Intelligent Approach for Clustering Mutations’ Nature of COVID-19 Genome

In December 2019, a group of people in Wuhan city of Hubei province of China were found to be affected by an infection called dark etiology pneumonia. The outbreak of this pneumonia infection was declared a deadly disease by the China Center for Disease Control and Prevention on January 9, 2020, named Novel Coronavirus 2019 (nCoV-2019). This nCoV-2019 is now known as COVID-19. There is a big list of infections of this coronavirus which is present in the form of a big family. This virus can cause several diseases that usually develop with a serious problem. According to the World Health Organization (WHO), 2019-nCoV has been placed as the modern generation of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) coronaviruses, so COVID-19 can repeatedly change its internal genome structure to extend its existence. Understanding and accurately predicting the mutational properties of the genome structure of COVID-19 can form a good leadership role in preventing and fighting against coronavirus. In this research paper, an analytical approach has been presented which is based on the k-means cluster technique of machine learning to find the clusters over the mutational properties of the COVID-19 viruses’ complete genome. This method would be able to act as a promising tool to monitor and track pathogenic infections in their stable and local genetics/hereditary varieties. This paper identifies five main clusters of mutations with as best in most cases in the coronavirus that could help scientists and researchers develop disease control vaccines for the transformation of coronaviruses.     

Automated contact tracing: a game of big numbers in the time of COVID-19

One of the more widely advocated solutions for slowing down the spread of COVID-19 has been automated contact tracing. Since proximity data can be collected by personal mobile devices, the natural proposal has been to use this for automated contact tracing providing a major gain over a manual implementation. In this work, we study the characteristics of voluntary and automated contact tracing and its effectiveness for mapping the spread of a pandemic due to the spread of SARS-CoV-2. We highlight the infrastructure and social structures required for automated contact tracing to work. We display the vulnerabilities of the strategy to inadequate sampling of the population, which results in the inability to sufficiently determine significant contact with infected individuals. Of crucial importance will be the participation of a significant fraction of the population for which we derive a minimum threshold. We conclude that relying largely on automated contact tracing without population-wide participation to contain the spread of the SARS-CoV-2 pandemic can be counterproductive and allow the pandemic to spread unchecked. The simultaneous implementation of various mitigation methods along with automated contact tracing is necessary for reaching an optimal solution to contain the pandemic.     

Clinical Characteristics and Outcomes of Severe or Critical COVID-19 Patients Presenting No Respiratory Symptoms or Fever at Onset

It is difficult to identify suspected cases of atypical patients with coronavirus disease 2019 (COVID-19), and data on severe or critical patients are scanty. This retrospective study presents the clinical, laboratory, and radiological profiles, treatments, and outcomes of atypical COVID-19 patients without respiratory symptoms or fever at onset. The study examined ten atypical patients out of 909 severe or critical patients diagnosed with COVID-19 in Wuhan Union Hospital West Campus between 25 January 2020 and 10 February 2020. Data were obtained from the electronic medical records of severe or critical patients without respiratory symptoms or fever at onset. Outcomes were followed up to discharge or death. Among 943 COVID-19 patients, 909 (96.4%) were severe or critical type. Of the severe or critical patients, ten (1.1%) presented without respiratory symptoms or fever at admission. The median age of the ten participants was 63 years (interquartile range (IQR): 57–72), and seven participants were men. The median time from symptom onset to admission was 14 d (IQR: 7–20). Eight of the ten patients had chronic diseases. The patients had fatigue (n = 5), headache or dizziness (n = 4), diarrhea (n = 5), anorexia (n = 3), nausea or vomiting (n = 3), and eye discomfort (n = 1). Four patients were found to have lymphopenia. Imaging examination revealed that nine patients had bilateral pneumonia and one had unilateral pneumonia. Eventually, two patients died and eight were discharged. In the discharged patients, the median time from admission to discharge lasted 24 d (IQR: 13–43). In summary, some severe or critical COVID-19 patients were found to have no respiratory symptoms or fever at onset. All such atypical cases should be identified and quarantined as early as possible, since they tend to have a prolonged hospital stay or fatal outcomes. Chest computed tomography (CT) scan and nucleic acid detection should be performed immediately on close contacts of COVID-19 patients to screen out those with atypical infections, even if the contacts present without respiratory symptoms or fever at onset.     

Particulate Alum via Pickering Emulsion for an Enhanced COVID-19 Vaccine Adjuvant

For rapid response against the prevailing COVID-19 (coronavirus disease 19), it is a global imperative to exploit the immunogenicity of existing formulations for safe and efficient vaccines. As the most accessible adjuvant, aluminum hydroxide (alum) is still the sole employed adjuvant in most countries. However, alum tends to attach on the membrane rather than entering the dendritic cells (DCs), leading to the absence of intracellular transfer and process of the antigens, and thus limits T-cell-mediated immunity. To address this, alum is packed on the squalene/water interphase is packed, forming an alum-stabilized Pickering emulsion (PAPE). “Inheriting” from alum and squalene, PAPE demonstrates a good biosafety profile. Intriguingly, with the dense array of alum on the oil/water interphase, PAPE not only adsorbs large quantities of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigens, but also harbors a higher affinity for DC uptake, which provokes the uptake and cross-presentation of the delivered antigens. Compared with alum-treated groups, more than six times higher antigen-specific antibody titer and three-fold more IFN-γ-secreting T cells are induced, indicating the potent humoral and cellular immune activations. Collectively, the data suggest that PAPE may provide potential insights toward a safe and efficient adjuvant platform for the enhanced COVID-19 vaccinations.     

COVID-19 pandemic dynamics in India,the SARS-CoV-2 Delta variant and implications for vaccination

The Delta variant is a major SARS-CoV-2 variant of concern first identified in India. To better understand COVID-19 pandemic dynamics and Delta, we use multiple datasets and model-inference to reconstruct COVID-19 pandemic dynamics in India during March 2020–June 2021. We further use the large discrepancy in one- and two-dose vaccination coverage in India (53% versus 23% by end of October 2021) to examine the impact of vaccination and whether prior non-Delta infection can boost vaccine effectiveness (VE). We estimate that Delta escaped immunity in 34.6% (95% CI: 0–64.2%) of individuals with prior wild-type infection and was 57.0% (95% CI: 37.9–75.6%) more infectious than wild-type SARS-CoV-2. Models assuming higher VE among non-Delta infection recoverees, particularly after the first dose, generated more accurate predictions than those assuming no such increases (best-performing VE setting: 90/95% versus 30/67% baseline for the first/second dose). Counterfactual modelling indicates that high vaccination coverage for first vaccine dose in India combined with the boosting of VE among recoverees averted around 60% of infections during July–mid-October 2021. These findings provide support to prioritizing first-dose vaccination in regions with high underlying infection rates, given continued vaccine shortages and new variant emergence.     

Prediction of COVID-19 Confirmed Cases Using Gradient Boosting Regression Method

The fast spread of coronavirus disease (COVID-19) caused by SARSCoV-2 has become a pandemic and a serious threat to the world. As of May 30, 2020, this disease had infected more than 6 million people globally, with hundreds of thousands of deaths. Therefore, there is an urgent need to predict confirmed cases so as to analyze the impact of COVID-19 and practice readiness in healthcare systems. This study uses gradient boosting regression (GBR) to build a trained model to predict the daily total confirmed cases of COVID-19. The GBR method can minimize the loss function of the training process and create a single strong learner from weak learners. Experiments are conducted on a dataset of daily confirmed COVID-19 cases from January 22, 2020, to May 30, 2020. The results are evaluated on a set of evaluation performance measures using 10-fold cross-validation to demonstrate the effectiveness of the GBR method. The results reveal that the GBR model achieves 0.00686 root mean square error, the lowest among several comparative models.     

School closures reduced social mixing of children during COVID-19 with implications for transmission risk and school reopening policies

School closures may reduce the size of social networks among children, potentially limiting infectious disease transmission. To estimate the impact of K–12 closures and reopening policies on children''s social interactions and COVID-19 incidence in California''s Bay Area, we collected data on children''s social contacts and assessed implications for transmission using an individual-based model. Elementary and Hispanic children had more contacts during closures than high school and non-Hispanic children, respectively. We estimated that spring 2020 closures of elementary schools averted 2167 cases in the Bay Area (95% CI: −985, 5572), fewer than middle (5884; 95% CI: 1478, 11.550), high school (8650; 95% CI: 3054, 15 940) and workplace (15 813; 95% CI: 9963, 22 617) closures. Under assumptions of moderate community transmission, we estimated that reopening for a four-month semester without any precautions will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1) and elementary school teachers (4.1%, 95% CI: −1.7, 12.0). However, we found that reopening policies for elementary schools that combine universal masking with classroom cohorts could result in few within-school transmissions, while high schools may require masking plus a staggered hybrid schedule. Stronger community interventions (e.g. remote work, social distancing) decreased the risk of within-school transmission across all measures studied, with the influence of community transmission minimized as the effectiveness of the within-school measures increased.     

Tele-COVID: A Telemedicine SOA-Based Architectural Design for COVID-19 Patients

In Wuhan, China, a novel Corona Virus (COVID-19) was detected in December 2019; it has changed the entire world and to date, the number of diagnosed cases is 38,756,289¹ and 1,095,216¹ people have died. This happened because a large number of people got affected and there is a lack of hospitals for COVID-19 patients. One of the precautionary measures for COVID-19 patients is isolation. To support this, there is an urgent need for a platform that makes treatment possible from a distance. Telemedicine systems have been drastically increasing in number and size over recent years. This increasing number intensifies the extensive need for telemedicine for the national healthcare system. In this paper, we present Tele-COVID which is a telemedicine application to treat COVID-19 patients from a distance. Tele-COVID is uniquely designed and implemented in Service-Oriented Architecture (SOA) to avoid the problem of interoperability, vendor lock-in, and data interchange. With the help of Tele-COVID, the treatment of patients at a distance is possible without the need for them to visit hospitals; in case of emergency, necessary services can also be provided.     

Case Study: Spark GPU-Enabled Framework to Control COVID-19 Spread Using Cell-Phone Spatio-Temporal Data

Nowadays, the world is fighting a dangerous form of Coronavirus that represents an emerging pandemic. Since its early appearance in China Wuhan city, manycountries undertook several strict regulations including lockdowns and social distancing measures. Unfortunately, these procedures have badly impacted the world economy. Detecting and isolating positive/probable virus infected cases using a tree tracking mechanism constitutes a backbone for containing and resisting such fast spreading disease. For helping this hard effort, this research presents an innovative case study based on big data processing techniques to build a complete tracking system able to identify the central areas of infected/suspected people, and the new suspected cases using health records integration with mobile stations spatio-temporal data logs. The main idea is to identify the positive cases historical movements by tracking their phone location for the last 14 days (i.e., the virus incubation period). Then, by acquiring the citizen’s mobile phone locations for the same period, the system will be able to measure the Euclideandistances between positive case locations and other nearby people to identify the incontact suspected-cases using parallel clustering and classification techniques. Moreover, the daily change of the clusters size and its centroids will be used to predict new regions of infection, as well as, new cases. Moreover, this approach will support infection avoidance by alerting people approaching areas of high probability of infection using their mobile GPS location. This case study has been developed as a simulation system consisting of three components; positive cases/citizens movement’s data generation subsystem, big data processing platform including CPU/GPU tasks, and data visualization/map geotagging subsystem. The processing of such a big data system requires intensive computing tasks. Therefore, GPU tasks carried out to achieve high performance and accelerate the data processing. According to the simulated systemresults, data partitioning and processing speed up measures have been examined.     

Intelligent Decision Support System for COVID-19 Empowered with Deep Learning

The prompt spread of Coronavirus (COVID-19) subsequently adorns a big threat to the people around the globe. The evolving and the perpetually diagnosis of coronavirus has become a critical challenge for the healthcare sector. Drastically increase of COVID-19 has rendered the necessity to detect the people who are more likely to get infected. Lately, the testing kits for COVID-19 are not available to deal it with required proficiency, along with-it countries have been widely hit by the COVID-19 disruption. To keep in view the need of hour asks for an automatic diagnosis system for early detection of COVID-19. It would be a feather in the cap if the early diagnosis of COVID-19 could reveal that how it has been affecting the masses immensely. According to the apparent clinical research, it has unleashed that most of the COVID-19 cases are more likely to fall for a lung infection. The abrupt changes do require a solution so the technology is out there to pace up, Chest X-ray and Computer tomography (CT) scan images could significantly identify the preliminaries of COVID-19 like lungs infection. CT scan and X-ray images could flourish the cause of detecting at an early stage and it has proved to be helpful to radiologists and the medical practitioners. The unbearable circumstances compel us to flatten the curve of the sufferers so a need to develop is obvious, a quick and highly responsive automatic system based on Artificial Intelligence (AI) is always there to aid against the masses to be prone to COVID-19. The proposed Intelligent decision support system for COVID-19 empowered with deep learning (ID2S-COVID19-DL) study suggests Deep learning (DL) based Convolutional neural network (CNN) approaches for effective and accurate detection to the maximum extent it could be, detection of coronavirus is assisted by using X-ray and CT-scan images. The primary experimental results here have depicted the maximum accuracy for training and is around 98.11 percent and for validation it comes out to be approximately 95.5 percent while statistical parameters like sensitivity and specificity for training is 98.03 percent and 98.20 percent respectively, and for validation 94.38 percent and 97.06 percent respectively. The suggested Deep Learning-based CNN model unleashed here opts for a comparable performance with medical experts and it is helpful to enhance the working productivity of radiologists. It could take the curve down with the downright contribution of radiologists, rapid detection of COVID-19, and to overcome this current pandemic with the proven efficacy.     

一种针对新型冠状病毒肺炎的准确、快速、便携式双功能电检测仪

新型冠状病毒肺炎(COVID-19)正在多个国家快速传播,已经导致了严重的全球大流行.由于目前没有针对此类病人的特效药和针对此病毒的疫苗,准确、快速地进行新冠病人检测成为了控制大流行最有效的措施.本文中我们开发了一种基于石墨烯场效应晶体管的便携式双功能电检测仪,其通过核酸互补杂交或者抗原-抗体特异性结合作用,能分别进行...     

An Efficient CNN-Based Hybrid Classification and Segmentation Approach for COVID-19 Detection

COVID-19 remains to proliferate precipitously in the world. It has significantly influenced public health, the world economy, and the persons’ lives. Hence, there is a need to speed up the diagnosis and precautions to deal with COVID-19 patients. With this explosion of this pandemic, there is a need for automated diagnosis tools to help specialists based on medical images. This paper presents a hybrid Convolutional Neural Network (CNN)-based classification and segmentation approach for COVID-19 detection from Computed Tomography (CT) images. The proposed approach is employed to classify and segment the COVID-19, pneumonia, and normal CT images. The classification stage is firstly applied to detect and classify the input medical CT images. Then, the segmentation stage is performed to distinguish between pneumonia and COVID-19 CT images. The classification stage is implemented based on a simple and efficient CNN deep learning model. This model comprises four Rectified Linear Units (ReLUs), four batch normalization layers, and four convolutional (Conv) layers. The Conv layer depends on filters with sizes of 64, 32, 16, and 8. A 2 × 2 window and a stride of 2 are employed in the utilized four max-pooling layers. A soft-max activation function and a Fully-Connected (FC) layer are utilized in the classification stage to perform the detection process. For the segmentation process, the Simplified Pulse Coupled Neural Network (SPCNN) is utilized in the proposed hybrid approach. The proposed segmentation approach is based on salient object detection to localize the COVID-19 or pneumonia region, accurately. To summarize the contributions of the paper, we can say that the classification process with a CNN model can be the first stage a highly-effective automated diagnosis system. Once the images are accepted by the system, it is possible to perform further processing through a segmentation process to isolate the regions of interest in the images. The region of interest can be assesses both automatically and through experts. This strategy helps so much in saving the time and efforts of specialists with the explosion of COVID-19 pandemic in the world. The proposed classification approach is applied for different scenarios of 80%, 70%, or 60% of the data for training and 20%, 30, or 40% of the data for testing, respectively. In these scenarios, the proposed approach achieves classification accuracies of 100%, 99.45%, and 98.55%, respectively. Thus, the obtained results demonstrate and prove the efficacy of the proposed approach for assisting the specialists in automated medical diagnosis services.     

Overcoming the limitations of COVID-19 diagnostics with nanostructures,nucleic acid engineering,and additive manufacturing

The COVID-19 pandemic revealed fundamental limitations in the current model for infectious disease diagnosis and serology, based upon complex assay workflows, laboratory-based instrumentation, and expensive materials for managing samples and reagents. The lengthy time delays required to obtain test results, the high cost of gold-standard PCR tests, and poor sensitivity of rapid point-of-care tests contributed directly to society’s inability to efficiently identify COVID-19-positive individuals for quarantine, which in turn continues to impact return to normal activities throughout the economy. Over the past year, enormous resources have been invested to develop more effective rapid tests and laboratory tests with greater throughput, yet the vast majority of engineering and chemistry approaches are merely incremental improvements to existing methods for nucleic acid amplification, lateral flow test strips, and enzymatic amplification assays for protein-based biomarkers. Meanwhile, widespread commercial availability of new test kits continues to be hampered by the cost and time required to develop single-use disposable microfluidic plastic cartridges manufactured by injection molding. Through development of novel technologies for sensitive, selective, rapid, and robust viral detection and more efficient approaches for scalable manufacturing of microfluidic devices, we can be much better prepared for future management of infectious pathogen outbreaks. Here, we describe how photonic metamaterials, graphene nanomaterials, designer DNA nanostructures, and polymers amenable to scalable additive manufacturing are being applied towards overcoming the fundamental limitations of currently dominant COVID-19 diagnostic approaches. In this paper, we review how several distinct classes of nanomaterials and nanochemistry enable simple assay workflows, high sensitivity, inexpensive instrumentation, point-of-care sample-to-answer virus diagnosis, and rapidly scaled manufacturing.     

关于新冠肺炎疫情防控中计量保障工作的几点思考

本文总结了新型冠状病毒肺炎疫情防控中所涉及的计量器具类别,以及对其进行检定、校准、检测等量值保障活动所适用的技术规范。围绕计量工作在新型冠状病毒肺炎疫情防控中的重要作用,文章重点从体温筛查、设备消毒、病毒检测、临床诊断、医疗救治、科学研究等方面分析了计量工作对新冠肺炎疫情防控的技术支撑和量值保障作用。为各疫情防控单位和医疗机构判断防控设备测量结果是否准确、可靠等问题是提供解决路径,也为各级计量技术机构和广大计量工作者针对疫情防控建立相关计量标准提供参考。     

Clinical Characteristics and Outcomes of Type 2 Diabetes Patients Infected with COVID-19: A Retrospective Study

Diabetes and its related metabolic disorders have been reported as the leading comorbidities in patients with coronavirus disease 2019 (COVID-19). This clinical study aims to investigate the clinical features, radiographic and laboratory tests, complications, treatments, and clinical outcomes in COVID-19 patients with or without diabetes. This retrospective study included 208 hospitalized patients (≥ 45 years old) with laboratory-confirmed COVID-19 during the period between 12 January and 25 March 2020. Information from the medical record, including clinical features, radiographic and laboratory tests, complications, treatments, and clinical outcomes, were extracted for the analysis. 96 (46.2%) patients had comorbidity with type 2 diabetes. In COVID-19 patients with type 2 diabetes, the coexistence of hypertension (58.3% vs 31.2%), coronary heart disease (17.1% vs 8.0%), and chronic kidney diseases (6.2% vs 0%) was significantly higher than in COVID-19 patients without type 2 diabetes. The frequency and degree of abnormalities in computed tomography (CT) chest scans in COVID-19 patients with type 2 diabetes were markedly increased, including ground-glass opacity (85.6% vs 64.9%, P < 0.001) and bilateral patchy shadowing (76.7% vs 37.8%, P < 0.001). In addition, the levels of blood glucose (7.23 mmol·L⁻¹ (interquartile range (IQR): 5.80–9.29) vs 5.46 mmol·L⁻¹ (IQR: 5.00–6.46)), blood low-density lipoprotein cholesterol (LDL-C) (2.21 mmol·L⁻¹ (IQR: 1.67–2.76) vs 1.75 mmol·L⁻¹ (IQR: 1.27–2.01)), and systolic pressure (130 mmHg (IQR: 120–142) vs 122 mmHg (IQR: 110–137)) (1 mmHg = 133.3 Pa) in COVID-19 patients with diabetes were significantly higher than in patients without diabetes (P < 0.001). The coexistence of type 2 diabetes and other metabolic disorders is common in patients with COVID-19, which may potentiate the morbidity and aggravate COVID-19 progression. Optimal management of the metabolic hemostasis of glucose and lipids is the key to ensuring better clinical outcomes. Increased clinical vigilance is warranted for COVID-19 patients with diabetes and other metabolic diseases that are fundamental and chronic conditions.     

COVID-19 and Learning Styles: GCET as Case Study

The COVID-19 pandemic has caused higher educational institutions around the world to close campus-based activities and move to online delivery. The aim of this paper is to present the case of Global College of Engineering and Technology (GCET) and how its practices including teaching, students/staff support, assessments, and exam policies were affected. The paper investigates the mediating role of no detriment policy impact on students’ result along with the challenges faced by the higher educational institution, recommendations and suggestions. The investigation concludes that the strategies adopted for online delivery, student support, assessments and exam policies have helped students to effectively cope with the teaching and learning challenges posed by the COVID-19 pandemic without affecting their academic results. The study shows that 99% of students were able to maintain the same or better level of performance during the 1st COVID-19 semester. One percent of students had shown a slight decrease in their performance (about 1%–2%) with respect to their overall marks pre-COVID-19. The no detriment policy has succoured those 1% of the students to maintain their overall performance to what it used to be pre-COVID-19 pandemic. Finally, the paper provides the list of challenges and suggestions for smooth conduction of online education.     

Buying Time for an Effective Epidemic Response: The Impact of a Public Holiday for Outbreak Control on COVID-19 Epidemic Spread

Rapid responses in the early stage of a new epidemic are crucial in outbreak control. Public holidays for outbreak control could provide a critical time window for a rapid rollout of social distancing and other control measures at a large population scale. The objective of our study was to explore the impact of the timing and duration of outbreak-control holidays on the coronavirus disease 2019 (COVID-19) epidemic spread during the early stage in China. We developed a compartment model to simulate the dynamic transmission of COVID-19 in China starting from January 2020. We projected and compared epidemic trajectories with and without an outbreak-control holiday that started during the Chinese Lunar New Year. We considered multiple scenarios of the outbreak-control holiday with different durations and starting times, and under different assumptions about viral transmission rates. We estimated the delays in days to reach certain thresholds of infections under different scenarios. Our results show that the outbreak-control holiday in China likely stalled the spread of COVID-19 for several days. The base case outbreak-control holiday (21 d for Hubei Province and 10 d for all other provinces) delayed the time to reach 100 000 confirmed infections by 7.54 d. A longer outbreak-control holiday would have had stronger effects. A nationwide outbreak-control holiday of 21 d would have delayed the time to 100 000 confirmed infections by nearly 10 d. Furthermore, we find that outbreak-control holidays that start earlier in the course of a new epidemic are more effective in stalling epidemic spread than later holidays and that additional control measures during the holidays can boost the holiday effect. In conclusion, an outbreak-control holiday can likely effectively delay the transmission of epidemics that spread through social contacts. The temporary delay in the epidemic trajectory buys time, which scientists can use to discover transmission routes and identify effective public health interventions and which governments can use to build physical infrastructure, organize medical supplies, and deploy human resources for long-term epidemic mitigation and control efforts.     

Cognitive impairment in a patient with COVID-19 on hemodialysis: Too dangerous to neglect!

Neurological manifestations of coronavirus disease 2019 (COVID-19) often have tragic repercussions. Although many reports of neurological complications of severe acute respiratory syndrome coronavirus 2 infection exist, none of them are of patients on hemodialysis, who have a fivefold greater risk of stroke than the general population. In this report, we emphasize the importance of being vigilant for mild stroke in high risk populations—such as patients on hemodialysis—with COVID-19, since these conditions have overlapping symptoms.