Comparative transcriptomic analyzes of human lung epithelial cells infected with wild-type SARS-CoV-2 and its variant with a 12-bp missing in the E gene.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that caused a global outbreak of coronavirus disease 2019 (COVID-19) pandemic. To elucidate the mechanism of SARS-CoV-2 replication and immunogenicity, we performed a comparative transcriptome profile of mRNA and long non-coding RNAs (lncRNAs) in human lung epithelial cells infected with the SARS-CoV-2 wild-type strain (8X) and the variant with a 12-bp deletion in the E gene (F8). In total, 3,966 differentially expressed genes (DEGs) and 110 differentially expressed lncRNA (DE-lncRNA) candidates were identified. Of these, 94 DEGs and 32 DE-lncRNAs were found between samples infected with F8 and 8X. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzes revealed that pathways such as the TNF signaling pathway and viral protein interaction with cytokine and cytokine receptor were involved. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to the immune response, which might explain the different replication and immunogenicity properties of the 8X and F8 strains. These results provide a useful resource for studying the pathogenesis of SARS-CoV-2 variants.

Comparative transcriptomic analyzes of human lung epithelial cells infected with wild-type SARS-CoV-2 and its variant with a 12-bp missing in the E gene

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that caused a global outbreak of coronavirus disease 2019 (COVID-19) pandemic. To elucidate the mechanism of SARS-CoV-2 replication and immunogenicity, we performed a comparative transcriptome profile of mRNA and long non-coding RNAs (lncRNAs) in human lung epithelial cells infected with the SARS-CoV-2 wild-type strain (8X) and the variant with a 12-bp deletion in the E gene (F8). In total, 3,966 differentially expressed genes (DEGs) and 110 differentially expressed lncRNA (DE-lncRNA) candidates were identified. Of these, 94 DEGs and 32 DE-lncRNAs were found between samples infected with F8 and 8X. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzes revealed that pathways such as the TNF signaling pathway and viral protein interaction with cytokine and cytokine receptor were involved. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to the immune response, which might explain the different replication and immunogenicity properties of the 8X and F8 strains. These results provide a useful resource for studying the pathogenesis of SARS-CoV-2 variants.

Improving COVID-19 CT classification of CNNs by learning parameter-efficient representation.

The COVID-19 pandemic continues to spread rapidly over the world and causes a tremendous crisis in global human health and the economy. Its early detection and diagnosis are crucial for controlling the further spread. Many deep learning-based methods have been proposed to assist clinicians in automatic COVID-19 diagnosis based on computed tomography imaging. However, challenges still remain, including low data diversity in existing datasets, and unsatisfied detection resulting from insufficient accuracy and sensitivity of deep learning models. To enhance the data diversity, we design augmentation techniques of incremental levels and apply them to the largest open-access benchmark dataset, COVIDx CT-2A. Meanwhile, similarity regularization (SR) derived from contrastive learning is proposed in this study to enable CNNs to learn more parameter-efficient representations, thus improve the accuracy and sensitivity of CNNs. The results on seven commonly used CNNs demonstrate that CNN performance can be improved stably through applying the designed augmentation and SR techniques. In particular, DenseNet121 with SR achieves an average test accuracy of 99.44% in three trials for three-category classification, including normal, non-COVID-19 pneumonia, and COVID-19 pneumonia. The achieved precision, sensitivity, and specificity for the COVID-19 pneumonia category are 98.40%, 99.59%, and 99.50%, respectively. These statistics suggest that our method has surpassed the existing state-of-the-art methods on the COVIDx CT-2A dataset. Source code is available at https://github.com/YujiaKCL/COVID-CT-Similarity-Regularization.

Intentions of Patients with Hypertension to Receive a Booster Dose of the COVID-19 Vaccine: A Cross-Sectional Survey in Taizhou, China.

COVID-19 patients with hypertension have increased hospital complications and mortality rates. Moreover, these patients also have lower antibody titers after receiving the coronavirus disease (COVID-19) vaccine. Therefore, patients with hypertension should receive a COVID-19 vaccine booster. To promote the uptake of COVID-19 vaccine booster among hypertensive patients, this study investigated patients' willingness and factors that influence patients with hypertension to receive the COVID-19 vaccine booster. From July 2021 to August, 410 patients with hypertension were surveyed. Overall, 76.8% of patients were willing to receive the COVID-19 vaccine booster, as 82.7% of patients without comorbidities and 72.7% of patients with comorbidities were willing to receive the vaccine booster. The main factors that influenced the willingness of patients with hypertension to receive a booster dose were the preventive effect of the vaccine (χ2 = 52.827, p < 0.05), vaccine safety (χ2 = 42.423, p < 0.05), vaccine knowledge (χ2 = 7.831, p < 0.05), presence of comorbidities (χ2 = 4.862, p < 0.05), disease control (χ2 = 5.039, p < 0.05), and antihypertensive treatments (χ2 = 12.565, p < 0.05). This study's findings highlight the need to promote knowledge about booster vaccination among patients and health management. These measures would improve patients' willingness and knowledge about the vaccine and their health status, which are the main factors that influence patients' intention to receive booster vaccines.

Investigations on the Respiratory Function in COVID-19 Patients: A Prospective Cohort Study.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) is a global public health crisis. However, whether it can cause respiratory dysfunction or physical and psychological disorders in patients remains unknown. Thus, this study was conducted to investigate the respiratory function, activities of daily living, quality of life, and mental status of patients with COVID-19. Participants and outcomes. Data was collected from the follow-up of eligible patients who attended the fever clinic of three hospitals in Jiangxi Province, from March to May 2020. The outcomes included respiratory muscle function, degree of dyspnea, aerobic capacity, activities of daily living, quality of life, and mental status. RESULTS: A total of 139 patients (72 men and 67 women) were included in this study. The proportions of mild, moderate, severe, and critical cases of COVID-19 were 7.1% (10 cases), 68.3% (95 cases), 20.1% (28 cases), and 4.2% (6 cases), respectively. The rates of abnormal maximal inspiratory pressure were 10.0%, 25.2%, 25.0%, and 16.7%, respectively. There were 50%, 65.3%, 50%, and 66.7% of the patients with abnormal dyspnea in the four clinical classifications, respectively. Patients generally show a decline in quality of life, anxiety, and depression symptoms. CONCLUSIONS: Respiratory dysfunction, decreased quality of life, and psychological disorders were present in each clinical classification of COVID-19. Therefore, it is necessary to carry out respiratory rehabilitation and psychological intervention for COVID-19 patients.

Azvudine is a thymus-homing anti-SARS-CoV-2 drug effective in treating COVID-19 patients.

Azvudine (FNC) is a nucleoside analog that inhibits HIV-1 RNA-dependent RNA polymerase (RdRp). Recently, we discovered FNC an agent against SARS-CoV-2, and have taken it into Phase III trial for COVID-19 patients. FNC monophosphate analog inhibited SARS-CoV-2 and HCoV-OC43 coronavirus with an EC50 between 1.2 and 4.3 µM, depending on viruses or cells, and selective index (SI) in 15-83 range. Oral administration of FNC in rats revealed a substantial thymus-homing feature, with FNC triphosphate (the active form) concentrated in the thymus and peripheral blood mononuclear cells (PBMC). Treating SARS-CoV-2 infected rhesus macaques with FNC (0.07 mg/kg, qd, orally) reduced viral load, recuperated the thymus, improved lymphocyte profiles, alleviated inflammation and organ damage, and lessened ground-glass opacities in chest X-ray. Single-cell sequencing suggested the promotion of thymus function by FNC. A randomized, single-arm clinical trial of FNC on compassionate use (n = 31) showed that oral FNC (5 mg, qd) cured all COVID-19 patients, with 100% viral ribonucleic acid negative conversion in 3.29 ± 2.22 days (range: 1-9 days) and 100% hospital discharge rate in 9.00 ± 4.93 days (range: 2-25 days). The side-effect of FNC is minor and transient dizziness and nausea in 16.12% (5/31) patients. Thus, FNC might cure COVID-19 through its anti-SARS-CoV-2 activity concentrated in the thymus, followed by promoted immunity.

Development of a Recombinant RBD Subunit Vaccine for SARS-CoV-2.

The novel coronavirus pneumonia (COVID-19) pandemic is a great threat to human society and now is still spreading. Although several vaccines have been authorized for emergency use, only one recombinant subunit vaccine has been permitted for widespread use. More subunit vaccines for COVID-19 should be developed in the future. The receptor binding domain (RBD), located at the S protein of SARS-CoV-2, contains most of the neutralizing epitopes. However, the immunogenicity of RBD monomers is not strong enough. In this study, we fused the RBD-monomer with a modified Fc fragment of human IgG1 to form an RBD-Fc fusion protein. The recombinant vaccine candidate based on the RBD-Fc protein could induce high levels of IgG and neutralizing antibody in mice, and these could last for at least three months. The secretion of IFN-γ, IL-2 and IL-10 in the RBD-stimulated splenocytes of immunized mice also increased significantly. Our results first showed that the RBD-Fc vaccine could induce both humoral and cellular immune responses and might be an optional strategy to control COVID-19.

Detecting Portable Executable Malware by Binary Code Using an Artificial Evolutionary Fuzzy LSTM Immune System

As the planet watches in shock the evolution of the COVID-19 pandemic, new forms of sophisticated, versatile, and extremely difficult-to-detect malware expose society and especially the global economy. Machine learning techniques are posing an increasingly important role in the field of malware identification and analysis. However, due to the complexity of the problem, the training of intelligent systems proves to be insufficient in recognizing advanced cyberthreats. The biggest challenge in information systems security using machine learning methods is to understand the polymorphism and metamorphism mechanisms used by malware developers and how to effectively address them. This work presents an innovative Artificial Evolutionary Fuzzy LSTM Immune System which, by using a heuristic machine learning method that combines evolutionary intelligence, Long-Short-Term Memory (LSTM), and fuzzy knowledge, proves to be able to adequately protect modern information system from Portable Executable Malware. The main innovation in the technical implementation of the proposed approach is the fact that the machine learning system can only be trained from raw bytes of an executable file to determine if the file is malicious. The performance of the proposed system was tested on a sophisticated dataset of high complexity, which emerged after extensive research on PE malware that offered us a realistic representation of their operating states. The high accuracy of the developed model significantly supports the validity of the proposed method. The final evaluation was carried out with in-depth comparisons to corresponding machine learning algorithms and it has revealed the superiority of the proposed immune system.

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp. 1647: Pseudo-Tetrapeptides Active Against Influenza A Viruses and Coronavirus HCoV-229E.

Many microorganisms have mechanisms that protect cells against attack from viruses. The fermentation components of Streptomyces sp. 1647 exhibit potent anti-influenza A virus (IAV) activity. This strain was isolated from soil in southern China in the 1970s, but the chemical nature of its antiviral substance(s) has remained unknown until now. We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete. The antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) analysis of its genome sequence revealed 38 biosynthetic gene clusters (BGCs) for secondary metabolites, and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis. Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene, cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds. Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues. Finally, 18 pseudo-tetrapeptides with an internal ureido linkage, omicsynins A1-A6, B1-B6, and C1-C6, were identified and/or isolated from fermentation broth. Among them, 11 compounds (omicsynins A1, A2, A6, B1-B3, B5, B6, C1, C2, and C6) are new compounds. Omicsynins B1-B4 exhibited potent antiviral activity against IAV with the 50% inhibitory concentration (IC50) of approximately 1 µmol∙L-1 and a selectivity index (SI) ranging from 100 to 300. Omicsynins B1-B4 also showed significant antiviral activity against human coronavirus HCoV-229E. By integrating multi-omics data, we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp. 1647, indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.

Application of microlecture teaching methods in standardized residency training during COVID-19 in Wuhan: a randomized, controlled study.

BACKGROUND: Providing high-quality training to residency students during the coronavirus 2019 (COVID-19) pandemic has been a goal of our institution. Since 2108, we began to take microlectures to students teaching. Microlectures are online presentations, and the microlecture teaching method has many advantages, such as a short teaching time, situational resource composition, diverse communication, strong pertinence and can attend microlectures from home. The aim of the present study was to evaluate the advantages of the microlecture teaching method on students in standardized residency training. METHODS: Students from our department were randomly divided into the traditional teaching group (control group) and the microlecture teaching group (observation group). The teaching duration for both groups was 3 months. All students were assessed on basic knowledge of the neurology before enrollment. After the teaching session, the students were assessed on teaching effect, theoretical operation, and clinical practice satisfaction. The students also evaluated the teachers, and the teachers evaluated the students. RESULTS: A total of 84 students participated in the study and were divided equally into the observation group (42 students) and the control group (42 students). The results showed that the rate of reaching the standard of teaching effect, achievement of theory and operation, satisfaction with clinical practice, the student's grades by teachers, and student satisfaction with teachers were significantly higher in the observation group than in the control group (all P<0.05). CONCLUSIONS: The microlecture teaching method can effectively improve the clinical teaching effect for neurology students and should be adopted in clinical teaching, especially during the COVID-19 pandemic.

Liuzijue is a promising exercise option for rehabilitating discharged COVID-19 patients.

BACKGROUND: Among discharged COVID-19 patients, the health-related quality of life is poor, and patients suffer from significant physical and psychological impairment. This study was designed to investigate the effects of Liuzijue exercise on the rehabilitation of COVID-19 patients. METHODS: Thirty three eligible patients with COVID-19 were enrolled in the study after discharge. All the participants practiced Liuzijue exercise once per day for 20 minutes over 4 weeks. Data were collected at baseline and the end of the intervention. Primary outcomes involved functional capacity and secondary outcomes involved quality of life. RESULTS: The maximal inspiratory pressure (MIP), peak inspiratory flow (PIF), and diaphragm movement in deep breathing (DM-DB) of patients increased significantly after 4 weeks of intervention. The dyspnea was also alleviated and exercise capacity was significantly improved. In terms of quality of life, physical functioning and role-physical scores were significantly increased. Moreover, Liuzijue could significantly alleviate the depression and anxiety status of the patients. CONCLUSION: Liuzijue exercise is a viable alternative home exercise program that produced better functional capacity and quality of life in discharged patients with COVID-19. These findings also showed the necessity of rehabilitation intervention for cured COVID-19 patients.

CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells.

In face of the everlasting battle toward COVID-19 and the rapid evolution of SARS-CoV-2, no specific and effective drugs for treating this disease have been reported until today. Angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, mediates the virus infection by binding to spike protein. Although ACE2 is expressed in the lung, kidney, and intestine, its expressing levels are rather low, especially in the lung. Considering the great infectivity of COVID-19, we speculate that SARS-CoV-2 may depend on other routes to facilitate its infection. Here, we first discover an interaction between host cell receptor CD147 and SARS-CoV-2 spike protein. The loss of CD147 or blocking CD147 in Vero E6 and BEAS-2B cell lines by anti-CD147 antibody, Meplazumab, inhibits SARS-CoV-2 amplification. Expression of human CD147 allows virus entry into non-susceptible BHK-21 cells, which can be neutralized by CD147 extracellular fragment. Viral loads are detectable in the lungs of human CD147 (hCD147) mice infected with SARS-CoV-2, but not in those of virus-infected wild type mice. Interestingly, virions are observed in lymphocytes of lung tissue from a COVID-19 patient. Human T cells with a property of ACE2 natural deficiency can be infected with SARS-CoV-2 pseudovirus in a dose-dependent manner, which is specifically inhibited by Meplazumab. Furthermore, CD147 mediates virus entering host cells by endocytosis. Together, our study reveals a novel virus entry route, CD147-spike protein, which provides an important target for developing specific and effective drug against COVID-19.

A SARS-CoV-2 variant with the 12-bp deletion at E gene.

The coronavirus disease 2019 (COVID-19) pandemic is still ongoing and has become an important public health threat. This disease is caused by a new coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, and so far, little is known about this virus. In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. There was no significant difference in the viral titer and infectivity of these two strains. The S protein content of the F8 viral culture was 0.39 µg/ml, much higher than that of 8X. An inactivated vaccine made from the F8 strain could trigger high levels of the IgG titer and neutralizing antibody titer, which could last for at least 6 weeks and were significantly higher than those from the 8X strain at 1 and 3 weeks post vaccination, respectively. In conclusion, we reported that both the E gene mutant and wild-type SARS-CoV-2 strains were isolated from the same clinical sample by plaque purification. A 12-bp deletion in the E gene was important for SARS-CoV-2 replication and immunogenicity.

Initial CT imaging characters of an imported family cluster of COVID-19.

The objective of this report is to better understand the initial CT imaging spectrum and the relationship between clinical characteristics and initial CT imaging features of an imported family cluster cases involving 7 laboratory-confirmed COVID-19 patients. We find that initial CT findings of 4 patients were positive within one week after the onset of symptoms and 1 patient was negative before the onset of symptoms. Two asymptomatic patients had typical CT abnormalities. The initial CT imaging manifestations are mainly peripheral or subpleural ground-glass opacities and ground-glass with consolidation. Our report is of potential guiding value for the initial CT screening of imported familial cluster cases since the imported cases have an identified time of infection.

Treating head and neck tumors during the SARS-CoV-2 epidemic, 2019 to 2020: Sichuan Cancer Hospital.

Since December 2019, a number of patients with novel coronavirus pneumonia (NCP) have been identified in Wuhan, Hubei Province, China. NCP has rapidly spread to other provinces and cities in China and other countries in the world. Due to the rapid increase in reported cases in China and around the world, on January 30, 2020, the World Health Organization (WHO) Emergency Committee announced that NCP is a Public Health Emergency of International Concern (PHEIC). However, there are relatively few suggestions and measures for tumor patients, especially patients with head and neck tumors. This article summarizes the prevention and control of disease in our medical institution to provide a reference for front-line head and neck surgeons.