Risk factors associated with indoor transmission during home quarantine of COVID-19 patients.

Purpose: The study aimed to identify potential risk factors for family transmission and to provide precautionary guidelines for the general public during novel Coronavirus disease 2019 (COVID-19) waves. Methods: A retrospective cohort study with numerous COVID-19 patients recruited was conducted in Shanghai. Epidemiological data including transmission details, demographics, vaccination status, symptoms, comorbidities, antigen test, living environment, residential ventilation, disinfection and medical treatment of each participant were collected and risk factors for family transmission were determined. Results: A total of 2,334 COVID-19 patients participated. Compared with non-cohabitation infected patients, cohabitated ones were younger (p = 0.019), more commonly unvaccinated (p = 0.048) or exposed to infections (p < 0.001), and had higher rates of symptoms (p = 0.003) or shared living room (p < 0.001). Risk factors analysis showed that the 2019-nCov antigen positive (OR = 1.86, 95%CI 1.40-2.48, p < 0.001), symptoms development (OR = 1.86, 95%CI 1.34-2.58, p < 0.001), direct contact exposure (OR = 1.47, 95%CI 1.09-1.96, p = 0.010) were independent risk factors for the cohabitant transmission of COVID-19, and a separate room with a separate toilet could reduce the risk of family transmission (OR = 0.62, 95%CI 0.41-0.92, p = 0.018). Conclusion: Patients showing negative 2019-nCov antigen tests, being asymptomatic, living in a separate room with a separate toilet, or actively avoiding direct contact with cohabitants were at low risk of family transmission, and the study recommended that avoiding direct contact and residential disinfection could reduce the risk of all cohabitants within the same house being infected with COVID-19.

Development of multiscale ultra-coarse-grained models for the SARS-CoV-2 virion from cryo-electron microscopy data.

The global spread of the new coronavirus COVID-19 has seriously affected human health and has caused a large number of deaths. Using molecular dynamics (MD) simulations to study the microscopic dynamic behavior of the virion provides an important means to study the pathogenic mechanism. In this work, we develop an ultra-coarse-grained (UCG) model of the SARS-CoV-2 virion from the authentic cryo-electron microscopy data, which enables MD simulation of the entire virion within microseconds. In addition, a hybrid all-atom and UCG (AA/UCG) virion model involving an all-atom spike protein is developed for the investigation of the spike protein interactions. A comparison of the conformational changes for the spike proteins as simulated in the hybrid model and that isolated in solution as in the free form reveals that the former is completely different from the latter. The simulation results demonstrate the necessity for the development of multiscale models to study the functions of proteins in the biomolecular complexes.

Transmission of SARS-CoV-2 Omicron Variant under a Dynamic Clearance Strategy in Shandong, China.

SARS-CoV-2 Omicron caused a large wave of COVID-19 cases in China in spring 2022. Shandong was one of the most affected regions during this epidemic yet was also among those areas that were able to quickly contain the transmission. We aimed to investigate the origin, genetic diversity, and transmission patterns of the Omicron epidemic in Shandong under a dynamic clearance strategy. We generated 1,149 Omicron sequences, performed phylogenetic analysis, and interpreted results in the context of available epidemiological information. We observed that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to majority of local cases. We found evidence suggesting that some local clusters were potentially associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. We identified a BA.1.1 genome with the R493Q reversion mutation in the spike receptor binding domain, potentially associated with an escape from vaccine and Omicron infection elicited neutralizing immunity. Our findings illustrated how the dynamic clearance strategy constrained this epidemic's size, duration, and geographical distribution. IMPORTANCE Starting in March 2022, the Omicron epidemic caused a large wave of COVID-19 cases in China. Shandong was one of the most affected regions during this epidemic but was also among those areas that were able to quickly contain the transmission. We investigated the origin, genetic diversity, and transmission patterns of Omicron epidemic in Shandong under a dynamic clearance strategy. We found that there were multiple introductions of distinct Omicron sublineages into Shandong from foreign countries and other regions in China, while a small number of introductions led to most local cases. We found evidence suggesting that some local clusters were associated with foreign imported cases. Superspreading events and cryptic transmissions contributed to the rapid spread of this epidemic. Our study illustrated the transmission patterns of Omicron epidemic in Shandong and provided a looking glass onto this epidemic in China.

Multi-mitigation strategies in medical supplies for epidemic outbreaks.

The outbreak of Coronavirus disease 2019 (COVID-19) highlights the importance of sufficient medical supplies stockpiling at the pre-event stage. In contrast, the potential disadvantages of maintaining adequate items at strategic locations (i.e., reserves) are considerable inventory-related costs. Unpredicted demand leads to a high degree of uncertainty. Efforts to mitigate the uncertainty should rely not only on prepositioning supplies at reserves but also on integrating various channels of medical materials. This paper proposes multi-mitigation strategies in medical supplies to ensure uninterrupted supply for hospitals and significant savings by introducing two-type suppliers, reserving and manufacturing suppliers. Thus, each hospital with uncertain demand is enabled to be served by various channels during pandemics: prepositioning in reserves, backups served by reserving suppliers, and medical commodities produced by manufacturing suppliers. Stochasticity is also incorporated into the raw materials available to produce. This research aims to develop an emergency response application that integrates preparedness action (reserve location, inventory level, and contract supplier's selection) with post-event operations (allocating medical materials from various channels). We formulate a two-stage stochastic mixed integer program to determine prepositioning strategy, including two-type suppliers' selection, and post-event allocation of multiple sources. A branch-and-Benders-cut method is developed for this problem and significantly outperforms both the classical Benders decomposition and Gurobi in the solution time. Different-sized test instances also verify the robustness of the proposed method. Based on a realistic and typical case study (inspired by the COVID-19 pandemic in Wuhan, China), significant savings, an increase in inventory utilization and an increase in demand fulfilment are obtained by our approach.

Humoral immunity and transcriptome differences of COVID-19 inactivated vacciane and protein subunit vaccine as third booster dose in human.

Under the background of the severe human health and world economic burden caused by COVID-19, the attenuation of vaccine protection efficacy, and the prevalence and immune escape of emerging variants of concern (VOCs), the third dose of booster immunization has been put on the agenda. Systems biology approaches can help us gain new perspectives on the characterization of immune responses and the identification of factors underlying vaccine-induced immune efficacy. We analyzed the antibody signature and transcriptional responses of participants vaccinated with COVID-19 inactivated vaccine and protein subunit vaccine as a third booster dose. The results from the antibody indicated that the third booster dose was effective, and that heterologous vaccination with the protein subunit vaccine as a booster dose induced stronger humoral immune responses than the homologous vaccination with inactivated vaccine, and might be more effective against VOCs. In transcriptomic analysis, protein subunit vaccine induced more differentially expressed genes that were significantly associated with many important innate immune pathways. Both the homologous and heterologous boosters could increase the effectiveness against COVID-19, and compared with the inactivated vaccine, the protein subunit vaccine, mediated a stronger humoral immune response and had a more significant correlation with the innate immune function module, which provided certain data support for the third booster immunization strategy.

Corporate philanthropic giving and nature of stock market reaction: Evidence from China: MDE

This study examines whether enterprises can obtain abnormal returns through philanthropic giving during public health emergencies, such as the COVID‐19 crisis, by using an event study approach to conduct an empirical analysis. The results show that if enterprises participate in philanthropic giving during the COVID‐19 crisis, they can obtain abnormal returns in the stock market. The extent of this market reaction is directly proportional to the level of philanthropic giving, and it is more significant for private enterprises, enterprises in regions that are more affected by the epidemic, enterprises in social responsibility sensitive industries, and enterprises with more timely donations.

Transcriptome Analysis of Peripheral Blood Mononuclear Cells in SARS-CoV-2 Naïve and Recovered Individuals Vaccinated With Inactivated Vaccine.

The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the host's molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.

Analysis of the Transmission of SARS-CoV-2 Delta VOC in Yantai, China, August 2021.

Objective: Starting 31 July 2021, a SARS-CoV-2 outbreak occurred in Yantai, Shandong Province. The investigation showed that this outbreak was closely related to the epidemic at Nanjing Lukou Airport. In view of the fact that there were many people involved in this outbreak and these people had a complex activity area, the transmission route cannot be analyzed by simple epidemiological investigation. Here we combined the SARS-COV-2 whole-genome sequencing with epidemiology to determine the epidemic transmission route of Yantai. Methods: Thirteen samples of SARS-CoV-2 outbreak cases from 31 July to 4 August 2021 were collected and identified by fluorescence quantitative PCR, then whole-genome deep sequencing based on NGS was performed, and the data were analyzed and processed by biological software. Results: All sequences were over 29,000 bases in length and all belonged to B.1.617.2, which was the Delta strain. All sequences shared two amino acid deletions and 9 amino acid mutations in Spike protein compared with reference sequence NC_045512.2 (Wuhan virus strain). Compared with the sequence of Lukou Airport Delta strain, the homology was 99.99%. In order to confirm the transmission relationship between patients, we performed a phylogenetic tree analysis. The results showed that patient 1, patient 2, and patient 9 belong to an independent branch, and other patients have a close relationship. Combined with the epidemiological investigation, we speculated that the epidemic of Yantai was transmitted by two routes at the same time. Based on this information, our prevention and control work was carried out in two ways and effectively prevented the further spread of this epidemic.

Neutralizing SARS-CoV-2 by dimeric side chain-to-side chain cross-linked ACE2 peptide mimetics.

We present the finding of a dimeric ACE2 peptide mimetic designed through side chain cross-linking and covalent dimerization. It has a binding affinity of 16 nM for the SARS-CoV-2 spike RBD, and effectively inhibits the SARS-CoV-2 pseudovirus in Huh7-hACE2 cells with an IC50 of 190 nM and neutralizes the authentic SARS-CoV-2 in Caco2 cells with an IC50 of 2.4 µM. Our study should provide a new insight for the optimization of peptide-based anti-SARS-CoV-2 inhibitors.

Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device.

The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.

Case report: Nutrition therapy and side-effects monitoring in critically ill coronavirus disease 2019 patients.

An outbreak of pneumonia proved to be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named Coronavirus Disease 2019 (COVID-19) by World Health Organization (WHO), has rapidly and widely spread to the whole world, affecting thousands of people. COVID-19 patients have poor gastrointestinal function and microecological disorders, which lead to the frequent occurrence of aspiration pneumonia, gastric retention, and diarrhea. In the meanwhile, it takes a certain period of time for nutrition therapy to reach the patient's physiological amount. Refeeding syndrome and hypoglycemia may occur during this period, causing the high risk of death in critical patients. Therefore, we reported the nutrition therapy and side-effects monitoring as well as the adjustment of the nutrition therapy of 2 critical COVID-19 patients, thus provide clinical evidence for nutrition therapy and prevention of the side effects.

SARS-CoV-2 not found in pressure injury exudates from COVID-19 patients.

BACKGROUND: The emergence of COVID-19 has become a global health emergency. The transmissibility of the disease is of great interest to healthcare workers and scientists alike. The primary route of transmission is via respiratory droplets, but viral RNA has also been found in feces and body fluids such as urine, serum, and semen. So far, there has been no report on whether SARS-CoV-2 is present in the exudates of cutaneous lesions. This study was designed to investigate whether SARS-CoV-2 can be found in the pressure injury exudates in patients with severe COVID-19 infections. METHODS: 46 critically ill COVID-19 patients who were admitted to the ICU of the Sino-French New City Branch of Tongji Hospital in Wuhan between February 4 and April 12 developed pressure injuries. 22 patients with pressure injuries had wound exudates. Wound and pharyngeal swabs of the 22 patients were collected and RT-PCRs were conducted to detect SARS-CoV-2 viral RNA. RESULTS: At the time of pressure injury, 5 patients still tested positive by pharyngeal swabs, the rest of the 17 patients tested negative. However, none of the wound exudate swabs from the participants tested positive for SARS-CoV-2 by RT-PCR. CONCLUSION: Our study suggests that it is rather unlikely that COVID-19 can be transmitted via pressure injury exudates, but we still recommend standardized personal protective equipment, face shield and an additional pair of gloves when treating pressure injuries.

Prediction on the number of confirmed Covid-19 with the FUDAN-CCDC mathematical model and its epidemiology, clinical manifestations, and prevention and treatment effects.

This study was to explore the development trend and clinical manifestations of COVID-19 better. The number of confirmed novel coronavirus pneumonia (COVID-19) was predicted based on the FUDAN-CCDC mathematical model (which was a new model namely based on the novel time delay dynamic model and the statistical data from Chinese Center for Disease Control (CCDC)). The epidemiology and clinical manifestations of COVID-19 were studied based on its clinical classification, and the prevention and treatment effects of antibacterial drugs on the COVID-19 were explored. Firstly, a FUDAN-CCDC mathematical model was established to predict the number of confirmed COVID-19 patients. Secondly, 500 COVID-19 patients with clear epidemiological history and confirmed by nucleic acid testing who were admitted to our Hospital from February 1, 2020 to May 1, 2020 were taken as research objects in this study. They were divided into 4 categories: mild cases, moderate cases, severe cases, and critical cases based on the standards given by the World Health Organization (WHO). The general data characteristics, epidemiological characteristics, clinical manifestations characteristics, laboratory indicator characteristics, and prevention and treatment effects of patients with COVID-19 were analyzed. The FUDAN-CCDC model predicted that the peak time of cumulative confirmed cases in Wuhan was from February 1 to February 5, the peak of cumulative confirmed cases was around 60,000, and the peak time of newly confirmed cases was from February 8 to February 11. Most of the patients with COVID-19 in critical cases were older, with an average age of 65.31 ±â€¯8.26 years old; it was mainly imported case (94 cases, 18.8%) at the beginning, and was mainly local cases (406 cases, 81.2%) later. The initial symptoms were fever (447 cases, 89.4%) and cough (304 cases, 60.8%), and the patients in severe and critical cases were often accompanied by respiratory failure and other late symptoms. There were differences in laboratory tests, patients in critical cases had increased procalcitonin (PCT) and less lymphocytes (LYM). The treatment of COVID-19 was mainly moxifloxacin tablets or injections and cefoperazone sodium sulbactam sodium for injection, with significant efficacy, but the cure rate of patients in severe and critical cases was low, which was 83.1% and 68.4% respectively. FUDAN-CCDC could be applied for prediction of the COVID-19 trend. COVID-19 patients with different clinical classifications were different in clinical symptoms, laboratory tests and treatment options, and the cure rate of patients in severe and critical cases was low. This article was conductive to improving the prevention and treatment of COVID-19, so as to provide a theoretical reference.

Expression of eosinophil in peripheral blood of patients with COVID-19 and its clinical significance.

AIMS: To investigate the eosinophil cell (EC) expression in peripheral blood of patients infected with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) and its clinical significance of diagnosis and prognosis. METHODS: 95 patients, whose nucleic acid test of SARS-CoV-2 was positive to make a definite diagnosis of COVID-19, were selected as the study group. They were admitted at the Chengdu Public Health Clinical Medical Center from January 21 to March 2, 2020. Another 95 healthy subjects and 95 non-infectious fever patients during the same period were selected as the control group. The BC-6900 blood cell analyzer was used to continuously observe and detect ECs in 95 patients with COVID-19 and the control group. The differences in expression levels of ECs in peripheral blood were analyzed. RESULTS: ECs were significantly decreased in 95 (75.8%) COVID-19 patients (P < .01). The absolute EC count IQR was 0.01 × 109/L (0 × 109/L - 0.04 × 109/L), and the EC percentage IQR was 0.3% (0.1% - 0.8%). As the patients' condition improved, the ECs returned to normal, but for those without improvement, ECs continued to decline. CONCLUSIONS: ECs decreased remarkably in patients with COVID-19, and gradually returned to normal after the improvement of the patients' condition, while EC continued to decrease in patients without improvement. It is suggested that ECs have certain clinical significance in the diagnosis and prognosis of COVID-19, and may be a useful index in the early warning of acute infectious diseases.

Chinese medical students' interest in COVID-19 pandemic.

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) happened in early December and it has affected China in more ways than one. The societal response to the pandemic restricted medical students to their homes. Although students cannot learn about COVID-19 through clinical practice, they can still pay attention to news of COVID-19 through various channels. Although, as suggested by previous studies, some medical students have already volunteered to serve during the COVID-19 pandemic, the overall willingness of Chinese medical students to volunteer for such has not been systematically examined. AIM: To study Chinese medical students' interest in the relevant knowledge on COVID-19 and what roles they want to play in the pandemic. METHODS: Medical students at Peking Union Medical College were surveyed via a web-based questionnaire to obtain data on the extent of interest in the relevant knowledge on COVID-19, attitude towards volunteerism in the pandemic, and career preference. Logistic regression modeling was used to investigate possible factors that could encourage volunteerism among this group in a pandemic. RESULTS: A total of 552 medical students responded. Most medical students showed a huge interest in COVID-19. The extent of students' interest in COVID-19 varied among different student-classes (P < 0.05). Senior students had higher scores than the other two classes. The number of people who were 'glad to volunteer' in COVID-19 represented 85.6% of the respondents. What these students expressed willingness to undertake involved direct, indirect, and administrative job activities. Logistic regression analysis identified two factors that negatively influenced volunteering in the pandemic: Student-class and hazards of the voluntary job. Factors that positively influenced volunteering were time to watch COVID-19 news, predictable impact on China, and moral responsibility. CONCLUSION: More innovative methods can be explored to increase Chinese medical students' interest in reading about the relevant knowledge on COVID-19 and doing voluntary jobs during the pandemic.

A Quantitative and Radiomics approach to monitoring ARDS in COVID-19 patients based on chest CT: a retrospective cohort study.

Rationale: Acute respiratory distress syndrome (ARDS) is one of the major reasons for ventilation and intubation management of COVID-19 patients but there is no noninvasive imaging monitoring protocol for ARDS. In this study, we aimed to develop a noninvasive ARDS monitoring protocol based on traditional quantitative and radiomics approaches from chest CT. Methods: Patients diagnosed with COVID-19 from Jan 20, 2020 to Mar 31, 2020 were enrolled in this study. Quantitative and radiomics data were extracted from automatically segmented regions of interest (ROIs) of infection regions in the lungs. ARDS existence was measured by Pa02/Fi02 <300 in artery blood samples. Three different models were constructed by using the traditional quantitative imaging metrics, radiomics features and their combinations, respectively. Receiver operating characteristic (ROC) curve analysis was used to assess the effectiveness of the models. Decision curve analysis (DCA) was used to test the clinical value of the proposed model. Results: The proposed models were constructed using 352 CT images from 86 patients. The median age was 49, and the male proportion was 61.9%. The training dataset and the validation dataset were generated by randomly sampling the patients with a 2:1 ratio. Chi-squared test showed that there was no significant difference in baseline of the enrolled patients between the training and validation datasets. The areas under the ROC curve (AUCs) of the traditional quantitative model, radiomics model and combined model in the validation dataset was 0.91, 0.91 and 0.94, respectively. Accordingly, the sensitivities were 0.55, 0.82 and 0.58, while the specificities were 0.97, 0.86 and 0.98. The DCA curve showed that when threshold probability for a doctor or patients is within a range of 0 to 0.83, the combined model adds more net benefit than "treat all" or "treat none" strategies, while the traditional quantitative model and radiomics model could add benefit in all threshold probability. Conclusions: It is feasible to monitor ARDS from CT images using radiomics or traditional quantitative analysis in COVID-19. The radiomics model seems to be the most practical one for possible clinical use. Multi-center validation with a larger number of samples is recommended in the future.