARIMA and poisson models. Forecasting is used to verify the validity of both ARIMA and poisson models. RESULTS: The effect of the pandemic was conditional upon the types of gun violence and impact models of intervention. The pandemic caused a temporary increase in fatal shootings while leading to a long-term increase in all non-fatal shootings, non-fatal shootings with injury, non-fatal shootings without injury, and gang related shootings. CONCLUSIONS: The pandemic has changed the volume of gun violence possibly due to increased strain and/or changed routine activities. This study not only promotes further research but also has policy implications for public health and safety. From a public policy perspective, criminal justice agencies should focus more attention and resources on gun violence resulting from a sense of strain and fear among individuals during the pandemic.

Delta (B1.617.2) variant of SARS-CoV-2 induces severe neurotropic patterns in K18-hACE2 mice.

A highly contagious virus, severe acute respiratory syndrome coronavirus 2, caused the coronavirus disease 19 (COVID-19) pandemic (SARS-CoV-2). SARS-CoV-2 genetic variants have been reported to circulate throughout the COVID-19 pandemic. COVID-19 symptoms include respiratory symptoms, fever, muscle pain, and breathing difficulty. In addition, up to 30% of COVID-19 patients experience neurological complications such as headaches, nausea, stroke, and anosmia. However, the neurotropism of SARS-CoV-2 infection remains largely unknown. This study investigated the neurotropic patterns between the B1.617.2 (Delta) and Hu-1 variants (Wuhan, early strain) in K18-hACE2 mice. Despite both the variants inducing similar pathogenic patterns in various organs, B1.617.2-infected K18-hACE2 mice demonstrated a higher range of disease phenotypes such as weight loss, lethality, and conjunctivitis when compared to those in Hu-1-infected mice. In addition, histopathological analysis revealed that B1.617.2 infects the brain of K18-hACE2 mice more rapidly and effectively than Hu-1. Finally, we discovered that, in B1.617.2-infected mice, the early activation of various signature genes involved innate cytokines and that the necrosis-related response was most pronounced than that in Hu-1-infected mice. The present findings indicate the neuroinvasive properties of SARS-CoV-2 variants in K18-hACE2 mice and link them to fatal neuro-dissemination during the disease onset.

Perception and safety analysis of COVID-19 vaccination in cancer patients: A multicenter, real-world study.

BACKGROUND: Although various coronavirus disease 2019 (COVID-19) vaccines have been delivered to the public worldwide, data on cancer populations are limited. Vaccine hesitancy related to safety concerns is observed among cancer patients. We report the perception of COVID-19 vaccines and their safety profile after vaccination among cancer patients. MATERIALS AND METHODS: Between April and November 2021, a multicenter survey was conducted on 318 patients treated in any hemato-oncology outpatient clinic among three hospitals under the Korea University Medical Center. The medical records of the patients were reviewed to obtain detailed clinical and hematological toxicity data. RESULTS: A perception survey was conducted among 293 patients. Among them, 53.9% were concerned about developing vaccine-related adverse events (VRAEs) and 23.5%, about negative effects on cancer treatment. During the study period, 255 and 186 patients participated in a safety survey after the first and second doses, respectively. After the first dose, 62% of patients reported VRAEs (2.4%, grade 3), whereas 48.9% reported VRAEs (2.7%, grade 3) after the second dose. For both doses, injection-site pain and sore arm pain were the most common VRAEs, followed by myalgia, fatigue, and headache. No grade 4/5 VRAEs were observed, and there were no differences in complete blood count after vaccination. Multivariate analysis revealed female sex, active cancer treatment, and mRNA vaccines as independent risk factors for VRAE development in cancer patients. CONCLUSION: Despite high levels of concern, COVID-19 vaccines were well tolerated by cancer patients, with a safety profile consistent with that of the general population.

A proteome-scale map of the SARS-CoV-2-human contactome.

Understanding the mechanisms of coronavirus disease 2019 (COVID-19) disease severity to efficiently design therapies for emerging virus variants remains an urgent challenge of the ongoing pandemic. Infection and immune reactions are mediated by direct contacts between viral molecules and the host proteome, and the vast majority of these virus-host contacts (the 'contactome') have not been identified. Here, we present a systematic contactome map of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the human host encompassing more than 200 binary virus-host and intraviral protein-protein interactions. We find that host proteins genetically associated with comorbidities of severe illness and long COVID are enriched in SARS-CoV-2 targeted network communities. Evaluating contactome-derived hypotheses, we demonstrate that viral NSP14 activates nuclear factor κB (NF-κB)-dependent transcription, even in the presence of cytokine signaling. Moreover, for several tested host proteins, genetic knock-down substantially reduces viral replication. Additionally, we show for USP25 that this effect is phenocopied by the small-molecule inhibitor AZ1. Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets.

Quantitative proteomics and biological activity of extracellular vesicles engineered to express SARS-CoV-2 spike protein.

SARS-CoV-2 viral infection led to the devastating COVID-19 pandemic, where illness stemmed from interactions between virions and recipient host cells resulting in multi-layered pathological consequences. The role of the infection portal is now understood to be the cellular angiotensin converting enzyme-2 (ACE2) receptor, which binds to viral spike (S) protein initiating virion internalisation process. Since SARS-CoV-2 virions bear some resemblance to endogenously produced small extracellular vesicles (sEVs) we reasoned that EVs engineered to express S protein (viral mimics) may interfere with viral infection. Here, we report generation of HEK293T cells producing sEVs enriched for transmembrane S-protein tagged with green fluorescent protein (S/GFP). Strikingly, S protein drove the GFP tag to the membrane of sEVs, while GFP alone was not efficiently included in the sEV cargo. High-throughput quantitative proteomics revealed that S/GFP sEVs contained over 1000 proteins including canonical components of the exosomal pathway such as ALIX, syntenin-1, and tetraspanins (CD81, CD9), but depleted for calnexin and cytochrome c. We found that 84 sEV proteins were significantly altered by the presence of S/GFP. S protein expressing EVs efficiently adhered to target cells in an ACE2-dependent manner, but they were poorly internalised. Importantly, prolonged administration of S/GFP EV to K18-hACE2 mice provided a significant protection against SARS-CoV-2 infection. Thus, the generation of sEV containing S protein can be considered as a novel therapeutic approach in reducing the transmission of SARS-CoV-2.

Randomized Open Investigation Determining Steroid Dose in Severe COVID-19: The ROIDS-Dose Clinical Trial.

Introduction Treatment with dexamethasone reduces mortality in patients with coronavirus disease 2019 (COVID-19) pneumonia requiring supplemental oxygen, but the optimal dose has not been determined. Objective To determine whether weight-based dexamethasone of 0.2 mg/kg is superior to 6 mg daily in reducing 28-day mortality in patients with COVID-19 and hypoxemia. Materials and methods A multicenter, open-label, randomized clinical trial was conducted between March 2021 and December 2021 at seven hospitals within Northwell Health. A total of 142 patients with confirmed COVID-19 and hypoxemia were included. Participants were randomized in a 1:1 ratio to dexamethasone 0.2 mg/kg intravenously daily (n = 70) or 6 mg daily (n = 72) for up to 10 days. Results There was no statistically significant difference in the primary outcome of 28-day all-cause mortality with deaths in 12 of 70 patients (17.14%) in the intervention group and 15 of 72 patients (20.83%) in the control group (p = 0.58). There were no statistically significant differences among the secondary outcomes. Conclusion In patients with COVID-19 and hypoxemia, the use of weight-based dexamethasone dosing was not superior to dexamethasone 6 mg in reducing all-cause mortality at 28 days. Clinical trial registration This study was registered under ClinicalTrials.gov (identifier: NCT04834375).

Impact of the COVID-19 and Socioeconomic Status on Access to Care for Otorhinolaryngology Patients.

Since December 2019, COVID-19 has greatly influenced public healthcare systems around the globe in various aspects, including limitation of healthcare accessibility due to lack of both human and financial resources, suspension of clinics, and fear of infection causing healthcare avoidance. The aim of this study was to investigate the impact of COVID-19 on access to healthcare for otorhinolaryngology patients from different socioeconomic status (SES) groups. Otorhinolaryngology patients' disease severity status, diagnosed at the first hospital visit, was investigated during the pre -and post-COVID-19 pandemic era in a single medical center located in Seoul, Korea. An ordinal regression model was used to assess the impact of both SES and the COVID-19 pandemic on otorhinolaryngology diseases. Within the chronic rhinosinusitis group, lower SES was associated with a higher disease severity at the first visit compared to higher SES (OR = 3.25). During the COVID-19 pandemic, while the total number of outpatients was reduced, the severity of these ENT diseases seemed to increase compared to the pre-pandemic severity in every SES group. Our study demonstrates the negative impact a worldwide pandemic can have on healthcare inequity and disease severity, and highlights the importance of re-allocating fundamental resources for those in need during periods of public health crisis.

Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response After Heterologous Immunizations With ChAdOx1/BNT162b2 in End-Stage Renal Disease Patients on Hemodialysis.

The Korean government decided to schedule heterologous vaccinations on dialysis patients for early achievement of immunization against Coronavirus disease 2019(COVID-19). However, the effects of heterologous immunizations in hemodialysis (HD) patients are unclear. One hundred (HD) patients from Gangdong Kyung Hee University Hospital and Kyung Hee Medical Center and 100 hospital workers from Gangdong Kyung Hee University Hospital were enrolled in this study. The HD patients received the mixing schedule of ChAdOx1/BNT162b2 vaccinations at 10-week intervals, while hospital workers received two doses of ChAdOx1 vaccines at 12-week intervals. Serum IgG to a receptor-binding domain (RBD) of the S1 subunit of the spike protein of SARS-CoV-2 was measured 1 month after the first dose, 2 months and 4 months after the second dose. The median [interquartile range] anti-RBD IgG was 82.1[34.5, 176.6] AU/ml in HD patients and 197.1[124.0, 346.0] AU/ml in hospital workers (P < 0.001) after the first dose. The percentage of positive responses (IgG > 50 AU/ml) was 65.0% and 96.0% among the both group, respectively (P < 0.001). The anti-RBD IgG levels increased significantly by 2528.8 [1327.6, 5795.1] AU/ml with a 100.0% positive response rate in HD patients 2 months after the second dose, which was higher than those in hospital workers 981.4[581.5, 1891.4] AU/ml (P < 0.001). Moreover, anti-RBD IgG remains constantly high, and positive response remains 100% in HD patients 4 months after the second dose. This study suggests that heterologous vaccinations with ChAdOx1/BNT162b2 can be an alternative solution on HD patients for early and strong induction of humoral response.

Correction: Saratale et al. Significance of Immune Status of SARS-CoV-2 Infected Patients in Determining the Efficacy of Therapeutic Interventions. J. Pers. Med. 2022, 12, 349.

In the original publication [...].

Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Response After Heterologous Immunizations With ChAdOx1/BNT162b2 in End-Stage Renal Disease Patients on Hemodialysis

The Korean government decided to schedule heterologous vaccinations on dialysis patients for early achievement of immunization against Coronavirus disease 2019(COVID-19). However, the effects of heterologous immunizations in hemodialysis (HD) patients are unclear. One hundred (HD) patients from Gangdong Kyung Hee University Hospital and Kyung Hee Medical Center and 100 hospital workers from Gangdong Kyung Hee University Hospital were enrolled in this study. The HD patients received the mixing schedule of ChAdOx1/BNT162b2 vaccinations at 10-week intervals, while hospital workers received two doses of ChAdOx1 vaccines at 12-week intervals. Serum IgG to a receptor-binding domain (RBD) of the S1 subunit of the spike protein of SARS-CoV-2 was measured 1 month after the first dose, 2 months and 4 months after the second dose. The median [interquartile range] anti-RBD IgG was 82.1[34.5, 176.6] AU/ml in HD patients and 197.1[124.0, 346.0] AU/ml in hospital workers (P < 0.001) after the first dose. The percentage of positive responses (IgG > 50 AU/ml) was 65.0% and 96.0% among the both group, respectively (P < 0.001). The anti-RBD IgG levels increased significantly by 2528.8 [1327.6, 5795.1] AU/ml with a 100.0% positive response rate in HD patients 2 months after the second dose, which was higher than those in hospital workers 981.4[581.5, 1891.4] AU/ml (P < 0.001). Moreover, anti-RBD IgG remains constantly high, and positive response remains 100% in HD patients 4 months after the second dose. This study suggests that heterologous vaccinations with ChAdOx1/BNT162b2 can be an alternative solution on HD patients for early and strong induction of humoral response.

Gires-Tournois Immunoassay Platform for Label-Free Bright-Field Imaging and Facile Quantification of Bioparticles.

Bright-field imaging of nanoscale bioparticles is a challenging task for optical microscopy because the light-matter interactions of bioparticles are weak on conventional surfaces due to their low refractive index and small size. Alternatively, advanced imaging techniques, including near-field microscopy and phase microscopy, have enabled visualization and quantification of the bioparticles, but they require assistance of sophisticated/customized systems and post-processing with complex established algorithms. Here, a simple and fast immunoassay device, Gires-Tournois immunoassay platform (GTIP) is presented, which provides unique color dynamics in response to optical environment changes and thus enables the label-free bright-field imaging and facile quantification of bioparticles using conventional optical microscopy. Bioparticles on GTIP slow down the velocity of reflected light, leading to vivid color change according to the local particle density and maximizing chromatic contrast for high spatial distinguishability. The particle distribution and density on the surface of the resonator are readily analyzed through 2D raster-scanning-based chromaticity analysis. GTIP offers multiscale sensing capability for target analytes that possess different refractive indices and sizes.

The COVID-19 Pandemic, Stay-at-Home Orders, and Gun Violence: A Story of Two Cities

This study examines the impact of the pandemic on gun violence in Philadelphia and Washington DC. Interrupted time-series analysis is used to examine weekly data from January 2017 to March 2021. Robust diagnostic checks confirm the validity of the fitted models. There were significant increases in gun violence during the pandemic, especially in the staged relaxation of social distancing. The timing of the increases in gun violence varies by location and fatality. Criminal justice agencies should place more attention and reallocate resources on gun violence in a timely manner in the volatile state of the nation. Finally, this study concludes with a discussion of the findings, limitations, and implications for future research.

Significance of Immune Status of SARS-CoV-2 Infected Patients in Determining the Efficacy of Therapeutic Interventions.

Coronavirus disease 2019 (COVID-19) is now being investigated for its distinctive patterns in the course of disease development which can be indicated with miscellaneous immune responses in infected individuals. Besides this series of investigations on the pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), significant fundamental immunological and physiological processes are indispensable to address clinical markers of COVID-19 disease and essential to identify or design effective therapeutics. Recent developments in the literature suggest that deficiency of type I interferon (IFN) in serum samples can be used to represent a severe progression of COVID-19 disease and can be used as the basis to develop combined immunotherapeutic strategies. Precise control over inflammatory response is a significant aspect of targeting viral infections. This account presents a brief review of the pathophysiological characteristics of the SARS-CoV-2 virus and the understanding of the immune status of infected patients. We further discuss the immune system's interaction with the SARS-CoV-2 virus and their subsequent involvement of dysfunctional immune responses during the progression of the disease. Finally, we highlight some of the implications of the different approaches applicable in developing promising therapeutic interventions that redirect immunoregulation and viral infection.