Impact of COVID-19 on ICU nurses’ psychology and influencing factors under COVID-19’s normalization, prevention and control: A cross-sectional survey (preprint)

Background: The first-line ICU nurses still play an important role in the nursing of patients diagnosed by designated hospitals during the normalization prevention and control of COVID-19. Discussing the mental health status of the first-line ICU nurses will help to provide more accurate measures to improve the mental status of the first-line ICU nurses and improve the quality of nursing. Aims: To explore the impact and possible influencing factors of the novel coronavirus (COVID-19) on the psychology of ICU nurses under the normalization, prevention and control. Design: A cross-sectional survey. Method: We chose 40 ICU nurses working in designated hospitals for novel coronavirus pneumonia in October to December of 2021. A post-traumatic stress disorder survey scale and questionnaire were used to investigate the situation and stressors of first-line ICU nurses. Results: The average score on post-traumatic stress disorder of first-line ICU nurses was(21.68 + 6.76 ) points under the normalization of prevention and control of COVID-19. Two nurses scored 38 points and had significant clinical symptoms, making the incidence of post-traumatic stress disorder 5%. The main stressors included the discomfort of wearing protective equipment and the concern for relatives at home. Conclusions: This study shows COVID-19 has little effect on the mental health of front-line ICU nurses and exerts a lighter degree of pressure during the normalization of COVID-19. We can also further improve the psychological status of front-line ICU nurses by improving the quality of protective equipment, increasing ICU staff, obtaining the understanding and support of family members, hierarchical training, and the care and support of managers to further improve the quality of nursing.

Specific Pupylation as IDEntity Reporter (SPIDER) for the identification of Protein-Biomolecule interactions (preprint)

Protein-biomolecule interactions play pivotal roles in almost all biological processes, the identification of the interacting protein is essential. By combining a substrate-based proximity labelling activity from the pupylation pathway of Mycobacterium tuberculosis , and the streptavidin (SA)-biotin system, we developed S pecific P upylation as IDE ntity R eporter (SPIDER) for identifying protein-biomolecular interactions. As a proof of principle, SPIDER was successfully applied for global identification of interacting proteins, including substrates for enzyme (CobB), the readers of m 6 A, the protein interactome of mRNA, and the target proteins of drug (lenalidomide). In addition, by SPIDER, we identified SARS-CoV-2 Omicron variant specific receptors on cell membrane and performed in-depth analysis for one candidate, Protein-g. These potential receptors could explain the differences between the Omicron variant and the Prototype strain, and further serve as target for combating the Omicron variant. Overall, we provide a robust technology which is applicable for a wide-range of protein-biomolecular interaction studies.

COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters (preprint)

Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, varies with regard to symptoms and mortality rates among populations. Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19. However, differences in immune responses and clinical features among COVID-19 patients remain largely unknown. Here, we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters (COVID-ONE humoral immune). COVID-ONE humoral immunity is based on a dataset that contains the IgG/IgM responses to 21 of 28 known SARS-CoV-2 proteins and 197 spike protein peptides against 2,360 COVID-19 samples collected from 783 patients. In addition, 96 clinical parameters for the 2,360 samples and information for the 783 patients are integrated into the database. Furthermore, COVID-ONE humoral immune provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups. A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters. After the "START" button is clicked, one can readily obtain a comprehensive analysis report for further interpretation. COVID-ONE-humoral immune is freely available at www.COVID-ONE.cn.

COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters (preprint)

Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, varies with regard to symptoms and mortality rates among populations. Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19. However, differences in immune responses and clinical features among COVID-19 patients remain largely unknown. Here, we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters (COVID-ONE humoral immune). COVID-ONE humoral immunity is based on a dataset that contains the IgG/IgM responses to 21 of 28 known SARS-CoV-2 proteins and 197 spike protein peptides against 2,360 COVID-19 samples collected from 783 patients. In addition, 96 clinical parameters for the 2,360 samples and information for the 783 patients are integrated into the database. Furthermore, COVID-ONE humoral immune provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups. A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters. After the START button is clicked, one can readily obtain a comprehensive analysis report for further interpretation. COVID-ONE-humoral immune is freely available at www.COVID-ONE.cn.

Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems (preprint)

Amid of COVID-19 pandemic devastating the public health around the world, it become urgent to maintain a sufficiently large supply of nucleic acid tests to screen suspected cases timely. Reusable molecular probes in current testing method could potentially lead to enormous amount of screening capacity, critical for the disease control. Herein, we for the first time report a kind of self-resetting molecular probes for repeatedly detecting SARS-CoV-2 RNA, enabled by orchestrating a biomimetic fuel dissipative system via dynamic DNA nanotechnology. A set of simulation toolkits was utilized for the design and optimization of the self-resetting probe, allowing for highly consistent signal amplitudes across cyclic detections of SARS-CoV-2 RNA. Idiosyncratically, FWHM regulated by dissipative kinetics exhibits a fingerprint signal for high confidential identification of single-nucleotide mutation in the virus sequence. We further exploited our self-resetting probes to examine multiple human-infectious RNA virus including SARS-CoV-2, ZIKV, MERS-CoV, and SARS-CoV to demonstrate its generic nucleic acid detection capability and superior orthogonality. Self-resetting probes were also deployed for detection of 110 clinical nasopharyngeal swabs and correctly classify all the clinical samples from 55 COVID-19 patients and 55 controls. We anticipate that the DNA nanotechnology-enabled self-resetting probe could circumvent the lack of sustainability in the diagnostics of COVID-19 and other infectious diseases, thus helping disease control and building a broader global public health agenda.

What Drives Closed-End Fund Discounts? Evidence from COVID-19 (preprint)

By exploiting the exogenous COVID-19 shock, this paper attempts to shed light on the closed-end fund (CEF) discount puzzle. CEF discounts increased after COVID-19, and I identify a causal role of sentiment in this effect. I show that COVID-19 reduced individual investor sentiment. Using the difference-in-differences (DiD) approach, I find that CEFs with higher sentiment beta or higher retail ownership experienced a larger increase in discounts after the COVID-19 shock. The DiD results are unlikely to be driven by alternative channels such as the liquidity, expense, payout, and leverage channels. Overall, the results support the sentiment-based explanation of CEF discounts.

Antibody Landscape Against SARS-CoV-2 Proteome Revealed Significant Differences between Non-Structural/ Accessory Proteins and Structural Proteins (preprint)

The immunogenicity of SARS-CoV-2 proteome is largely unknown, especially for non-structural proteins and accessory proteins. Here we collected 2,360 COVID-19 sera and 601 control sera. We analyzed these sera on a protein microarray with 20 proteins of SARS-CoV-2, built an antibody response landscape for IgG and IgM. We found that non-structural proteins and accessory proteins NSP1, NSP7, NSP8, RdRp, ORF3b and ORF9b elicit prevalent IgG responses. The IgG patterns and dynamic of non-structural/ accessory proteins are different from that of S and N protein. The IgG responses against these 6 proteins are associated with disease severity and clinical outcome and declined sharply about 20 days after symptom onset. In non-survivors, sharp decrease of IgG antibodies against S1 and N protein before death was observed. The global antibody responses to non-structural/ accessory proteins revealed here may facilitate deeper understanding of SARS-CoV-2 immunology.Funding: This work was partially supported by the National Key Research and Development Program of China Grant (No.2016YFA0500600), National Natural Science Foundation of China (No. 31970130, 31600672, 31670831, 31370813, 31900112 and 21907065).Conflict of Interest: The authors declare no competing interests.Ethical Approval: The study was approved by the Ethical Committee of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (ITJ-C20200128). Written informed consent was obtained from all participants enrolled in this study.

A SARS-CoV-2 Reference Standard Quantified by Multi-digital PCR Platforms for Quality Assessment of Molecular Tests (preprint)

SARS-CoV-2 is the seventh coronavirus known to infect humans and has caused an emerging and rapidly evolving global pandemic (COVID-19) with significant morbidity and mortality. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. The limit of detection (LoD) is a crucial feature for a diagnostic assay to detect SARS-CoV-2 in clinical samples, and a reference standard with a well-characterized concentration or titer is of the utmost importance for LoD studies. Although several reference standards of plasmids or synthetic RNA carrying specific genomic regions of SARS-CoV-2 have already been announced, a reference standard for inactivated virus particles with accurate concentration is still needed to evaluate the complete procedure including nucleic acid extraction and to accommodate customized primer-probe sets targeting different genome sequences. Here, we performed a collaborative study to estimate the NAT-detectable units as viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6x105 {+/-} 6.5x104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.

Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution (preprint)

SARS-CoV-2 specific IgG responses play critical roles for patients to recover from COVID-19, in-depth dissecting of the IgG responses on systems level is of great interest. Herein, we adopted a newly developed high-throughput epitope mapping technology (AbMap), analyzed 55 COVID-19 convalescent sera and 226 antibody samples enriched by specific proteins or peptides from these sera. We revealed three areas that are rich of IgG epitopes, two are on Spike protein but outside of RBD, and one is on Nucleocapsid protein. We identified 29 significant epitopes on Spike protein, from two of these significant epitopes, two critical epitope residues were found, i. e., D936 and P1263, which are highly related to the infectivity of SARS-CoV-2. In summary, we provided the first global map of IgG binding epitopes for SARS-CoV-2 at single amino acid resolution. This map will facilitate the precise development of therapeutic antibodies and vaccines.

Linear Epitope Landscape of SARS-CoV-2 Spike Protein Constructed from 1,051 COVID-19 Patients (preprint)

Neutralization antibodies and vaccines for treating COVID-19 are desperately needed. For precise development of antibodies and vaccines, the key is to understand which part of SARS-CoV-2 Spike protein is highly immunogenic on a systematic way. We generate a linear epitope landscape of Spike protein by analyzing serum IgG response of 1,051 COVID-19 patients with a peptide microarray. We reveal two regions that rich of linear epitopes, i.e., CTD and a region close to the S2’ cleavage site and fusion peptide. Unexpectedly, we find RBD is lack of linear epitope. Besides 3 moderate immunogenic peptides from RBD, 16 highly immunogenic peptides from other regions of Spike protein are determined. These peptides could serve as the base for precise development of antibodies and vaccines for COVID-19 on a systematic level.Funding: This work was partially supported by National Key Research and Development Program of China Grant (No. 2016YFA0500600), Science and Technology Commission of Shanghai Municipality (No. 19441911900), Interdisciplinary Program of Shanghai Jiao Tong University (No. YG2020YQ10), National Natural Science Foundation of China (No. 31970130, 31600672, 31670831, and 31370813).Conflict of Interest: The authors declare no competing interest.

Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients (preprint)

SARS-CoV-2 outbreak is a world-wide pandemic. The Spike protein plays central role in cell entry of the virus, and triggers significant immuno-response. Our understanding of the immune-response against S protein is still very limited. Herein, we constructed a peptide microarray and analyzed 55 convalescent sera, three areas with rich linear epitopes were identified. Potent neutralizing antibodies enriched from sera by 3 peptides, which do not belong to RBD were revealed.

Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors (preprint)

Development of an anti-SARS-CoV-2 therapeutic is hindered by the lack of physiologically relevant model systems that can recapitulate host-viral interactions in human cell types, specifically the epithelium of the lung. Here, we compare induced pluripotent stem cell (iPSC)-derived alveolar and airway epithelial cells to primary lung epithelial cell controls, focusing on expression levels of genes relevant for COVID-19 disease modeling. iPSC-derived alveolar epithelial type II-like cells (iAT2s) and iPSC-derived airway epithelial lineages express key transcripts associated with lung identity in the majority of cells produced in culture. They express ACE2 and TMPRSS2, transcripts encoding essential host factors required for SARS-CoV-2 infection, in a minor subset of each cell sub-lineage, similar to frequencies observed in primary cells. In order to prepare human culture systems that are amenable to modeling viral infection of both the proximal and distal lung epithelium, we adapt iPSC-derived alveolar and airway epithelial cells to two-dimensional air-liquid interface cultures. These engineered human lung cell systems represent sharable, physiologically relevant platforms for SARS-CoV-2 infection modeling and may therefore expedite the development of an effective pharmacologic intervention for COVID-19.

Clinical Characteristics and Short-Term Outcomes of Severe Patients with COVID-19 in Wuhan, China (preprint)

ObjectiveA novel pneumonia (COVID-19) which is sweeping the globe was started in December, 2019, in Wuhan, China. Most deaths occurred in severe and critically cases, but information on prognostic risk factors for severe ill patients is incomplete. Further research is urgently needed to guide clinicians, so we prospectively evaluate the clinical outcomes of 114 severe ill patients with COVID-19 for short-term in the Union Hospital in Wuhan, China. MethodsIn this single-centered, prospective and observational study, we enrolled 114 severe ill patients with confirmed COVID-19 from Jan 23, 2020 to February 22, 2020. Epidemiological, demographic and laboratory information were collected at baseline, data on treatment and outcome were collected until the day of death or discharge or for the first 28 days after severe ill diagnosis, whichever was shorter. Univariate and multivariate Cox proportional hazard models were used to determine hazard ratios (HRs) and 95% confidence intervals (CIs) of poor outcome. ResultsAmong enrolled 114 patients, 94 (82.5%) had good outcome while 20 (17.5%) had poor outcome. No significant differences were showed in age, gender and the prevalence of coexisting disorders between outcome groups. Results of multivariate Cox analyses indicated that higher levels of oxygen saturation (HR, 0.123; 95% CI, 0.041-0.369), albumin (HR, 0.060; 95% CI, 0.008-0.460) and arterial partial pressure of oxygen (HR, 0.321; 95% CI, 0.106-0.973) were associated with decreased risk of developing poor outcome within 28 days. In the other hand, higher levels of leucocytes (HR, 5.575; 95% CI, 2.080-14.943), neutrophils (HR, 2.566; 95% CI, 1.022-6.443), total bilirubin (HR, 6.171; 95% CI, 2.458- 15.496), globulin (HR, 2.526; 95% CI, 1.027-6.211), blood urea nitrogen (HR, 5.640; 95% CI, 2.193-14.509), creatine kinase-MB (HR, 3.032; 95% CI, 1.203-7.644), lactate dehydrogenase (HR, 4.607; 95% CI, 1.057-20.090), hypersensitive cardiac troponin I (HR, 5.023; 95% CI, 1.921-13.136), lactate concentration (HR,15.721; 95% CI, 2.099-117.777), Interleukin-10 (HR, 3.551; 95% CI, 1.280-9.857) and C-reactive protein (HR, 5.275; 95% CI, 1.517-18.344) were associated with increased risk of poor outcome development. We also found that traditional Chinese medicine can significantly improve the patients condition, which is conducive to the transformation from severe to mild. ConclusionIn summary, we firstly reported this single-centered, prospective and observational study for short-term outcome in severe patients with COVID-19. We found that cytokine storm and uncontrolled inflammation responses, liver, kidney, cardiac dysfunction may play important roles in final outcome of severe ill patients with COVID-19. Our study will provide clinicians to be benefit to rapidly estimate the likelihood risk of short-term poor outcome for severe patients.