How Social Support Enhances Individual Resilience in the Public Health Crisis: Testing a Dual-Process Serial Mediation Model (preprint)

Under the background of the COVID-19 pandemic, our paper attempts to advance a dual-process model from online social support to individual resilience via diverse social capital (bonding and bridging) and political beliefs (political efficacy, political trust and city identification). Drawing on a survey of 446 residents in Shanghai, China, the findings indicate that neither informational nor emotional social support directly affects individual resilience, but indirectly influences it through different pathways. Specifically, bridging social capital mediates informational social support and individual resilience, but bonding social capital might not follow a similar path. Notably, political efficacy and political trust are involved in the above mediation between informational social support and individual resilience. Besides, the serial mediation effect of emotional social support on individual resilience via bonding social capital and then city identification or political trust is also significant. Our findings are expected to guide people to better recover from the current public health crisis and prepare for the future wave.

Security analysis of sports competition under the influence of covid-19 / Análise de segurança da competição esportiva sob a influência da covid-19 / Análisis de seguridad de la competición deportiva bajo la influencia del covid-19

ABSTRACT Introduction The continuous growth of COVID-19 has harmed sports competitions. Although the existing method of non-opening to spectators is very effective for preventing and controlling COVID-19, it will also seriously blow the sports economy's development. Objective Explore the safety of sports competition under the influence of COVID-19 to realize sports practice in a safe and regulated condition. Methods Firstly, the current public's willingness to participate in the competition was analyzed by questionnaire survey. Then, using the literature search method, this paper discusses the safety needs of sports competitions under the normalization of the prevention and control of COVID-19 in the research area at the present stage. Results By completely controlling the crowd shift rule and skillfully controlling the crowd pace, the transmission risk in the competition process can be effectively reduced. Conclusion The relevant departments and stadium managers should fully analyze the current epidemic prevention and control needs and strengthen spectator safety management in the study area in combination with regional characteristics and the actual spectator situation. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.

RESUMO Introdução O crescimento contínuo da COVID-19 tem tido um impacto negativo sobre as competições esportivas. Embora o método existente de não-abertura aos espectadores seja muito eficaz para a prevenção e controle da COVID-19, ele também trará um sério golpe ao desenvolvimento da economia esportiva. Objetivo Explorar a segurança da competição esportiva sob a influência da COVID-19, de forma a realizar a prática esportiva em uma condição segura e regulamentada. Métodos Primeiramente, a disposição do público atual para participar da competição foi analisada por meio de pesquisa por questionário. Em seguida, utilizando o método de pesquisa bibliográfica, este trabalho discute as necessidades de segurança das competições esportivas sob a normalização da prevenção e controle da COVID-19 na área de pesquisa na presente fase. Resultados Controlando completamente a regra do deslocamento da multidão e controlando habilmente o ritmo da multidão, o risco de transmissão no processo de competição pode ser efetivamente reduzido. Conclusão Os departamentos e gerentes de estádios pertinentes devem analisar plenamente as necessidades atuais de prevenção e controle de epidemias e fortalecer a gestão da segurança dos espectadores na área de estudo em combinação com as características regionais e a situação real dos espectadores. Nível de evidência II; Estudos terapêuticos - investigação dos resultados do tratamento.

RESUMEN Introducción El continuo crecimiento del COVID-19 ha tenido un impacto negativo en las competiciones deportivas. Aunque el método actual de no abrir para los espectadores es muy eficaz para la prevención y el control del COVID-19, también supondrá un duro golpe para el desarrollo de la economía deportiva. Objetivo Explorar la seguridad de la competición deportiva bajo la influencia del COVID-19, para llevar a cabo la práctica deportiva en condiciones seguras y reguladas. Métodos En primer lugar, se analizó la disposición del público actual a participar en el concurso mediante una encuesta por cuestionario. A continuación, utilizando el método de búsqueda bibliográfica, este trabajo analiza las necesidades de seguridad de las competiciones deportivas en el marco de la normalización de la prevención y el control del COVID-19 en el ámbito de la investigación en la etapa actual. Resultados Si se controla completamente la regla de desplazamiento de la multitud y se controla hábilmente el ritmo de la multitud, se puede reducir eficazmente el riesgo de transmisión en el proceso de competición. Conclusión Los departamentos competentes y los gestores de los estadios deben analizar a fondo las necesidades actuales de prevención y control de epidemias y reforzar la gestión de la seguridad de los espectadores en la zona de estudio en combinación con las características regionales y la situación real de los espectadores. Nivel de evidencia II; Estudios terapéuticos - investigación de los resultados del tratamiento.

Security analysis of sports competition under the influence of covid-19 / Análise de segurança da competição esportiva sob a influência da covid-19 / Análisis de seguridad de la competición deportiva bajo la influencia del covid-19

ABSTRACT Introduction The continuous growth of COVID-19 has harmed sports competitions. Although the existing method of non-opening to spectators is very effective for preventing and controlling COVID-19, it will also seriously blow the sports economy's development. Objective Explore the safety of sports competition under the influence of COVID-19 to realize sports practice in a safe and regulated condition. Methods Firstly, the current public's willingness to participate in the competition was analyzed by questionnaire survey. Then, using the literature search method, this paper discusses the safety needs of sports competitions under the normalization of the prevention and control of COVID-19 in the research area at the present stage. Results By completely controlling the crowd shift rule and skillfully controlling the crowd pace, the transmission risk in the competition process can be effectively reduced. Conclusion The relevant departments and stadium managers should fully analyze the current epidemic prevention and control needs and strengthen spectator safety management in the study area in combination with regional characteristics and the actual spectator situation. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.

RESUMO Introdução O crescimento contínuo da COVID-19 tem tido um impacto negativo sobre as competições esportivas. Embora o método existente de não-abertura aos espectadores seja muito eficaz para a prevenção e controle da COVID-19, ele também trará um sério golpe ao desenvolvimento da economia esportiva. Objetivo Explorar a segurança da competição esportiva sob a influência da COVID-19, de forma a realizar a prática esportiva em uma condição segura e regulamentada. Métodos Primeiramente, a disposição do público atual para participar da competição foi analisada por meio de pesquisa por questionário. Em seguida, utilizando o método de pesquisa bibliográfica, este trabalho discute as necessidades de segurança das competições esportivas sob a normalização da prevenção e controle da COVID-19 na área de pesquisa na presente fase. Resultados Controlando completamente a regra do deslocamento da multidão e controlando habilmente o ritmo da multidão, o risco de transmissão no processo de competição pode ser efetivamente reduzido. Conclusão Os departamentos e gerentes de estádios pertinentes devem analisar plenamente as necessidades atuais de prevenção e controle de epidemias e fortalecer a gestão da segurança dos espectadores na área de estudo em combinação com as características regionais e a situação real dos espectadores. Nível de evidência II; Estudos terapêuticos - investigação dos resultados do tratamento.

RESUMEN Introducción El continuo crecimiento del COVID-19 ha tenido un impacto negativo en las competiciones deportivas. Aunque el método actual de no abrir para los espectadores es muy eficaz para la prevención y el control del COVID-19, también supondrá un duro golpe para el desarrollo de la economía deportiva. Objetivo Explorar la seguridad de la competición deportiva bajo la influencia del COVID-19, para llevar a cabo la práctica deportiva en condiciones seguras y reguladas. Métodos En primer lugar, se analizó la disposición del público actual a participar en el concurso mediante una encuesta por cuestionario. A continuación, utilizando el método de búsqueda bibliográfica, este trabajo analiza las necesidades de seguridad de las competiciones deportivas en el marco de la normalización de la prevención y el control del COVID-19 en el ámbito de la investigación en la etapa actual. Resultados Si se controla completamente la regla de desplazamiento de la multitud y se controla hábilmente el ritmo de la multitud, se puede reducir eficazmente el riesgo de transmisión en el proceso de competición. Conclusión Los departamentos competentes y los gestores de los estadios deben analizar a fondo las necesidades actuales de prevención y control de epidemias y reforzar la gestión de la seguridad de los espectadores en la zona de estudio en combinación con las características regionales y la situación real de los espectadores. Nivel de evidencia II; Estudios terapéuticos - investigación de los resultados del tratamiento.

Maternal-Neonatal Outcomes of Obstetric Deliveries Performed in Negative Pressure Isolation Rooms during the COVID-19 Omicron Variant Pandemic in Taiwan: A Retrospective Cohort Study of a Single Institution.

Objective: To investigate the maternal-neonatal outcomes of obstetric deliveries performed in negative pressure isolated delivery rooms (NPIDRs) during the coronavirus disease 2019 (COVID-19) omicron variant pandemic period in a single tertiary center in northern Taiwan. Methods: Confirmed positive and suspected-positive COVID-19 cases delivered in NPIDRs and COVID-19-negative mothers delivered in conventional delivery rooms (CDRs) in the period of 1 May 2022 to 31 May 2022 during the COVID-19 omicron variant pandemic stage were reviewed. The maternal-neonatal outcomes between the two groups of mothers were analyzed. All deliveries were performed following the obstetric and neonatologic protocols conforming to the epidemic prevention regulations promulgated by the Taiwan Centers for Disease Control (T-CDC). Multiple gestations, deliveries at gestational age below 34 weeks, and major fetal anomalies were excluded from this study. Results: A total of 213 obstetric deliveries were included. Forty-five deliveries were performed in NPIDRs due to a positive COVID-19 polymerase chain reaction (PCR) test (n = 41) or suspected COVID-19 positive status (n = 4). One hundred and sixty-eight deliveries with negative COVID-19 PCR tests were performed in CDRs. There was no statistical difference in maternal characteristics between the two groups of pregnant women. All COVID-19-confirmed cases either presented with mild upper-airway symptoms (78%) or were asymptomatic (22%); none of these cases developed severe acute respiratory syndrome. The total rate of cesarean section was not statistically different between obstetric deliveries in NPIDRs and in CDRs (38.1% vs. 40.0%, p = 0.82, respectively). Regardless of delivery modes, poorer short-term perinatal outcomes were observed in obstetric deliveries in NPIDRs: there were significant higher rates of neonatal respiratory distress (37.8% vs. 10.7%, p < 0.001, respectively), meconium-stained amniotic fluid (22.2% vs. 4.2%, p < 0.001, respectively) and newborn intensive care unit admission (55.6% vs. 8.3%, p < 0.001, respectively) in obstetric deliveries performed in NPIDRs than in CDRs. Maternal surgical outcomes were not significantly different between the two groups of patients. There was no vertical transmission or nosocomial infection observed in COVID-19 confirmed cases in this study period. Conclusions: Our study demonstrates that obstetric deliveries for positive and suspected COVID-19 omicron-variant cases performed in NPIDRs are associated with poorer short-term perinatal outcomes. Reasonable use of personal protective equipment in NPIDRs could effectively prevent nosocomial infection during obstetric deliveries for pregnant women infected with the COVID-19 omicron variant.

Developing Pseudovirus-Based Neutralization Assay against Omicron-Included SARS-CoV-2 Variants

The global spread of SARS-CoV-2 and its variants poses a serious threat to human health worldwide. Recently, the emergence of Omicron has presented a new challenge to the prevention and control of the COVID-19 pandemic. A convenient and reliable in vitro neutralization assay is an important method for validating the efficiency of antibodies, vaccines, and other potential drugs. Here, we established an effective assay based on a pseudovirus carrying a full-length spike (S) protein of SARS-CoV-2 variants in the HIV-1 backbone, with a luciferase reporter gene inserted into the non-replicate pseudovirus genome. The key parameters for packaging the pseudovirus were optimized, including the ratio of the S protein expression plasmids to the HIV backbone plasmids and the collection time for the Alpha, Beta, Gamma, Kappa, and Omicron pseudovirus particles. The pseudovirus neutralization assay was validated using several approved or developed monoclonal antibodies, underscoring that Omicron can escape some neutralizing antibodies, such as REGN10987 and REGN10933, while S309 and ADG-2 still function with reduced neutralization capability. The neutralizing capacity of convalescent plasma from COVID-19 convalescent patients in Wuhan was tested against these pseudoviruses, revealing the immune evasion of Omicron. Our work established a practical pseudovirus-based neutralization assay for SARS-CoV-2 variants, which can be conducted safely under biosafety level-2 (BSL-2) conditions, and this assay will be a promising tool for studying and characterizing vaccines and therapeutic candidates against Omicron-included SARS-CoV-2 variants.

Attitude and behavior toward bystander cardiopulmonary resuscitation during COVID-19 outbreak

Background: Outbreaks of emerging infectious diseases, such as COVID-19, have negative impacts on bystander cardiopulmonary resuscitation (BCPR) for fear of transmission while breaking social distancing rules. The latest guidelines recommend hands-only cardiopulmonary resuscitation (CPR) and facemask use. However, public willingness in this setup remains unknown. Methods: A cross-sectional, unrestricted volunteer Internet survey was conducted to assess individuals' attitudes and behaviors toward performing BCPR, pre-existing CPR training, occupational identity, age group, and gender. The raking method for weights and a regression analysis for the predictors of willingness were performed. Results: Among 1,347 eligible respondents, 822 (61%) had negative attitudes toward performing BCPR. Healthcare providers (HCPs) and those with pre-existing CPR training had fewer negative attitudes (p < 0.001);HCPs and those with pre-existing CPR training and unchanged attitude showed more positive behaviors toward BCPR (p < 0.001). Further, 9.7% of the respondents would absolutely refuse to perform BCPR. In contrast, 16.9% would perform BCPR directly despite the outbreak. Approximately 9.9% would perform it if they were instructed, 23.5%, if they wore facemasks, and 40.1%, if they were to perform hands-only CPR. Interestingly, among the 822 respondents with negative attitudes, over 85% still tended to perform BCPR in the abovementioned situations. The weighted analysis showed similar results. The adjusted predictors for lower negative attitudes toward BCPR were younger age, being a man, and being an HCP;those for more positive behaviors were younger age and being an HCP. Conclusions: Outbreaks of emerging infectious diseases, such as COVID-19, have negative impacts on attitudes and behaviors toward BCPR. Younger individuals, men, HCPs, and those with pre-existing CPR training tended to show fewer negative attitudes and behaviors. Meanwhile, most individuals with negative attitudes still expressed positive behaviors under safer measures such as facemask protection, hands-only CPR, and available dispatch instructions. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

A Wide-bandwidth Nanocomposite-Sensor Integrated Smart Mask for Tracking Multi-phase Respiratory Activities for COVID-19 Endemic (preprint)

A global sentiment in early 2022 is that the COVID-19 virus could become endemic just like common cold flu viruses soon. The most optimistic view is that, with minimal precautions, such as vaccination, boosters and optional masking, life for most people will proceed as normal soon. However, as warned by A. Katzourakis of Oxford University recently [1], we must set aside lazy optimism, and must be realistic about the likely levels of death, disability and sickness that will be brought on by a COVID-19 endemic. Moreover, the world must also consider that continual circulation of the virus could give rise to new variants such as the new BA.2 variant (a subvariant of Omicron) continues to spread across the US and parts of Europe. Data from the CDC is already showing that BA.2 has been tripling in prevalence every two weeks [2]. Hence, globally, we must use available and proven weapons to continue to fight the COVID-19 viruses, i.e., effective vaccines, antiviral medications, diagnostic tests and stop an airborne virus transmission through social distancing, and mask wearing. For this work, we have demonstrated a smart mask with an optimally-coupled ultra-thin flexible soundwave sensors for tracking, classifying, and recognizing different respiratory activities, including breathing, speaking, and two-/tri-phase coughing; the masks functionality can also be augmented in the future to monitor other human physiological signals. Although researchers have integrated sensors into masks to detect respiratory activities in the past, they only based on measuring temperature and air flow during coughing, i.e., counting only the number of coughs. However, coughing is a process consisting of several phases, including an explosion of the air with glottal opening producing some noise-like waveform, a decrease of airflow to decrease sound amplitude, and a voiced stage which is the interruption of the air flow due to the closure of glottal and periodical vibration of partly glottis, which is not always present. Therefore, sensors used for cough detection should not be only sensitive to subtle air pressure but also the high-frequency vibrations, i.e., a pressure sensor that needs to be responsive to a wide input amplitude and bandwidth range, in order to detect air flows between hundreds of hertz from breath, and acoustic signals from voice that could reach [~] 8000 Hz. Respiratory activities data from thirty-one (31) human subjects were collected. Machine learning methods such as Support Vector Machines and Convolutional Neural Networks were used to classify the collected sensor data from the smart mask, which show an overall macro-recall of about 93.88% for the three respiratory sounds among all 31 subjects. For individual subjects, the 31 human subjects have the average macro-recall of 95.23% (ranging from 90% to 100%) for these 3 respiratory activities. Our work bridges the technological gap between ultra-lightweight but high-frequency response sensor material fabrication, signal transduction and conditioning, and applying machining learning algorithms to demonstrate a reliable wearable device for potential applications in continual healthy monitoring of subjects with cough symptoms during the eventual COVID-19 endemic. The monitoring and analysis of cough sound should be highly beneficial for human health management. These health monitoring data could then be shared with doctors via cloud storage and transmission technique to help disease diagnosis more effectively. Also, communication barriers caused by wearing masks can be alleviated by combining with the speech recognition techniques. In general, this research helps to advance the wearable device technology for tracking respiratory activities, similar to an Apple Watch or a Fitbit smartwatch in tracking physical and physiological activities.

Intellectual Property, Drug Regulatory, and Health Governance

During the current global COVID-19 pandemic, drugs and medical devices have again shown how they can be a critical weapon in the battlefield of health governance. However, due to the inherent characters of a longdeveloping period, high costs, and unexpected risks, the products and biotechnology industry need a comprehensive regime supported by state sovereignties to provide sufficient resources, control unpredictable risks, and protect their interests. This paper uses drugs as an example and Taiwan laws as the background to discuss how the products play a critical role in health governance from intellectual property and regulatory perspectives.

Network of “drug-target-SARS-CoV-2 Related Genes” Through Integrated Analysis of Pharmacology and Geo Database (preprint)

BackgroundCoronavirus Disease 2019 (COVID-19) respiratory disease rapidly caused a global pandemic and social and economic disruption. The combination of Traditional Chinese medicine (TCM) and Conventional Western medicine (CWM) is more effective for COVID-19 treatment. Moreover, TCM and CWM are important data source for developing new drug targets and promote strategies treat SARS-CoV-2 infections. However, many studies have analyzed the therapeutic mechanism of CWM or TCM alone for COVID-19, it is still unclear the interaction mechanism between TCM and CWM on COVID-19.MethodsThis paper integrates network pharmacology and GEO database to mine and identify COVID-19 molecular therapeutic targets, providing potential targets and new ideas for COVID-19 gene therapy and new drug development. It includes: 1) using TCMSP, TTD, PubChem and CTD databases to analyze drug interactions and associated phenotypes for SARS-CoV-2, to correlate drug and disease interaction mechanisms to screen key drug targets; 2) using GEO database to correlate differential genes and drug targets to screen potential antiviral gene therapy targets, to construct regulatory network and key points of SARS-CoV-2 therapeutic drugs; 3) using computer simulation of molecular docking to screen virus-related proteins for new drugs. ResultsIntegrated analysis of network pharmacology discovered that baicalein, estrone and quercetin are the pivotal active ingredients in TCM and CWM. Combining drug target genes in pharmacology database and virus induced genes in GEO database, the result showed the core hub genes related to COVID-19: STAT1, IL1B, IL6, IL8, PTGS2 and NFKBIA, and these genes were significantly downregulated in A549 and NHBE cells by SARS-CoV-2 infection. Moreover, chemical interaction and molecular docking analysis of hub genes showed that folic acid might as be potential therapeutic drug for COVID-19 treatment, and SARS-CoV-2 nucleocapsid phosphoprotein was a potential drug target. The network of “drug-target-SARS-CoV-2 related genes” provide noval potential compounds and targets for further studies of SARS-CoV-2.ConclusionsIntegrated analysis of network pharmacology and big data mining provided noval potential compounds and targets for further studies of SARS-CoV-2. Our research implied folic acid and SARS-CoV-2 N as therapeutic target in TCM and CWM. Our research also suggests that targeting SARS-CoV-2 N protein is likely to be a common mechanism of TCM and CWM. On the one hand, the identification of pivotal genes provides a target for COVID-19 molecular therapy, on the other hand, it provides ideas for the analysis of interaction mechanism between virus and host.

Emergency department response to coronavirus disease 2019 outbreak with a fever screening station and "graded approach" for isolation and testing.

BACKGROUND: Ever since coronavirus disease 2019 (COVID-19) emerged in Wuhan, China, in December 2019, it has had a devastating effect on the world through exponential case growth and death tolls in at least 146 countries. Rapid response and timely modifications in the emergency department (ED) for infection control are paramount to maintaining basic medical services and preventing the spread of COVID-19. This study presents the unique measure of combining a fever screening station (FSS) and graded approach to isolation and testing in a Taiwanese medical center. METHODS: An FSS was immediately set up outside the ED on January 27, 2019. A graded approach was adopted to stratify patients into "high risk," "intermediate risk," and "undetermined risk" for both isolation and testing. RESULTS: A total of 3755 patients were screened at the FSS, with 80.3% visiting the ED from home, 70.9% having no travel history, 21.4% having traveled to Asia, and 10.0% of TVGH staff. Further, 54.9% had fever, 35.5% had respiratory symptoms, 3.2% had gastrointestinal symptoms, 0.6% experienced loss of smell, and 3.1% had no symptoms; 81.3% were discharged, 18.6% admitted, and 0.1% died. About 1.9% were admitted to the intensive care unit, 10.3% to the general ward, and 6.4% were isolated. Two patients tested positive for COVID-19 (0.1%) and 127 (3.4%) tested positive for atypical infection; 1471 patients were tested for COVID-19; 583 were stratified as high-risk, 781 as intermediate-risk, and 107 as undetermined-risk patients. CONCLUSION: Rapid response for infection control is a paramount in the ED to confront the COVID-19 outbreak. The FFS helped divide the flow of high- and intermediate-risk patients; it also decreased the ED workload during a surge of febrile patients. A graded approach to testing uses risk stratification to prevent nosocomial infection of asymptomatic patients. A graded approach to isolation enables efficient allocation of scarce medical resources according to risk stratification.

Relationship between the COVID-19 exposure and depression and anxiety: mediating role of social support / 中国学校卫生

Objective@#To investigate the social support of medical students during the outbreak of COVID-19 and its mediating effect on the correlation between epidemic exposure and depression with anxiety.@*Methods@#A total of 5 593 medical students were enrolled, and Social Support Rating Scale(SSRS), Patient Health Questionnaire-9 and 7-tiem Generalize Anxiety Disorder Scale were used to measure.@*Results@#The social support score of SSRS of male students was lower than that of female students (t=-4.36, P<0.05) and juniors and seniors scored lower than other grades(F=4.84, P<0.05). Epidemic exposure proportion was positively correlated with both depressive proportionand anxiety proportion(r=0.05, 0.06, P<0.01), while epidemic exposure and depressive proportion and anxiety proportion were negatively correlated with social support score(r=-0.05, -0.25, -0.19, P<0.01). After controlling for gender and grade, the mediating effect of social support in the correlation between epidemic exposure and depression accounted for 26.6% of the total effect, and the mediating effect of subjective support and supportive utilization was 32.3% and 25.7% respectively. After controlling for gender and grade, the mediating effect of social support in the correlation between epidemic exposure and depression accounted for 20.0% of the total effect, and the mediating effect of subjective support and supportive utilization was 15.9% and 12.2% respectively.@*Conclusion@#Social support has partially mediating effect in the correlation between epidemic exposure with depression and anxiety.

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.

Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.

Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses (preprint)

The outbreak of the new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus, Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.

Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing.

As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing.