SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype.

Since the emergence of the Omicron variants at the end of 2021, they quickly became the dominant variants globally. The Omicron variants may be more easily transmitted compared to the earlier Wuhan and the other variants. In this study, we aimed to elucidate mechanisms of the altered infectivity associated with the Omicron variants. We systemically evaluated mutations located in the S2 sequence of spike and identified mutations that are responsible for altered viral fusion. We demonstrated that mutations near the S1/S2 cleavage site decrease S1/S2 cleavage, resulting in reduced fusogenicity. Mutations in the HR1 and other S2 sequences also affect cell-cell fusion. Based on nuclear magnetic resonance (NMR) studies and in silico modeling, these mutations affect fusogenicity possibly at multiple steps of the viral fusion. Our findings reveal that the Omicron variants have accumulated mutations that contribute to reduced syncytial formation and hence an attenuated pathogenicity.

Targeting the Fusion Process of SARS-CoV-2 Infection by Small Molecule Inhibitors.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a serious threat to global public health, underscoring the urgency of developing effective therapies. Therapeutics and, more specifically, direct-acting antiviral development are still very much in their infancy. Here, we report that two hepatitis C virus (HCV) fusion inhibitors identified in our previous study, dichlorcyclizine and fluoxazolevir, broadly block human coronavirus entry into various cell types. Both compounds were effective against various human-pathogenic CoVs in multiple assays based on vesicular stomatitis virus (VSV) pseudotyped with the spike protein and spike-mediated syncytium formation. The antiviral effects were confirmed in SARS-CoV-2 infection systems. These compounds were equally effective against recently emerged variants, including the delta variant. Cross-linking experiments and structural modeling suggest that the compounds bind to a hydrophobic pocket near the fusion peptide of S protein, consistent with their potential mechanism of action as fusion inhibitors. In summary, these fusion inhibitors have broad-spectrum antiviral activities and may be promising leads for treatment of SARS-CoV-2, its variants, and other pathogenic CoVs. IMPORTANCE SARS-CoV-2 is an enveloped virus that requires membrane fusion for entry into host cells. Since the fusion process is relatively conserved among enveloped viruses, we tested our HCV fusion inhibitors, dichlorcyclizine and fluoxazolevir, against SARS-CoV-2. We performed in vitro assays and demonstrated their effective antiviral activity against SARS-CoV-2 and its variants. Cross-linking experiments and structural modeling suggest that the compounds bind to a hydrophobic pocket in spike protein to exert their inhibitory effect on the fusion step. These data suggest that both dichlorcyclizine and fluoxazolevir are promising candidates for further development as treatment for SARS-CoV-2.

Dynamic changes and clinical significance of COVID-19 specific antibodies in rehabilitated patients

Objective To investigate the dynamic changes and clinical significance of specific antibodies in patients with coronavirus disease 2019 (COVID-19). Methods A retrospective study was conducted to collect 141 adult COVID-19 survivors who were followed up in the Eighth Hospital affiliated to Guangzhou Medical University from February 6, 2020, to March 24, 2021. The patients were divided into severe group (severe and critical) and non-severe group (light and ordinary) according to the diagnosis at discharge. The antibody changes of the two groups were compared and analyzed at 1 week, 2 weeks, 1 month, 3 months, 6 months and 1 year after discharge. Results After discharge from hospital, the positive rate of IgG in the severe group was 95.00% after 1 week and 100.00% in the following year, in the positive rate of IgG in the non-severe group was 59.50% after 1 week, 90.08% in 6 months and 76.03% in one year. The level of serum IgG in the severe group was significantly higher than that in non-severe group (Z=-2.441, P=0.015). One-year follow-up: the serum IgG in the severe group was significantly higher than that in the non-severe group (Z=-3.410, P=0.001). The serum IgM level of the severe group after one year follow-up was lower than that of the six months follow-up, the difference was statistically significant (Z=-2.259, P=0.024). The serum IgG and IgM level of the non-severe group after one year follow-up was lower than that of the six months follow-up, the difference was statistically significant (Z=-7.37, P<0.01;Z=3.850, P<0.01). Conclusion The level of serum protective antibody in COVID-19 patients remained high within 6 months after discharge, and remained stable within 1 year after discharge. The antibody titers in the severe group were significantly higher than those in the non-severe group and lasted for at least one year. COVID-19 survivors receive 1 year of natural immune protection, and patients with critical conditions receive immunity for longer periods of time. © 2022 The authors.

Immunogenicity of a 3rd Dose of Mrna Covid-19 Vaccine in Kidney Transplant Recipients Who Failed to Respond to 2 Prior Doses

Purpose: Kidney transplant recipients (KTRs) have diminished immune response and protection after 2-dose mRNA COVID-19 vaccination. It is unknown if additional doses improve neutralization of variants of concern (VOC) in KTRs with prior poor seroresponse. Method(s): Adult KTRs with negative (<0.8 U/mL) or low (<=50 U/ml) anti-RBD Ig (Roche Elecsys anti-SARS-CoV-2-S) after 2-dose mRNA series were given a homologous 3rd dose (D3). Anti-RBD and VOC surrogate neutralization (%ACE2i) were measured 30 days post D3;responses were stratified by baseline anti-RBD. Reactogenicity, serial SARS-CoV-2 swabs, and donor-specific antibody (DSA) were assessed. Result(s): 81 KTRs (50% negative anti-RBD) received D3 (72% BNT162b2, 28% mRNA-1273) at median 167 days post D2 (Table). Median (IQR) anti-RBD increase was 410 (8-2309) U/mL with 69% (40% negative vs 98% low anti-RBD) achieving day 30 anti-RBD >50 U/ml (Fig1a). 22% remained seronegative. Non-response was associated with lower baseline lymphocyte count (median 770 vs 1160 cells/ uL;p=0.05) and IgG (median 779 vs 979 mg/dL;p<0.01), but not demographics, vaccine, or immunosuppressives. Median (IQR) delta variant %ACE2i increased from 6% (3-7) to 10% (4-22) (p<0.001), a 1% (0-5) increase in negative vs 13% (5-25) in low anti-RBD. %ACE2i was linearly associated with anti-RBD >=100 U/ mL (all VOC shown in Fig1b);64% of KTRs with anti-RBD >=250 U/mL had delta %ACE2i >20. There were 3 cases of mild-moderate COVID-19 >=7 days post-D3, with pre-infection anti-RBD <0.4, 22, 76 U/mL and delta %ACE2i 6, 9, and 16, respectively. There was no acute rejection, nor increased or de novo DSA. Conclusion(s): A 3rd mRNA vaccine dose increased anti-RBD and VOC neutralization in KTRs without inducing clinical alloimmunity, yet 45% with negative baseline anti-RBD remained seronegative without delta variant neutralization. Trials are ongoing to test immune response augmentation in this subgroup via temporary immunosuppression reduction or heterologous boosting.

Combined Influence of Commenting and Forwarding on Information Propagation on the Chinese Sina Microblog

After the outbreak of the COVID-19 pandemic, social media platforms offer an essential channel for the public to obtain and discuss the latest development of the epidemic situation and vaccine research. On the Chinese Sina Microblog, which is one of the most popular social platforms in China, two unique interaction mechanisms promote the change of the intensity and breadth of online information propagation, namely 'commenting' and 'forwarding'. Based on that, we propose a Susceptible-Commenting-Forwarding-Immune (SCFI) dynamic model and use the actual public opinion event on the Chinese Sina Microblog to adopt a data-model dual-drive research approach. We focus on the differences between the influence of 'commenting community' and 'forwarding community' on the promotion of information propagation, which is conducive to grasping the law of public opinion propagation. Our experimental results show that the multiple interactive mechanisms can particularly affect public opinion propagation. Our conclusions can contribute to designing effective communication strategies for governments and related agencies to guide public opinion in response to public health emergencies. © 2022 IEEE.

Adaptive Droplet Routing for MEDA Biochips via Deep Reinforcement Learning

Digital microfluidic biochips (DMFBs) based on a micro-electrode-dot-array (MEDA) architecture provide fine-grained control and sensing of droplets in real-time. However, excessive actuation of microelectrodes in MEDA biochips can lead to charge trapping during bioassay execution, causing the failure of microelectrodes and erroneous bioassay outcomes. A recently proposed enhancement to MEDA allows run-time measurement of microelectrode health information, thereby enabling synthesis of adaptive routing strategies for droplets. However, existing synthesis solutions are computationally infeasible for large MEDA biochips that have been commercialized. In this paper, we propose a synthesis framework for adaptive droplet routing in MEDA biochips via deep reinforcement learning (DRL). The framework utilizes the real-time microelectrode health feedback to synthesize droplet routes that proactively minimize the likelihood of charge trapping. We show how the adaptive routing strategies can be synthesized using DRL. We implement the DRL agent, the MEDA simulation environment, and the bioassay scheduler using the OpenAI Gym environment. Our framework obtains adaptive routing policies efficiently for COVID-19 testing protocols on large arrays that reflect the sizes of commercial MEDA biochips available in the marketplace, significantly increasing probabilities of successful bioassay completion compared to existing methods. © 2022 EDAA.

Multi-View Auxiliary Diagnosis Algorithm for Lung Nodules

Lung is an important organ of human body. More and more people are suffering from lung diseases due to air pollution. These diseases are usually highly infectious. Such as lung tuberculosis, novel coronavirus COVID-19, etc. Lung nodule is a kind of high-density globular lesion in the lung. Physicians need to spend a lot of time and energy to observe the computed tomography image sequences to make a diagnosis, which is inefficient. For this reason, the use of computer-assisted diagnosis of lung nodules has become the current main trend. In the process of computer-aided diagnosis, how to reduce the false positive rate while ensuring a low missed detection rate is a difficulty and focus of current research. To solve this problem, we propose a three-dimensional optimization model to achieve the extraction of suspected regions, improve the traditional deep belief network, and to modify the dispersion matrix between classes. We construct a multi-view model, fuse local three-dimensional information into two-dimensional images, and thereby to reduce the complexity of the algorithm. And alleviate the problem of unbalanced training caused by only a small number of positive samples. Experiments show that the false positive rate of the algorithm proposed in this paper is as low as 12%, which is in line with clinical application standards. © 2022 Tech Science Press. All rights reserved.

Securing Biochemical Samples Using Molecular Barcoding on Digital Microfluidic Biochips*

Microfluidic biochips are being adopted today in point-of-care diagnostics, e.g., COVID-19 testing;therefore, it is critical to ensure integrity of bio-sample before bioassays are run on-chip. A security technique called molecular barcoding was recently proposed to thwart sample-forgery attacks in DNA forensics. Molecular barcoding refers to addition of unique DNA molecules in bio-samples, and the sequence of the added DNA sample serves as a distinct 'barcode' for the sample. The existence of the added molecule can be validated using polymerase chain reaction (PCR) and gel electrophoresis. However, this security solution has several limitations: (1) the lack of robustness of the barcode molecules when they are added to other genomic DNA (e.g., samples collected for diagnostics);(2) the need for special bulk instrumentation for validation;(3) the need for human intervention during the overall process. To overcome the limitations, we design a set of robust molecular barcodes that can be validated using both traditional polymerase chain reaction and loop mediated isothermal amplification (LAMP). The validation using LAMP can be executed on a small-in-size and portable digital microfluidic biochip (DMFB). Our LAMP workflow includes a color-changing visual indicator for simple, rapid identification of the barcode existence in solutions. We first demonstrate the proposed security workflow using benchtop techniques. Next, we fabricate a printed circuit board (PCB)-based DMFB with heaters and demonstrate, for the first time, the LAMP assay on a DMFB. © 2021 IEEE.

Parallel Droplet Control in MEDA Biochips Using Multi-Agent Reinforcement Learning

Microfluidic biochips are being utilized for clinical diagnostics, including COVID-19 testing, because they provide sample-to-result turnaround at low cost. Recently, microelectrode-dot-array (MEDA) biochips have been proposed to advance microfluidics technology. A MEDA biochip manipulates droplets of nano/picoliter volumes to automatically execute biochemical protocols. During bioassay execution, droplets are transported in parallel to achieve high-throughput outcomes. However, a major concern associated with the use of MEDA biochips is microelectrode degradation over time. Recent work has shown that formulating droplet transportation as a reinforcement-learning (RL) problem enables the training of policies to capture the underlying health conditions of microelectrodes and ensure reliable fluidic operations. However, the above RL-based approach suffers from two key limitations: 1) it cannot be used for concurrent transportation of multiple droplets;2) it requires the availability of CCD cameras for monitoring droplet movement. To overcome these problems, we present a multi-agent reinforcement learning (MARL) droplet-routing solution that can be used for various sizes of MEDA biochips with integrated sensors, and we demonstrate the reliable execution of a serial-dilution bioassay with the MARL droplet router on a fabricated MEDA biochip. To facilitate further research, we also present a simulation environment based on the PettingZoo Gym Interface for MARL-guided droplet-routing problems on MEDA biochips.

Discovery of Small Molecule Entry Inhibitors Targeting the Fusion Peptide of SARS-CoV-2 Spike Protein.

SARS-CoV-2 entry into host cells relies on the spike (S) protein binding to the human ACE2 receptor. In this study, we investigated the structural dynamics of the viral S protein at the fusion peptide (FP) domain and small molecule binding for therapeutics development. Following comparative modeling analysis and docking studies of our previously identified fusion inhibitor chlorcyclizine, we performed a pharmacophore-based virtual screen and identified two novel chemotypes of entry inhibitors targeting the FP. The compounds were evaluated in the pseudoparticle viral entry assay and SARS-CoV-2 cytopathic effect assay and showed single-digital micromole inhibition against SARS-CoV-2 as well as SARS-CoV-1 and MERS. The characterization of the FP binding site of SARS-CoV-2 S protein provides a promising target for the structure-based development of small molecule entry inhibitors as drug candidates for the treatment of COVID-19.

Online Outpatient Services During the COVID-19 Pandemic

In the early stages of the Covid-19 pandemic in China, many people felt anxiety and panic, which led to an increase in visits to outpatient clinics. To relieve the pressure on these clinics, a new medical service, the Online Outpatient, was introduced. Starting in late January, 2020, by February 29, there had been more than 5500 online consultations, with 95.2% of these having been satisfactorily completed. To analyze the important role and success of the Online Outpatient, consultation data extracted for 4102 valid cases from the Online Outpatient system at the Sichuan Provincial People’s Hospital were analyzed using statistical methods, such as chi-square tests, the Cochran-Mantel-Haenszel Test, and non-parametric tests. It was found that 83.62% had been advised to stay at home, which reduced the number of people going to the hospital, and relieved the pressure on the outpatient departments. While around 44% or 1806 of the online outpatients had claimed to be suffering from anxiety, 80.34% of these admitted feeling relief from their anxiety after consulting. Therefore, the online outpatient medical consultation service was successful in both alleviating client anxiety and panic and relieving the pressure on offline outpatient departments. This new type of medical service could assist in managing hospital outpatients during public health emergencies. © 2021, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Renal injury in hypertensive patients plays a role in promoting the worsening condition after they are infected with sars-cov-2

Objective: To explore potential mechanism about the experience that hypertension is associated with poor outcome in patients with coronavirus disease 2019 (COVID-19). Methods: In this retrospective study, 134 hypertensive patients diagnosed with COVID-19 were included from February 1, 2020 to March 15, 2020. We assessed the associations between renal injury on admission and risks of acute kidney injury (AKI) and in-hospital mortality and analyzed the dynamic changes of serum creatinine and blood urea nitrogen (BUN). Result: Among the 134 COVID-19 patients, 95 (70.9%) were discharged and survived, and 39 (29.1%) died. On admission, BUN and serum creatinine were elevated in 24 (17.9%) and 39 (29.1%) patients, respectively. Estimated glomerular filtration rate (eGFR) < 60 ml/min/1.73 m2 was reported in 18 (13.4%) patients. Multiple regression analysis showed that elevated baseline BUN and eGFR less than 60 ml/min/1.73 m2 on admission were independent risk factors for both AKI and in-hospital death in COVID-19 patients with hypertension. Level of serum creatinine or BUN increased faster in patients with elevated baseline serum creatinine or BUN respectively than those with normal levels. Conclusion: Renal injury of hypertensive patients can result in poor outcomes including AKI and death after they are infected with SARS-CoV-2, and clinicians should be vigilant for these patients with abnormal renal function at admission.

Upper gastrointestinal bleeding in a pediatric patient with sickle cell disease and COVID-19

INTRODUCTION: Gastrointestinal (GI) symptoms can be the first presenting finding in children infected with the severe acute respiratory syndrome coronavirus-2 (SARSCoV- 2). The novel coronavirus disease 2019 (COVID-19) has a higher rate of mortality and critical illness in adults, however, severe presentations in children are increasingly reported. Patients with chronic illness are at a higher risk of complications from the infection, but there is no data in patients sickle cell disease (SCD). METHODS: A 12-year-old African American boy with SCD, subtype HbSS, presented with acute worsening hematemesis, 2 days of non-bloody diarrhea, and back pain that responded a dose of ibuprofen. He had a history of splenectomy and multiple episodes of acute chest syndrome (ACS) and vaso-occlusive crises. On presentation, he was febrile, tachycardic, and hypotensive, without signs of respiratory distress. His hemoglobin had dropped to 4.1 g/ dL. His nasopharyngeal swab was positive for SARS-CoV-2. He required multiple blood transfusions and other supportive measures to treat his shock state. Esophagoduodenoscopy (EGD) showed diffuse hemorrhagic gastropathy without ulcerations, but no biopsy was taken. RESULTS: The patient's presenting symptoms of diarrhea and fever were consistent with published data on children with COVID-19. He also had leukocytosis, elevated inflammatory markers, and an abnormal coagulation profile. These are seen in more severe cases and are currently described under the multisystem inflammatory syndrome of children. His respiratory status remained stable despite having multiple ACS episodes in the past. Upper GI bleeding is not yet described in pediatric COVID-19. Most cases of upper GI bleeding in children are attributed to NSAIDs exposure, but it's unlikely that one dose of ibuprofen causes such severe bleeding. Histopathologic samples from COVID-19 patients show evidence of lymphocytic infiltrate and interstitial edema in the gastric mucosa, with detection of SARS-CoV-2 nucleocapsid protein in gastric epithelial cells. We hypothesize that the severe hemorrhagic gastritis resulted from SARS-CoV-2-induced coagulopathy and viral invasion. This was further compounded by the acute insult from an NSAID and the underlying mucosal infarction and vascular congestion from sickling.

Traditional village protection based on big data under the impact of COVID-19

Under the influence of novel corona virus pneumonia epidemic, the protection of traditional villages is put forward higher request. The spread of the epidemic among villages will make the situation of epidemic prevention and control more difficult. As an important part of culture, traditional villages have high historical value. In this paper, the traditional village protection method, a new geographical data algorithm IData storage method. Compared with the traditional ArcGIS method, it improves the efficiency and accuracy of topographic map entry. IData's data factory can use the symbolic technology of skeleton lines to represent all the figures in the national standard mode, and any complex figure can only be represented by one element. Idate can quickly load data and render symbols in a drawing. With the powerful data processing engine of IData data factory, we can check out the errors that other software can't find and process the data automatically. Records of the loss of traditional villages can be recorded quickly. The establishment and protection of traditional villages have had a beneficial impact.

Pattern recognition of decorative elements based on neural network

The Covid-19 first occurs in Wuhan, China in December 2019. After that, the virus has spread all over the world and at the time of writing this paper the total number of confirmed cases are above 11 million with over 600,000 deaths. The pattern recognition of complex environment can be used to determine if a COVID-19 breath pattern can be established with accuracy. The traditional decorative pattern detection method has a high degree of recognition in simple scene. However, the efficiency of decorative pattern detection in complex scenes is low and the recognition accuracy is not high. Firstly, the evaluation index of target detection method is designed. Through this paper, it is found that the success rate of some targets is naturally better than other targets, and easy to distinguish from the background. In order to improve the recognition success rate of the object in the complex environment and determine the position and attitude of the object, the pattern as the artificial identification in the environment is proposed. The interior art decoration pattern is selected as the experimental pattern and the pattern classification evaluation index is designed. The experimental results show that the method proposed in this paper can optimize the pattern subsets which are confused with each other and easy to distinguish from the background. It has a certain reference value for decorative pattern recognition in complex environment for COVID-19 epidemic. © 2020 - IOS Press and the authors. All rights reserved.

Relationship between initial CT signs and symptoms onset time in COVID-19 patients outside Wuhan

Objective: To explore the correlation between initial chest CT signs and onset time in patients with coronavirus disease 2019 (COVID-19) outside Wuhan area and to identify the early changes in chest CT signs. Methods: We made a retrospective analysis of the clinical features and CT signs of confirmed cases of COVID-19 in Shaanxi Province from January 22 to February 10, 2020. The CT signs were mainly analyzed for ground glass opacities (GGO), consolidation and GGO combined with consolidation in the lung, and the degree of lung injury in each patient was scored at the same time. The correlation of CT signs and lung injury score with onset time was analyzed, and the data were non-linearly fitted (quadratic fitting curve) to judge the changes of CT signs and scores with time. Results: A total of 293 lesions were detected in 91 patients with COVID-19, including 143 (48.8%) GGO, 116 (39.6%) GGO with consolidation and 34 (11.6%) simple consolidation. The nonlinear fitting analysis revealed that the GGO had a downward trend with the onset time, the quadratic fitting curve of GGO combined with consolidation showed a positive "U" shape, and the solid change showed an inverted "U" shape;and the three signs had a turning point on the 7th day. At the same time, the lung injury score of the patients peaked on the 7th day. Conclusion: The main CT manifestations of patients with COVID-19 are GGO and GGO combined with consolidation, and the 7th day of onset may be the key time point for the change of CT signs. © 2020, Editorial Board of Journal of Xi'an Jiaotong University (Medical Sciences). All right reserved.

Asymptomatic COVID-19 infection in patients with cancer at a cancer-specialized hospital in Wuhan, China - Preliminary results.

OBJECTIVE: Patients with cancer are usually immunosuppressive and susceptible to COVID-19 infection. Asymptomatic COVID-19 cases are infective and cannot be identified by symptom-based screening. There is an urgent need to control virus spread by asymptomatic carriers at cancer centres. We aim to describe the characteristics, screening methods, and outcomes of cancer patients with asymptomatic COVID-19 infection and to further explore anti-tumour treatment for this population. PATIENTS AND METHODS: We reviewed patients with cancer who were admitted to Hubei Cancer Hospital in Wuhan from February 1, 2020, to April 4, 2020. We collected demographic data, laboratory findings, treatment information, nucleic acid and serum test results, chest computed tomography (CT) information and survival status of cancer patients diagnosed with asymptomatic COVID-19 infection. RESULTS: A total of 16 cancer patients with asymptomatic COVID-19 infection were confirmed. The most common cancer type was breast cancer. The blood cell counts of most patients were in the normal range. Lymphocytes of 100% of asymptomatic carriers were in the normal range. Thirteen (81.3%) patients were positive for virus-specific IgM antibodies, and three (18.8%) were positive by PCR; only one (6.3%) patient showed novel coronavirus pneumonia features on CT. Three (18.3%) patients died, and the cause of death was considered malignancy caused by delaying anti-tumour treatment. CONCLUSIONS: Our study shows that the lymphocytes of 100% of asymptomatic carriers were in the normal range. This result indicates that the host immunity of asymptomatic carriers is not significantly disrupted by COVID-19. Single PCR detection is not sufficient to screen among asymptomatic individuals, and a combination of PCR tests, serological tests and CT is of great importance. Unless the tumour is life-threatening or rapidly progressing, we advise restarting active anti-tumour therapy after PCR tests become negative.