title: COVID-19: a retrospective cohort study with focus on the over-80s and hospital-onset disease

text: Abstract: Objectives: To describe the presenting features and outcomes of patients with COVID-19 in a UK hospital, with a focus on those patients over 80 years and patients with hospital onset infection. Design: Retrospective cohort study with data extracted from the electronic records of patients with PCR-confirmed COVID-19 admitted to our institution. Setting: Suburban general hospital serving the most populous London borough. Participants: The first 450 inpatients admitted to our hospital with swab-confirmed COVID-19 infection. Primary outcome: The primary outcome measure was death during the index hospital admission. Results: The median (IQR) age was 72 (56, 83), with 150 (33%) over 80 years old and 60% male. Presenting clinical and biochemical features were consistent with those reported elsewhere. The ethnic breakdown of patients admitted was similar to that of our underlying local population with no excess of BAME deaths. Inpatient mortality was high at 38%. Patients over 80 presented earlier in their disease course and were significantly less likely to present with the typical features of cough, breathlessness and fever. Cardiac co-morbidity and markers of cardiac dysfunction were more common, but not those of bacterial infection. Mortality was significantly higher in this group (60% vs 28%, p <0.001). 31 (7%) of patients were classified as having hospital-onset COVID-19 infection. The peak of hospital-onset infections occurred at the same time as the overall peak of admitted infections. Despite being older and more frail, the outcomes for this cohort were no worse. Conclusions: Inpatient mortality was high, especially among the over-80s, who were more likely to present atypically. The ethnic composition of our caseload was similar to the underlying population. While a significant number of patients presented with COVID-19 while already in hospital, their outcomes were no worse.


title: Initial Simulation of SARS-CoV2 Spread and Intervention Effects in the Continental US

text: Here we use a metapopulation model applied at county resolution to simulate the spread and growth of COVID-19 incidence in the continental United States. We calibrate the model against county-level incidence data collected between February 21, 2020 and March 13, 2020, and estimate epidemiological parameters including the fraction of undocumented infections and their contagiousness1. Using the calibrated model, we project the outbreak in the continental US for 180 days after March 13, 2020, and evaluate the effects of social distancing and travel restrictions on the outbreak.


title: Importance of untested infectious individuals for the suppression of COVID-19 epidemics

text: A mathematical model which accounts for tested and untested infectious individuals is calibrated during the early stages of COVID-19 outbreaks in Germany, the Hubei province, Italy, Spain and the UK. The predicted percentage of untested infected individuals depends on the specific outbreak but we found that they typically represent 50% to 80% of the infected individuals. Even when unreported cases are taken into account, we estimate that less than 8% of the population would have been exposed to SARS-CoV-2 by 09/04/2020 in the analysed outbreaks. These levels are far from the 70-85% needed to ensure herd immunity and we predict a resurgence of infection if ongoing lockdowns in the analysed outbreaks are fully lifted. We propose that partially lifted lockdowns together with fast and thorough testing allowing for quick isolation of both symptomatic and asymptomatic cases could lead to suppression of secondary waves of COVID-19 epidemics.


title: Pharma mobilizes to combat the coronavirus

text: The World Health Organization has declared the fast-moving coronavirus outbreak in China a “public health emergency of international concern,” a measure that can spur coordinated global efforts to combat it With infections steadily rising, major drug companies are mobilizing to develop diagnostics, vaccines, and possible treatments for the virus, 2019-nCoV According to WHO, as of Jan 30 more than 7,800 people worldwide are confirmed to have been infected by the virus, and another 12,000-plus cases are suspected Almost all of the cases are in China, where 170 people have died Although smaller biotech firms were among the first to publicly respond to the outbreak, big pharma firms say they have been quietly working on tests and treatments for several weeks Roche has sent the first commercial diagnostic to China, and Johnson & Johnson says it is using the same technologies deployed for the rapid development of an Ebola vaccine to( )


title: High prevalence of putative invasive pulmonary aspergillosis in critically ill COVID-19 patients

text: We are currently facing a frightening increase in COVID-19 patients admitted to the ICU. Aiming at screening for fungal secondary pneumonia, we collected the data of our first 27 ICU patients, who underwent bronchoalveolar lavage or bronchial aspirates. We classified the patients based on the recently published study on invasive aspergillosis in influenza patients in your journal (Schauwvlinghe et al., 2018.) and found 33% of our COVID-19 patients with putative invasive pulmonary aspergillosis. Observing such a high prevalence in COVID-infected patients was somehow unexpected since the 30% prevalence of invasive aspergillosis in influenza patients has been attributed to the action of oseltamivir on anti-Aspergillus immunity. Almost all critically ill COVID-19 patients develop ARDS and are likely to receive high-dose steroids or immunomodulatory therapies to prevent worsening as suggested by reports from China. In the COVID-19 patients with putative invasive aspergillosis, antifungal prophylactic therapy may be questioned to avoid increased lung inflammation that may compromise the outcome. This issue remains to be addressed in future clinical trials. We are strongly convinced that testing deep lung specimens for Aspergillus in severe COVID-19 patients should be recommended. This message is major, given the high mortality rate of COVID-19 patients in the ICU.


Pakistan, Covid-19, and the end of the neo-liberal disorder


title: Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome

text: OBJECTIVES: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has been rapidly spreading worldwide. Although the causal relationship among mutations and the features of SARS-CoV-2 such as rapid transmission, pathogenicity, and tropism, remains unclear, our results of genomic mutations in SARS-CoV-2 may help to interpret the interaction between genomic characterization in SARS-CoV-2 and infectivity with the host. METHODS: A total of 4,254 genomic sequences of SARS-CoV-2 were collected from the Global Initiative on Sharing all Influenza Data (GISAID). Multiple sequence alignment for phylogenetic analysis and comparative genomic approach for mutation analysis were conducted using Molecular Evolutionary Genetics Analysis (MEGA), and an in-house program based on Perl language, respectively. RESULTS: Phylogenetic analysis of SARS-CoV-2 strains indicated that there were 3 major clades including S, V, and G, and 2 subclades (G.1 and G.2). There were 767 types of synonymous and 1,352 types of non-synonymous mutation. ORF1a, ORF1b, S, and N genes were detected at high frequency, whereas ORF7b and E genes exhibited low frequency. In the receptor-binding domain (RBD) of the S gene, 11 non-synonymous mutations were observed in the region adjacent to the angiotensin converting enzyme 2 (ACE2) binding site. CONCLUSION: It has been reported that the rapid infectivity and transmission of SARS-CoV-2 associated with host receptor affinity are derived from several mutations in its genes. Without these genetic mutations to enhance evolutionary adaptation, species recognition, host receptor affinity, and pathogenicity, it would not survive. It is expected that our results could provide an important clue in understanding the genomic characteristics of SARS-CoV-2.


title: Appendix 6 Pharmaceutical Products Commonly Used in Avian Medicine

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title: Cell-Type-Specific Expression of Renin-Angiotensin-System Components in the Human Body and Its Relevance to SARS-CoV-2 Infection

text: We have analyzed the cell-type-specific expression of the renin-angiotensin system (RAS) components across 141 cell types or subtypes as defined by single-cell RNA-seq (scRNA-seq) analysis. ACE2, one of the components of RAS, also facilitates SARS-CoV-2 entry into cells in cooperation with its associated protease TMPRSS2. Therefore, our analysis also contributes to the understanding of SARS-CoV-2 infection, spreading of the virus throughout the body, and potential viral interference with RAS in COVID-19 patients.


title: Lessons drawn from China and South Korea for managing COVID-19 epidemic: insights from a comparative modeling study

text: We conducted a comparative study of COVID-19 epidemic in three different settings: mainland China, the Guangdong province of China and South Korea, by formulating two disease transmission dynamics models incorporating epidemic characteristics and setting-specific interventions, and fitting the models to multi-source data to identify initial and effective reproduction numbers and evaluate effectiveness of interventions. We estimated the initial basic reproduction number for South Korea, the Guangdong province and mainland China as 2.6 (95% confidence interval (CI): (2.5, 2.7)), 3.0 (95%CI: (2.6, 3.3)) and 3.8 (95%CI: (3.5,4.2)), respectively, given a serial interval with mean of 5 days with standard deviation of 3 days. We found that the effective reproduction number for the Guangdong province and mainland China has fallen below the threshold 1 since February 8th and 18th respectively, while the effective reproduction number for South Korea remains high, suggesting that the interventions implemented need to be enhanced in order to halt further infections. We also project the epidemic trend in South Korea under different scenarios where a portion or the entirety of the integrated package of interventions in China is used. We show that a coherent and integrated approach with stringent public health interventions is the key to the success of containing the epidemic in China and specially its provinces outside its epicenter, and we show that this approach can also be effective to mitigate the burden of the COVID-19 epidemic in South Korea. The experience of outbreak control in mainland China should be a guiding reference for the rest of the world including South Korea.


title: Potency and timing of antiviral therapy as determinants of duration of SARS CoV-2 shedding and intensity of inflammatory response

text: Treatments are desperately needed to lower the hospitalization and case fatality rates of SARS CoV-2 infection. In order to meaningfully impact the COVID-19 pandemic, promising antiviral therapies must be identified within the next several months. However, the number of clinical trials that can be performed in this timeframe is limited. We therefore developed a mathematical model which allows projection of all possible therapeutic approaches. Our model recapitulates off-treatment viral dynamics and predicts a three-phase immune response. Addition of treatment with remdesivir, hydroxychloroquine, neutralizing antibodies or cellular immunotherapy demonstrates that if in vivo drug potency is high, then rapid elimination of virus is possible. Potent therapies dosed soon after peak viral load when infected people typically develop symptoms, are predicted to decrease shedding duration and intensity of the effector immune response, but to have little effect on viral area under the curve, which is driven by high levels of early SARS CoV-2 replication. Potent therapy dosed prior to peak viral load, when infection is usually pre-symptomatic, is predicted to be the only option to lower viral area under the curve. We also identify that clinically meaningful drug resistance is less likely to emerge with a highly potent agent that is dosed after peak viral load. Our results support an early test and treat approach for COVID-19, but also demonstrate the need to identify early viral shedding kinetic features that are the most predictive surrogates of clinical severity and transmission risk.


Neurologists Scramble to Respond to COVID-19 with Telemedicine: The Challenges and Opportunities


title: Cancelling March Madness exposes opportunities for a more sustainable sports tourism economy

text: One of the earliest signals of the severity of the spread of COVID-19 in the United States and other countries was the swift cancelation of many highly prominent amateur and professional sporting events and seasons like the NCAA Division I Men’s Basketball Tournament, known as “March Madness.” The loss of March Madness is treated as a moment of creative tension, when disruptions can facilitate reflection and lead to positive change. We discuss the economic, socio-cultural, and environmental effects of shuttering the tournament and suggest that an understanding of the impacts of COVID-19 offers an opportunity to bring about an alternative, more sustainable sports tourism economy. The cancellation of March Madness resulted in the loss of millions of dollars in tourism revenue for local economies and deprived traveler-fans of pilgrimages to arenas, important socio-cultural gathering spaces for American basketball fans. However, it also prevented the emission of a sizable quantity of greenhouse gasses based on our carbon footprint calculated from the previous year’s tournament. Ultimately, from the disruptive closing down of sport and event tourism, a post-pandemic sports tourism landscape should emerge that takes more seriously the triple-bottom line notion of balancing a reduction of greenhouse gas emissions with the creation and maintenance of resilient local economies all while both acknowledging the important role sport plays in society and keeping tourism actors healthy.


title: Epidemiological Development of Novel Coronavirus Pneumonia in China and Its Forecast

text: ABSTRACT BACKGROUND AND OBJECTIVE The novel coronavirus (SARS-Cov-2) infected coronavirus disease 2019 (COVID-19) was broken out in Wuhan and Hubei province for more than a month. It severely threats people's health of thousands in Chin and even other countries. In order to prevent its wide spread, it is necessary to understand the development of the epidemic with precise mathematical language. METHODS The various data of novel coronavirus pneumonia were collected from the official websites of the National Health Committee of the People's Republic of China. According to epidemic and administrative division, three groups were divided to analyze the data, Hubei Province (including Wuhan), nationwide without Hubei and Henan Province. With classic SIR models, the fitting epidemiological curves of incidence have made, and basic reproduction number (R0) was also calculated as well. Therefore the disease's infection intensity, peak time and the epidemiological end time can be deduced.


Ozone disinfectants like soclean CPAP sanitizer can be used to sterilize cloth and n95 masks in the protection against COVID-19


title: Modeling and Short-Term Forecasts of Indicators for COVID-19 Outbreak in 25 Countries at the end of March

text: Background: The coronavirus, which originated in Wuhan, causing the disease called COVID-19, spread more than 200 countries and continents end of the March. There is a lot of data since the virus started. However, these data will be explanatory when accurate analyzes are made and will allow future predictions to be made. In this study, it was aimed to model the outbreak with different time series models and also predict the indicators. Methods: The data was collected from 25 countries which have different process at least 20 days. ARIMA(p,d,q), Simple Exponential Smoothing, Holts Two Parameter, Browns Double Exponential Smoothing Models were used. The prediction and forecasting values were obtained for the countries. Trends and seasonal effects were also evaluated. Results: China has almost under control according to forecasting. The cumulative death prevalence in Italy and Spain will be the highest, followed by the Netherlands, France, England, China, Denmark, Belgium, Brazil and Sweden respectively as of the first week of April. The highest daily case prevalence was observed in Belgium, America, Canada, Poland, Ireland, Netherlands, France and Israel between 10% and 12%.The lowest rate was observed in China and South Korea. Turkey was one of the leading countries in terms of ranking these criteria. The prevalence of the new case and the recovered were higher in Spain than Italy. Conclusions: More accurate predictions for the future can be obtained using time series models with a wide range of data from different countries by modelling real time and retrospective data.


title: Fused Filament Fabrication of Biodegradable PLA/316L Composite Scaffolds: Effects of Metal Particle Content

text: Abstract Polylactic acid (PLA) is a biodegradable polymer suitable for fabricating porous scaffolds in bone tissue engineering. Fillers are often added into PLA matrix to fabricate composite scaffolds in order to improve the performance of pure PLA. In the present study, we fabricated PLA/316L composite scaffolds with stainless steel particle contents from 5 vol% to 15 vol% using fused filament fabrication (FFF) process. The effects on dimensions of pore and strut, surface roughness, as well as thermal, mechanical, and in-vitro degradation properties of the scaffolds were studied. The results showed that the dimensional accuracy was improved, and the surface roughness was tailored by the addition of steel powders that were dispersedly distributed on the strut surface. In addition, PLA/316L composite scaffolds exhibited a lower coefficient of thermal expansion than pure PLA, while glass transition temperature and crystalline phase transition temperature were not significantly affected by steel powder. Moreover, compressive strength and elastic modulus were enhanced when powder loading was set at 10 vol% or 15 vol%. In-vitro degradation tests showed no significant differences on degradation rates between PLA and PLA/316L composite scaffolds.


title: On the Front (Phone) Lines: Results of a COVID-19 Hotline in Northeast Ohio

text: ABSTRACT Importance: Severe acute respiratory syndrome coronavirus (SARS-CoV-2) and the associated coronavirus disease of 2019 (COVID-19) have presented immense challenges for health care systems. Many regions have struggled to adapt to disruptions to health care practice and employ systems that effectively manage the demand for services. Objective: To examine the effectiveness of the first five weeks of a 24/7 physician-staffed COVID-19 hotline. Design: Cohort study using electronic health records. Setting: A single large health care system in Northeast Ohio. Participants: During 5 weeks of operation, 10,112 patients called the hotline (callers) and were evaluated by a registered nurse (RN) using standardized protocols. Of these, 4,213 (42%) were referred for a physician telehealth visit (telehealth patients). The mean age of callers was 42 years. 67% were female, 51% white, and 46% were on Medicaid or uninsured. Intervention: Physician telehealth visits for COVID-19. Main Outcomes and Measures: We describe clinical diagnosis, patient characteristics (age, sex race/ethnicity, smoking status, insurance status), and visit disposition. We use logistic regression to evaluate associations between patient characteristics, visit disposition and subsequent emergency department use, hospitalization, and SARS-Cov-2 PCR testing. Results: Common caller concerns included cough, fever, and shortness of breath. Most telehealth patients (79%) were advised to self-isolate at home, 14% were determined to be unlikely to have COVID-19, 3% were advised to seek emergency care, and 4% had miscellaneous other dispositions. A total of 287 (7%) patients had a subsequent ED visit, and 44 (1%) were hospitalized with a COVID-19 diagnosis. Of the callers, 482 (5%) had a COVID-19 test reported with 69 (14%) testing positive. Among patients advised to stay at home, 83% had no further face-to-face visits. In multivariable results, only a physician recommendation to seek emergency care was associated with emergency room use (OR=4.73, 95%CI 1.37-16.39, p=.014). Only older age was associated with having a positive test result. Conclusions and Relevance: Robust, physician-directed telehealth services can meet a wide range of needs during the acute phase of a pandemic, conserving scarce resources such as personal protective equipment and testing supplies and preventing the spread of infections to patients and health care workers.


title: COVID-19 in Kenya

text: COVID-19 meaning Coronavirus disease which is severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) discovered in the year December 2019 at Wuhan in China after an outbreak an infectious disease causing respiratory illness-pneumonia. SARS-CoV-2 was previously known as 2019 novel Coronavirus disease or 2019-nCov. Kenya has 122 positive cases of COVID-19 as at 4thApril 2020, four deaths and three recoveries as reported by the Government of Kenya.


title: Disinfection effect of pulsed xenon ultraviolet irradiation on SARS-CoV-2 and implications for environmental risk of COVID-19 transmission

text: Prolonged survival of SARS-CoV-2 on environmental surfaces and personal protective equipment (PPE) may lead to these surfaces transmitting disease to others. This article reports the effectiveness of a pulsed xenon ultraviolet (PX-UV) disinfection system in reducing the load of SARS-CoV-2 on hard surfaces and N95 respirators. Chamber slides and N95 respirator material were directly inoculated with SARS-CoV-2 and exposed to different durations of PX-UV disinfection. For hard surfaces, disinfection for 1, 2, and 5 minutes resulted in 3.53 Log10, >4.54 Log10, and >4.12 Log10 reductions in viral load, respectively. For N95 respirators, disinfection for 5 minutes resulted in >4.79 Log10 reduction in viral load. We found that PX-UV significantly reduces SARS-CoV-2 on hard surfaces and N95 respirators. With the potential to rapidly disinfectant environmental surfaces and N95 respirators, PX-UV devices are a promising technology for the reduction of environmental and PPE bioburden and to enhance both HCW and patient safety by reducing the risk of exposure to SARS-CoV-2.


title: Sterilization of N95 respirators: The time for action is upon us!

text: Re-processing of primary protective equipment is the need of the hour with healthcare systems all over the world strained due to the shortage precipitated by severe acute respiratory syndrome coronavirus 2. The common methods of re-sterilization do not hold well for filtering facepiece respirators (FFRs) as they affect their structure and function. We propose the validation and eventual use of gamma irradiation, an already existing method of re-sterilization, to disinfect FFRs in bulk.


title: The Clinical Efficacy of BQJGHJ (a Traditional Chinese Medicine Compound Pharmaceutics) in the Treatment of Chickens Artificially Infected with Infectious Bronchitis Virus/ 板芩桔甘合剂对传染性支气管炎病毒人工感染雏鸡的临床疗效分析

text: This study was conducted to investigate the clinical efficacy of BQJGHJ, a traditional Chinese medicine compound pharmaceutics, in the treatment of chickens artificially infected with Infectious bronchitis virus (IBV). One hundred and twenty chicks were divided into blank group, model group (IBV infection), positive drug group (IBV infection & Gan Dan oral liquid), and BQJGHJ high, middle and low dose groups (IBV infection & BQJGHJ), 20 chicks in each group. Except for the blank group, the other groups were modeled by infecting IBV-M41 strain, 4 days after modeling, the medicines were administrated through drinking water for 5 days. The clinical symptoms of each group were observed every day, the scores of clinical symptoms were recorded, the effective rate was counted, and the cure rate was used as the evaluation index. On the 3rd, 5th and 7th day post the first administration, the blood samples were collected from the wing vein and the serum were separated. The contents of IFN-γ, IL-6 and IL-10 in chicks serum were detected by ELISA. The results indicated that the cure rates of BQJGHJ high, middle and low dose groups were 75.0%, 80.0% and 65.0%, and the effective rates were 90.0%, 95.0% and 80.0%, respectively. The content of IL-10 in serum of chicks in model group decreased and the content of IL-6 increased, which was significantly different from that in blank group (P<0.05 or P<0.01). On day 3 and 5 of administration, the contents of IFN-γ (P<0.01 at day 5 in high dose group, P>0.05 for others) and IL-10(P<0.01 at day 5 in eath BQJGHJ gruop and positive drug group) in serum of chicks in BQJGHJ high, middle and low dose groups and positive drug groups increased, while the contents of IL-6 in serum of chicks decreased, which were significantly different from those in model group (P<0.05). On the 2nd day after withdrawal, the contents of IFN-γ and IL-10 in serum of chicks in BQJGHJ high, middle and low dose groups and positive drug groups increased, while the contents of IL-6 in serum decreased, which were significantly different from those in model group (P<0.05 or P<0.01); There was no significant difference in the contents of IFN-γ and IL-6, IL-10 in serum of chicks between each BQJGHJ group and the positive drug group (P>0.05). BQJGHJ can increase the content of IFN-γ, IL-10 in serum of chicks with infectious bronchitis, reduce the content of IL-6 in serum of chicks with infectious bronchitis, so as to achieve the effect of treating infectious bronchitis in chicks.


title: COVID-19-related coagulopathy – Is transferrin a missing link?

text: SARS-CoV-2 is the causative agent of COVID-19. Severe COVID-19 disease has been associated with disseminated intravascular coagulation and thrombosis, but the mechanisms underlying COVID-19-related coagulopathy remain unknown. Since the risk of severe COVID-19 disease is higher in males than in females and increases with age, we combined proteomics data from SARS-CoV-2-infected cells with human gene expression data from the Genotype-Tissue Expression (GTEx) database to identify gene products involved in coagulation that change with age, differ in their levels between females and males, and are regulated in response to SARS-CoV-2 infection. This resulted in the identification of transferrin as a candidate coagulation promoter, whose levels increases with age and are higher in males than in females and that is increased upon SARS-CoV-2 infection. A systematic investigation of gene products associated with the GO term “blood coagulation” did not reveal further high confidence candidates, which are likely to contribute to COVID-19-related coagulopathy. In conclusion, the role of transferrin should be considered in the course of COVID-19 disease and further examined in ongoing clinic-pathological investigations.


title: Estimating population immunity without serological testing

text: We propose an approximate methodology for estimating the overall level of immunity against COVID-19 in a population that has been affected by the recent epidemic. The methodology relies on the currently available mortality data and utilizes the properties of the SIR model. We illustrate the application of the method by estimating the recent levels of immunity in 10 US states with highest case numbers of COVID-19.


Obesity during the COVID-19 pandemic: cause of high risk or an effect of lockdown? A population-based electronic health record analysis in 1 958 184 individuals.


title: Investigating mechanism of Qingfei Dayuan Granules for treatment of COVID-19 based on network pharmacology and molecular docking/ 基于网络药理学和分子对接探讨清肺达原颗粒治疗新型冠状病毒肺炎（COVID-19）的作用机制

text: Objective: To explore the main active components, key targets and signaling pathways of Qingfei Dayuan Granules in treating of COVID-19 based on network pharmacology and molecular docking. Methods: TCMSP, ETCM and YATCM databases were used to search the chemical constituents of Qingfei Dayuan Granules, and the threshold values of OB ≥ 30% and DL ≥0.18 were used to screen the potential active compounds. SIB and STITCH databases were used to query the targets corresponding to the active compounds, and the PPI network and network topology parameters were obtained by using STRING database. Cytoscape 3.6.0 was used to screen the hub targets. The key targets were analyzed by Gene Ontology (GO), the Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment and tissue enrichment using DAVID 6.8 software. The molecular docking was performed by AutoDock Tools 1.5.6 software. Results: A total of 251 active compounds and 1 037 targets were obtained, 107 key targets and 185 corresponding compounds were screened. The key targets involved ESR1, AR, EGFR, KDR, MMP2, and 52 genes were coexpressed with ACE2. The results of GO function enrichment analysis showed that Qingfei Dayuan Granules mainly regulated the biological processes of cell surface signaling transduction, molecular function, phosphorylation and transcription. KEGG pathway enrichment mainly involved chemokine signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, natural killer cell mediated cytotoxicity and Toll like receptor signaling pathway. The results of tissue enrichment showed that the key gene expression sites were mainly in lung and epithelial cells, involving a variety of immune cells, such as T cells, B cells, lymphocytes, etc. Molecular docking showed that the compounds with good binding power to SARS-CoV-2-RBD-ACE2 complex in Qingfei Dayuan granules were mainly come from Bupleuri Radix, Codonopsis Radix, Anemarrhenae Rhizoma, and Glycyrrhizae Radix et Rhizoma. Saikosaponin, glycyrrhizic acid, anemarsaponin had good binding power with SARS-CoV-2-S-RBD-ACE2, which may be potential active components against SARS-CoV-2. Conclusion: Qingfei Dayuan Granules has the characteristics of multi-components, multi-targets and multi-pathway regulation. Saikosaponin, glycyrrhizic acid, and anemarsaponin may be the potential active components against SARS-CoV-2. The mechanisms of its treatment against COVID-19 may be related to the regulation of the co-expressed genes with ACE2, inhibition of inflammation and immune related signaling pathways, and the destruction of the complex structure of SARS-CoV-2-S-RBD-ACE2.


title: Early detection of severe COVID-19 disease patterns define near real-time personalised care, bioseverity in males, and decelerating mortality rates.

text: BACKGROUND: COVID-19 is a global health emergency. Recent data indicate a 50% mortality rate across UK intensive care units. METHODS: A single institution, two-centre retrospective analysis following implementation of a Decision Support tool and real-time data dashboard for early detection of patients requiring personalised enhanced care, focussing particularly on respiratory rate, diastolic blood pressure, oxygenation indices, C-reactive protein, D-dimer and ferritin. Protocols differing from conventional practice included high-dose prophylactic anticoagulation for all COVID-19 positive patients and antioxidant prescription. RESULTS: By 22nd April 2020, 923 patients tested COVID-19 positive. 569 patients (61.7%) were male. The majority presented with advanced disease: interquartile ranges were C-reactive protein 44.9-179mg/L, D-dimer 1070-3802ng/L, and ferritin 261-1208g/L. Completed case fatality rates were 25.1% [95% CI 20.0, 30.0] in females, 40.5% [95% CI 35.9, 45.0] in males. 139 patients were admitted to intensive care where current death rates are 16.2% [95% CI 3.8, 28.7] in females, 38.2% [95% CI 28.6, 47.8] in males with no trends for differences based on ethnicity. A real-time traffic lights dashboard enabled rapid assessment of patients using critical parameters to accelerate adjustments to management protocols. In total 513 (55.6%) of patients were flagged as high risk for thromboembolic disease, exceeding the numbers flagged for respiratory deteriorations (N=391, 42.4%), or cytokine storm (N=68, 7.4%). There was minimal evidence that age was associated with disease severity, but males had higher levels of all dashboard indices, particularly C-reactive protein and ferritin (p<0.0001) which displayed no relationship with age. CONCLUSIONS: Survival rates are encouraging. Protocols employed (traffic light-driven personalised care, protocolised early therapeutic anticoagulation based on D-dimer >1,000ng/L and/or CRP>200 mg/L, personalised ventilatory strategies and antioxidants) are recommended to other units. Males are at greater risk of severe disease, most likely as the obligate SARS-CoV-2 receptor is on the X-chromosome, and require especially close, and early attention.


title: Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population

text: In six of seven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients, VH clonotypes, encoded by either immunoglobin heavy variable (IGHV)3-53 or IGHV3-66 and immunoglobin heavy joining (IGHJ)6, were identified in IgG1, IgA1, and IgA2 subtypes, with minimal mutations, and could be paired with diverse light chains, resulting in binding to the SARS-CoV-2 receptor-binding domain (RBD). Because most human antibodies against the RBD neutralized the virus by inhibiting host cell entry, we selected one of these clonotypes and demonstrated that it could potently inhibit viral replication. Interestingly, these VH clonotypes pre-existed in six of 10 healthy individuals, predominantly as IgM isotypes, which could explain the expeditious and stereotypic development of these clonotypes among SARS-CoV-2 patients.


title: Rapid diagnosis of SARS-CoV-2 infection by detecting IgG and IgM antibodies with an immunochromatographic device: a prospective single-center study

text: Objectives: SARS-CoV-2 infection constitutes a diagnostic challenge in patients from 2-3 weeks after the onset of symptoms, due to the low positivity rate of the PCR, especially in upper respiratory samples. Serologic tests based on ELISA have been developed and evaluated as useful complements to PCR in these situations. However, there is scarce information about the usefulness of rapid tests based on immunochromatography. The aim of our study was to analyze the diagnostic performance of these rapid tests in COVID-19 pneumonia patients. Methods: We evaluated an immunochromatographic test (AllTest COV-19 IgG / IgM kit) which detects IgG and IgM antibodies. First, we performed a validation of the serologic test using serum samples from 45 healthy control patients (group 1) and 55 confirmed by PCR cases of COVID-19 (group 2) in order to establish the specificity and sensitivity, respectively. Then we prospectively employed the test in 63 patients diagnosed with pneumonia of unknown etiology that were SARS-CoV-2 negative by PCR (group 3), to establish the diagnostic performance in these patients. Results: All patients from group 1 (healthy controls) resulted negative for the serologic test (specificity = 100%). Regarding group 2 (PCR positive) patients, the median time from the onset of symptoms was 11 days and the test was positive for either IgM or IgG in 26 out of 55 patients (overall sensitivity = 47.3%). However, in those patients with 14 days or more from onset of symptoms, the sensitivity was 73.9%. Regarding group 3 patients, the median days from onset of symptoms was 17 and the test was positive in 56 out of 63 patients (88.9% positivity rate). In these group 3 patients with 14 days or more from onset of symptoms, the positivity rate was 91.1%. Conclusions: Our study shows that serologic rapid tests can be used as a complement of PCR to diagnose SARS-CoV-2 infection after 14 days from the onset of symptoms. These immunochromatographic devices could be especially useful in hospitalized patients with pneumonia of unknown etiology with 14 or more days from the onset of symptoms and in whom the PCR has been negative.


Belief in the age of coronavirus: Dread, science and mystery


title: Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences

text: Motivation Infectious diseases from novel viruses are becoming a major public health concern. Fast identification of virus–host interactions can reveal mechanistic insights of infectious diseases and shed light on potential treatments and drug discoveries. Current computational prediction methods for novel viruses are based only on protein sequences. Yet, it is not clear to what extent other important features, such as the symptoms caused by the viruses, could contribute to a predictor. Disease phenotypes (i.e., symptoms) are readily accessible from clinical diagnosis and we hypothesize that they may act as a potential proxy and an additional source of information for the underlying molecular interactions between the pathogens and hosts. Results We developed DeepViral, a deep learning method that predicts potential protein–protein interactions between human and viruses. First, human proteins and viruses were embedded in a shared space using their associated phenotypes, functions, taxonomic classification, as well as formalized background knowledge from biomedical ontologies. By extending a sequence learning model with phenotype features, our model can not only significantly improve over previous sequence-based approaches for inter-species interaction prediction, but also identify pathways of viral targets under a realistic experimental setup for novel viruses. Availability https://github.com/bio-ontology-research-group/DeepViral Contact robert.hoehndorf@kaust.edu.sa


title: The consistent burden in published estimates of delirium occurrence in medical inpatients over four decades: a systematic review and meta-analysis study

text: Introduction Delirium is associated with a wide range of adverse patient safety outcomes. We sought to identify if trends in healthcare complexity were associated with changes in reported delirium in adult medical patients in the general hospital over the last four decades. Methods We used identical criteria to a previous systematic review, including studies using DSM and ICD-10 criteria for delirium diagnosis. Random effects meta-analysis pooled estimates across studies, meta-regression estimated temporal changes, funnel plots assessed publication bias. Results Overall delirium occurrence was 23% (95% CI 19%-26%) (33 studies). There was no change between 1980-2019, nor was case-mix (average age of sample, proportion with dementia) different. There was evidence of increasing publication bias over time. Discussion The incidence and prevalence of delirium in hospitals appears to be stable, though publication bias may mask true changes. Nonetheless, delirium remains a challenging and urgent priority for clinical diagnosis and care pathways.


title: The proportion of deaths cases in confirmed patients of COVID-19 is still increasing for cumulative cases reported up to 25 April 2020

text: In this work I analyse how proportions of fatal cases after COVID-19 infection change since outbreak of the disease. Using publicity available data I model the change in deaths probability from day 30 of outbreak until 25 April 2020. The global trend is that the proportion of fatal cases is still increasing and that many countries have not yet reached the maximum deaths proportion. However, there are visual differences between countries and in some countries the proportions are clearly below or above the global trend. A positive correlation between deaths cases and recorded infections indicates that a higher infection number results in increased mortality numbers.


title: Early estimates of COVID-19 infections in small, medium and large population clusters

text: Since its emergence in December 2019, COVID-19 has rapidly developed into a pandemic with many countries declaring emergency conditions to contain its spread. The impact of the disease, while has been relatively low in the Sub Saharan Africa (SSA) so far, is expected to be devastating given the less developed and fragmented health care system in the continent. In addition, most emergency measures such as border closings, cancellations of inbound flights, social distancing, and promotion of hand hygiene may not be as effective due to the clustered way people live in large as well as smaller population centers. As SSA waits for the start of large epidemics as seem in other regions, there exist acute need for estimates of the potential impacts of the disease once it gets strong hold in the region. To address this need, we developed a mathematical model with key parameters obtained from recent studies, to estimate the number of infections with in the first 90 days of the transmission under different scenarios of population sizes, initial number of cases, and coverage of contact tracing and isolation. Our results show that if implemented early, 80% contact tracing may "flattens the curve" of local epidemics, brings the pandemic to a manageable level for all population sizes we assessed. In countries with limited workforce, hospital resources and ICU care, a robust contact tracing program could yield in outcomes that prevent several millions of infections and thousands of deaths across the continent.


title: Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China

text: Background The seroprevalence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be a more reliable approach to detect true infected population, particularly in asymptomatic persons. Few studies focus on the diagnosis of COVID-19 patients using serological tests. To detect and assess asymptomatic infections of COVID-19 among people in Wuhan, the epicenter of the COVID-19 pandemic in China, and provide evidence for planning adequate public health measures, we collected and analyzed the clinical data in the Wuhan General Hospital mandatory for 16- to 64-year-old asymptomatic people. This retrospective study estimated the seroprevalence of IgM and IgG and compared the epidemiological characteristics of asymptomatic SARS-CoV-2-infected population. Methods Demographical and radiological data were collected from the Wuhan General Hospital between March 26 and April 28, 2020. Serological tests for IgM and IgG antibodies against SARS-CoV-2 were conducted with a colloidal gold method. Nucleic acid sequences of viruses were detected with RT-PCR. Statistical analyses were carried out using SPSS 20.0 software. Findings Between March 26 and April 28, 2020, 18,391 asymptomatic back-to-work participants were enrolled. Among them, 89 had positivity for IgM (0.48%, 95% confidence interval (CI): 0.38-0.58%); 620 cases had IgG positivity (3.37%, 95% CI: 3.11-3.64%), and 650 cases had either IgG positivity or IgM positivity (3.53%, 95% CI: 3.26-3.80%). After standardizing for the genders and ages in the population of Wuhan, the overall standardized seroprevalence of IgG was 3.33% (95% CI: 3.07-3.59%) and the standardized seroprevalence of IgG was 3.01% (95% CI: 2.69-3.33%) among males and 3.66% (95 % CI: 3.23-4.09%) among females. The standardized seroprevalence of IgG was higher in women than in men with a significant difference ({chi}2 = 2,060.3, p < 0.01). By a detection method adjustment, the seroprevalence of IgG was 1.57% (95% CI: 1.39-1.75%) in all medical records, of which males were 1.96% (95% CI: 1.64-2.28%), and females were 1.19% (95% CI: 0.99-1.39%). The assay-adjusted seroprevalence of IgG was higher in women than in men, and the difference was significant ({chi}2 = 5,871.0, p < 0.01). The differences were significant for the seroprevalence of IgG among people who went back to work in different categories of workplace ({chi}2 = 198.44, p < 0.01). The differences in seroprevalence for IgG positivity or IgM positivity among people who went back to work in different urban and rural areas was also significant ({chi}2 = 45.110, p < 0.01). Calculated as IgG and/or IgM antibody positivity, the number of new infections was reduced by 64.8% from March 26 to April 28, 2020. Based on the census population aged 16-64 years in Wuhan in 2017, we estimated that 172,340 (95% CI: 157,568-187,112) asymptomatic people aged 16-64 years were infected with SARS-CoV-2 in Wuhan between March 25 and April 28, 2020. This estimate was 3.4-times higher than the officially reported 50,333 infections on April 28. Interpretation The seropositivity rate in Wuhan indicated that RT-PCR-confirmed patients only represented a small part of the total number of cases. Seropositivity progressively decreased in the Wuhan population from March 26 to April 28, 2020, comparable to Japan and Denmark, but well below the level reported in New York, Iran, Italy, and Germany. The prevalence of asymptomatic infection was higher in women than in men among people who went back to work in Wuhan. The low seroprevalence suggests that most of the population remains susceptible to COVID-19. Funding The Emergency Management Project of the National Natural Science Foundation of China (81842035) and Advisory Research Project of the Chinese Academy of Engineering in 2019 (2019-XZ-70).


Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay


title: The diagnostic accuracy of nucleic acid point-of-care tests for human coronavirus: A systematic review and meta-analysis

text: Many recent studies reported coronavirus point of care tests (POCTs) based on isothermal amplification. However, the performances of these tests have not been systematically evaluated. We searched databases for studies that provide data to calculate sensitivity, specificity and diagnostic odds ratio (DOR). We included 43 studies on 5204 specimens. Most studies had high risk of patient selection and index test bias but low risk in other domains. Most studies (n = 21) used reverse-transcribed loop-mediated isothermal amplification (RT-LAMP) to diagnose Coronavirus disease 2019 (COVID-19). Summary estimated ln(DOR) for RT-LAMP of RNA purified COVID-19 samples is 6.50 (95%CI 5.25-7.76), similar to the previously reported value for RT-LAMP of other RNA virus. RT-LAMP from crude samples has significantly lower ln(DOR) at 4.46 (95%CI 3.53-5.38). SAMBA-II has the highest ln(DOR) at 8.00 (95%CI 6.14-9.87). Abbott ID Now performance is similar to RT-LAMP of crude sample. The performances of CRISPR diagnosis and RT-LAMP are not significantly different. Types of coronaviruses and publication status have no significant effect on diagnosis performance. Existing nucleic acid POCTs, particularly RT-LAMP, CRISPR diagnosis and SAMBA-II, have good diagnostic performance. Future work should focus on improving a study design to minimize the risk of biases.


The Malnutritional Status of the Host as a Virulence Factor for New Coronavirus SARS-CoV-2


title: Multicycle Autoclave Decontamination of N95 Filtering Facepiece Respirators

text: Introduction: During pandemic situations like the one caused by the emergent coronavirus SARS-CoV-2, healthcare systems face the challenge of limited personal protective equipment and impaired supply chains. This problem poses a threat to healthcare workers, first responders, and the public, which demands solutions that can span the gap between institutional shortages and resupplies. Objectives: To examine the efficacy of autoclave-based decontamination for the reuse of single-use surgical masks and N95 filtering facepiece respirators (FFRs). This method is the most readily available form of decontamination in the hospital and laboratory settings. Methods: Three models of N95 FFRs and two procedural masks were evaluated in this study. A moist heat autoclave using four different autoclave cycles: 115°C for one hour, 121.1°C for 30 minutes, 130°C for two minutes, and 130°C for four minutes was used. After the autoclave process, the FFRs were NIOSH fit tested and particle counting was performed for both coarse particles of 5 micrometers (µM) and fine particles from 0.1µM to 1.0µM. Results: We observed negligible alterations in the functionality and integrity of 3M 1805 and 3M 1870/1870+ N95 FFRs after three autoclave cycles. Surgical masks also showed minimal changes in functionality and integrity. The 3M 1860 FFR failed fit test after a single autoclave decontamination cycle. Discussion and Conclusion: The study finds that specific surgical masks and N95 FFR models can withstand autoclave decontamination for up to three cycles. Additionally, the autoclave cycles tested were those that could be readily achieved by both clinical and research institutions.


title: Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number and pathogen genome identity (GENI) score: modeling molecular epidemiology

text: Background: Global spread of COVID-19 created an unprecedented infectious disease crisis that progressed to a pandemic with >180,000 cases in >100 countries. Reproductive number (R) is an outbreak metric estimating the transmission of a pathogen. Initial R values were published based on the early outbreak in China with limited number of cases with whole genome sequencing. Initial comparisons failed to show a direct relationship viral genomic diversity and epidemic severity was not established for SARS-Cov-2. Methods: Each country's COVID-19 outbreak status was classified according to epicurve stage (index, takeoff, exponential, decline). Instantaneous R estimates (Wallinga and Teunis method) with a short and standard serial interval examined asymptomatic spread. Whole genome sequences were used to quantify the pathogen genome identity score that were used to estimate transmission time and epicurve stage. Transmission time was estimated based on evolutionary rate of 2 mutations/month. Findings: The country-specific R revealed variable infection dynamics between and within outbreak stages. Outside China, R estimates revealed propagating epidemics poised to move into the takeoff and exponential stages. Population density and local temperatures had variable relationship to the outbreaks. GENI scores differentiated countries in index stage with cryptic transmission. Integration of incidence data with genome variation directly increases in cases with increased genome variation. Interpretation: R was dynamic for each country and during the outbreak stage. Integrating the outbreak dynamic, dynamic R, and genome variation found a direct association between cases and genome variation. Synergistically, GENI provides an evidence-based transmission metric that can be determined by sequencing the virus from each case. We calculated an instantaneous country-specific R at different stages of outbreaks and formulated a novel metric for infection dynamics using viral genome sequences to capture gaps in untraceable transmission. Integrating epidemiology with genome sequencing allows evidence-based dynamic disease outbreak tracking with predictive evidence.


title: Sonography of the Lungs: Diagnosis and Surveillance of Patients With COVID-19

text: The outbreak of a novel coronavirus (COVID-19) with symptoms that mimic bronchitis and other chest infections has created a need for quick diagnosis to prevent disease spread. Traditionally, computed tomography (CT) has been used as the primary method to identify infection and staging of the virus. While effective, repeated use of ionizing radiation, particularly in susceptible patient populations, can add risk as the disease is monitored through full recovery. Sonography of the chest may be a viable alternative for diagnosis and monitoring of COVID-19. In addition, new technology such as the remote robotic ultrasound equipment being used at Zhejiang Provincial People’s Hospital in Hangzhou, China, has the potential to facilitate sonographic evaluation with minimal disease exposure to the sonologist and to other patients by eliminating the need for patient transport to imaging facilities. Additional studies will need to be conducted to evaluate the effectiveness of sonography versus other imaging modalities in the diagnosis and treatment of COVID-19 and other novel diseases.


Trust is crucial in lockdown-and beyond


title: Nifedipine and Amlodipine Are Associated With Improved Mortality and Decreased Risk for Intubation and Mechanical Ventilation in Elderly Patients Hospitalized for COVID-19

text: Dihydropyridine calcium channel blockers (CCB) are typically used agents in the clinical management of hypertension. Yet, they have also been utilized in the treatment of various pulmonary disorders with vasoconstriction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been implicated in the development of vasoconstrictive, proinflammatory, and pro-oxidative effects. A retrospective review was conducted on CCB use in hospitalized patients in search of any difference in outcomes related to specific endpoints: survival to discharge and progression of disease leading to intubation and mechanical ventilation. The electronic medical records for all patients that tested positive for SARS-CoV-2 that were at or above the age of 65 and that expired or survived to discharge from a community hospital in Brooklyn, NY, between the start of the public health crisis due to the viral disease up until April 13, 2020, were included. Of the 77 patients that were identified, 18 survived until discharge and 59 expired. Seven patients from the expired group were excluded since they died within one day of presentation to the hospital. Five patients were excluded from the expired group since their age was above that of the eldest patient in the survival group (89 years old). With 65 patients left, 24 were found to have been administered either amlodipine or nifedipine (CCB group) and 41 were not (No-CCB group). Patients treated with a CCB were significantly more likely to survive than those not treated with a CCB: 12 (50%) survived and 12 expired in the CCB group vs. six (14.6%) that survived and 35 (85.4%) that expired in the No-CCB treatment group (P<.01; p=0.0036). CCB patients were also significantly less likely to undergo intubation and mechanical ventilation. Only one patient (4.2%) was intubated in the CCB group whereas 16 (39.0%) were intubated in the No-CCB treatment group (P<.01; p=0.0026). Nifedipine and amlodipine were found to be associated with significantly improved mortality and a decreased risk for intubation and mechanical ventilation in elderly patients hospitalized with COVID-19. Further clinical studies are warranted. Including either nifedipine or amlodipine in medication regimens for elderly patients with hypertension hospitalized for COVID-19 may be considered.


title: The reproduction number of COVID-19 and its correlation with public health interventions

text: Throughout the past four months, no number has dominated the public media more persistently than the reproduction number of COVID-19. This powerful but simple concept is widely used by the public media, scientists, and political decision makers to explain and justify political strategies to control the COVID-19 pandemic. Here we explore the effectiveness of political interventions using the reproduction number of COVID-19 across Europe. We propose a dynamic SEIR epidemiology model with a time-varying reproduction number, which we identify using machine learning and uncertainty quantification. During the early outbreak, the reproduction number was 4.5+/-21.4, with maximum values of 6.5 and 5.9 in Spain and France. As of today, it has dropped to 0.7+/-20.2, with minimum values of 0.4 and 0.3 in Austria and France. We found a strong correlation between passenger air travel and the reproduction number with a time delay of 12.6+/-22.7 days. Our new dynamic SEIR model provides the flexibility to simulate various outbreak control and exit strategies to inform political decision making and identify safe solutions in the benefit of global health.


title: Uncertainty stress, and its impact on disease fear and prevention behaviors during the COVID-19 epidemic in China: A panel study

text: Objective To examine changing trends of uncertainty stress, and its impact on disease fear and prevention behaviors during the Chinese COVID-19 epidemic using a prospective observational study. Methods The study employed a longitudinal design. Participants were recruited for an online panel survey from chat groups on social media platforms. There were 5 waves of interviews. Information on uncertainty stress and related variables were collected via the online survey. Descriptive statistics and the GIM program were used for data analysis. Results Participants numbered 150 for the linkable baseline survey and 102 (68%) for the final survey. Uncertainty stress({beta}: -0.047, S.E: 0.118, p>0.05) did not show a statistically significant temporal change trend over the observation period. Disease fear manifested a statistically significant downwards trend ({beta}: -0.342, S.E: 0.157, p<0.05), and prevention behaviors indicated an upwards trend ({beta}: 0.048, S.E: 0.021, p<0.05) during the observation period. Uncertainty stress was positively associated with disease fear ({beta}: 0.45046, S.E: 0.05964, p<0.0001), and negatively associated with self-efficacy ({beta}: -0.6698, S.E: 0.01035, p<0.0001), and prevention behaviors ({beta}: -0.02029, S.E: 0.00876, p: 0.0209). Conclusion This study yielded new information about uncertainty stress among Chinese people during the COVID-19 epidemic. Policy changes and public education are essential for minimizing the negative effects of uncertainty stress in disease prevention.


title: An Agent Based Model methodology for assessing spread and health systems burden for Covid-19 using a synthetic population from India

text: Covid-19 disease, caused by SARS-CoV-2 virus, has infected over four million people globally. It has been declared as a global public health emergency by the World Health Organization. Researchers and governments are striving to do their best to fight against this pandemic. Several Mathematical models mostly based on compartmental modeling are being used for projections for Covid-19 in India. These projections are used for policy level decisions and public health prevention activities. Compartmental models are mostly used for Covid-19 projections. Unlike compartmental models, which consider population average, the Agent based models (ABM) models consider individual behavior in the models for projections. ABMs, yet rarely used for Covid-19, provide better insights into projections compared to compartmental models. We present an ABM approach with a small synthetic population of India, to examine the patterns and trends of the Covid-19 in terms of infected, admitted, critical cases requiring intensive care and/ or ventilator support, mortality and recovery. The parameters for the ABM model are defined and model run for a period of 365 days for three different non-pharmaceutical intervention (NPI) scenarios. AnyLogic platform was used for the ABM simulations. Results revealed that the peak values and slope of the curve declined as NPI became more stringent. The results could provide a platform for researchers and modelers to explore this approach for conducting ABM for Covid-19 projections with inclusion of interventions and health system preparedness.


Special Coverage on COVID-19: No One is Ready for This


title: Studying the pathophysiology of coronavirus disease 2019 - a protocol for the Berlin prospective COVID-19 patient cohort (Pa- COVID-19)

text: Purpose Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide causing a global health emergency. Pa-COVID-19 aims to provide comprehensive data on clinical course, pathophysiology, immunology and outcome of COVID-19, in order to identify prognostic biomarkers, clinical scores, and therapeutic targets for improved clinical management and preventive interventions. Methods Pa-COVID-19 is a prospective observational cohort study of patients with confirmed SARS-CoV-2 infection treated at Charite - Universitaetsmedizin Berlin. We collect data on epidemiology, demography, medical history, symptoms, clinical course, pathogen testing and treatment. Systematic, serial blood sampling will allow deep molecular and immunological phenotyping, transcriptomic profiling, and comprehensive biobanking. Longitudinal data and sample collection during hospitalization will be supplemented by long-term follow-up. Results Outcome measures include the WHO clinical ordinal scale on day 15 and clinical, functional and health-related quality of life assessments at discharge and during follow-up. We developed a scalable dataset to (i) suit national standards of care (ii) facilitate comprehensive data collection in medical care facilities with varying resources and (iii) allow for rapid implementation of interventional trials based on the standardized study design and data collection. We propose this scalable protocol as blueprint for harmonized data collection and deep phenotyping in COVID-19 in Germany. Conclusion We established a basic platform for harmonized, scalable data collection, pathophysiological analysis, and deep phenotyping of COVID-19, which enables rapid generation of evidence for improved medical care and identification of candidate therapeutic and preventive strategies. The electronic database accredited for interventional trials allows fast trial implementation for candidate therapeutic agents.


title: La maladie à coronavirus COVID-19 en Afrique subsaharienne : la place de la santé au travail

text: Résumé Le milieu de travail africain subsaharien pour faire face à la pandémie à COVID-19, doit s’appuyer sur les missions de la santé au travail au niveau du secteur structuré et la promotion du bien-être et de la santé au travail pour le secteur informel. Les mesures de prévention technique collective (sensibilisation, formation, propreté), individuelle (équipements de protection individuelle, vaccination) et de prévention médicale (dépistage, surveillance) rejoignent les recommandations préconisées par les autorités. Summary In response to the COVID-19 pandemic, the workplace in Sub-Saharan Africa should build on the missions of occupational health in the formal sector and on the promotion of well-being and occupational health in the informal sector. Technical prevention measures adopted at the collective level (awareness-raising, training and hygiene) and at the individual level (personal protective equipment and vaccination) as well as disease prevention measures (screening and surveillance) are in line with the recommendations advocated by the authorities.


title: COVID-19 UK Lockdown Forecasts and R0

text: Introduction The first reported UK case of COVID-19 occurred on 31 January 2020, and a lockdown of unknown duration began on 24 March. One model to forecast disease spread depends on clinical parameters and transmission rates. Output includes the basic reproduction number R0 and the log growth rate r in the exponential phase. Methods UK data on reported deaths is used to estimate r. A likelihood for the transmission parameters is defined from a gaussian density for r using the mean and standard error of the estimate. Parameter samples from the Metropolis-Hastings algorithm lead to an estimate and credible interval for R0 and forecasts for severe and critical cases, and deaths during a lockdown. Results In the exponential phase, the UK growth rate for log(deaths) is r = 0.224 with s.e. 0.005. R0 = 5.81 with 90% CI (5.08 , 6.98). In a 12 week lockdown from 24 March with transmission parameters reduced to 20% of their previous values, around 63,000 severely ill patients will need hospitalisation by mid June, 37,000 critically ill will need intensive care, whilst over 81,000 are expected to die. Had the lockdown begun on 17 March around 16,500 severe, 9,250 critical cases and 18,500 deaths would be expected by early June. With 10% transmission, severe and critical cases peak in April. Discussion The R0 estimate is around twice the value quoted by the UK government. The NHS faces extreme pressures, even if transmission is reduced ten-fold. An earlier lockdown could have saved many lives.


title: Using country-level variables to classify countries according to the number of confirmed COVID-19 cases: An unsupervised machine learning approach

text: Background: The COVID-19 pandemic has attracted the attention of researchers and clinicians whom have provided evidence about risk factors and clinical outcomes Research on the COVID-19 pandemic benefiting from open-access data and machine learning algorithms is still scarce yet can produce relevant and pragmatic information With country-level pre-COVID-19-pandemic variables, we aimed to cluster countries in groups with shared profiles of the COVID-19 pandemic Methods: Unsupervised machine learning algorithms (k-means) were used to define data-driven clusters of countries;the algorithm was informed by disease prevalence estimates, metrics of air pollution, socio-economic status and health system coverage Using the one-way ANOVA test, we compared the clusters in terms of number of confirmed COVID-19 cases, number of deaths, case fatality rate and order in which the country reported the first case Results: The model to define the clusters was developed with 155 countries The model with three principal component analysis parameters and five or six clusters showed the best ability to group countries in relevant sets There was strong evidence that the model with five or six clusters could stratify countries according to the number of confirmed COVID-19 cases (p<0 001) However, the model could not stratify countries in terms of number of deaths or case fatality rate Conclusions: A simple data-driven approach using available global information before the COVID-19 pandemic, seemed able to classify countries in terms of the number of confirmed COVID-19 cases The model was not able to stratify countries based on COVID-19 mortality data


title: A Quantitative Lung Computed Tomography Image Feature for Multi-Center Severity Assessment of COVID-19

text: The COVID-19 pandemic has affected millions and congested healthcare systems globally. Hence an objective severity assessment is crucial in making therapeutic decisions judiciously. Computed Tomography (CT)-scans can provide demarcating features to identify the severity of pneumonia, commonly associated with COVID-19, in the affected lungs. Here, a semi-quantitative severity assessing lung CT image feature is demonstrated for COVID-19 patients. An open-source multi-center Italian database was used, among which 61 cases were incorporated in the study (age 27-86, 71% males) from 27 CT imaging centers. Lesions in the form of opacifications, crazy-paving patterns, and consolidations were heuristically marked and the severity determining feature L_norm was quantified and established to be statistically distinct for the three classes i.e., mild, moderate, and severe (p-value < 0.0001). The thresholds of L_norm for a 3-class classification were determined based on the optimum sensitivity/specificity combination from ROC analyses. The feature L_norm classified the cases in the three severity categories with 89.34% accuracy when L_norm was calculated based on experts' heuristic annotations. Substantial to almost-perfect intra-rater and inter-rater agreements were achieved involving expert and non-expert based evaluations ({kappa}-score 0.79-0.97). We trained machine learning based classification models and showed L_norm alone has a superior diagnostic accuracy over standard image intensity and texture features. Classification accuracy was further increased when L_norm was used to delineate the severe cases from non-severe ones (98.9%) with high sensitivity (97.7%), and specificity (97.49%). Therefore, key highlights of this severity assessment feature are accuracy, lower dependency on expert availability, and wide utility across multiple imaging centers.


title: The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases

text: RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2’dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2’ OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2’dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here we show that a conserved Arg residue uses a two-pronged strategy to select against 2’dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2’OH group to promote NTP binding, but selectively inhibits incorporation of 2’dNTPs by interacting with their 3’OH group to favor the catalytically-inert 2’-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.


title: Use Crow-AMSAA Method to predict the cases of the Coronavirus 19 in Michigan and U.S.A

text: The Crow-AMSAA method is used in engineering reliability world to predict the failures and evaluate the reliability growth. The author intents to use this model in the prediction of the Coronavirus 19 (COVID19) cases by using the daily reported data from Michigan, New York City, U.S.A and other countries. The piece wise Crow-AMSAA (CA) model fits the data very well for the infected cases and deaths at different phases while the COVID19 outbreak starting. The slope β of the Crow-AMSAA line indicates the speed of the transmission or death rate. The traditional epidemiological model is based on the exponential distribution, but the Crow-AMSAA is the Non Homogeneous Poisson Process (NHPP) which can be used to modeling the complex problem like COVID19, especially when the various mitigation strategies such as social distance, isolation and locking down were implemented by the government at different places.


title: Pre-existing Cardiovascular Disease in United States Population at High Risk for Severe COVID-19 Infection

text: Background and Purpose There is increasing recognition of a relatively high burden of pre-existing cardiovascular disease in Corona Virus Disease 2019 (COVID 19) infected patients. We determined the burden of pre-existing cardiovascular disease in persons residing in United States (US) who are at risk for severe COVID-19 infection. Methods Age (60 years or greater), presence of chronic obstructive pulmonary disease, diabetes, mellitus, hypertension, and/or malignancy were used to identify persons at risk for admission to intensive care unit, or invasive ventilation, or death with COVID-19 infection. Persons were classified as low risk (no risk factors), moderate risk (1 risk factor), and high risk (two or more risk factors present) using nationally representative sample of US adults from National Health and Nutrition Examination Survey 2017 and 2018 survey. Results Among a total of 5856 participants, 2386 (40.7%) were considered low risk, 1325 (22.6%) moderate risk, and 2145 persons (36.6%) as high risk for severe COVID-19 infection. The proportion of patients who had pre-existing stroke increased from 0.6% to 10.5% in low risk patients to high risk patients (odds ratio [OR]19.9, 95% confidence interval [CI]11.6-34.3). The proportion of who had pre-existing myocardial infection (MI) increased from 0.4% to 10.4% in low risk patients to high risk patients (OR 30.6, 95% CI 15.7-59.8). Conclusions A large proportion of persons in US who are at risk for developing severe COVID 19 infection are expected to have pre-existing cardiovascular disease. Further studies need to identify whether targeted strategies towards cardiovascular diseases can reduce the mortality in COVID-19 infected patients.


A call for caution in extrapolating chest CT sensitivity for COVID-19 derived from hospital data to patients among general population


title: Spaces of care and resistance in China: public engagement during the COVID-19 outbreak

text: As the COVID-19 pandemic continues to unfold, the approach of the Chinese government remains under the spotlight, obscuring the complex landscape of responses to the outbreak within the country. Drawing upon the author’s social media experiences as well as textual analysis of a wide range of sources, this paper explores how the Chinese public responded to the outbreak in complex and nuanced ways through social media. The findings challenge conventional views of Chinese social media as simply sites of self-censorship and surveillance. On the contrary, during the COVID-19 outbreak, social media became spaces of active public engagement, in which Chinese citizens expressed care and solidarity, engaged in claim-making and resistance, and negotiated with authorities. This paper situates this public engagement within a broader context of China’s health-care reforms, calling attention to persistent structural and political issues, as well as the precarious positionalities of health-care workers within the health system.


SPECIAL COVID-19 COVERAGE: Breaking News: The Harm of Treating Fear in COVID-19


title: Fractional-order susceptible-infected model: definition and applications to the study of COVID-19 main protease

text: We propose a model for the transmission of perturbations across the amino acids of a protein represented as an interaction network. The dynamics consists of a Susceptible-Infected (SI) model based on the Caputo fractional-order derivative. We find an upper bound to the analytical solution of this model which represents the worse-case scenario on the propagation of perturbations across a protein residue network. This upper bound is expressed in terms of Mittag-Leffler functions of the adjacency matrix of the network of inter-amino acids interactions. We then apply this model to the analysis of the propagation of perturbations produced by inhibitors of the main protease of SARS CoV-2. We find that the perturbations produced by strong inhibitors of the protease are propagated far away from the binding site, confirming the long-range nature of intra-protein communication. On the contrary, the weakest inhibitors only transmit their perturbations across a close environment around the binding site. These findings may help to the design of drug candidates against this new coronavirus.


title: Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression

text: In this study, we ascertain the associations between BCG vaccination policies and progression of COVID-19 through analysis of various time-adjusted indicators either directly extracted from the incidence and death reports, or estimated as parameters of disease progression models. We observe weak correlation between BCG vaccination status and indicators related to disease reproduction characteristics. We did not find any associations with case fatality rates (CFR), but the differences in CFR estimates are at present likely dominated by differences in testing and case reporting between countries.


title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy

text: Background The management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. It is unclear whether these subjects should be tested in the absence of symptoms and if those can guide diagnosis. Methods Occupational and clinical characteristics of all the consecutive HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, 2020, to March 31, 2020, were collected. Frequencies of positive tests were compared according to selected variables. Multivariable logistic regression analyses were then applied. Findings Positive tests were 138 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.4-10.3), with a marked difference between symptomatic (20.2%, 95%CI: 16.7-24.1) and asymptomatic (3.7%, 95%CI: 2.7-5.1) subjects (p<0.001). Physicians were the group with the highest frequency of positive tests (10.6%, 95%CI: 8.3-13.4) whereas clerical workers and technicians displayed the lowest frequency (2.9%, 95%CI: 0.8-7.3). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors of a positive test were taste and smell alterations (odds ratio [OR]= 29.7) and fever (OR = 7.21). The median time from first positive test to a negative test was 23 days (95%CI: 19-24). Interpretation In this Italian group of HCWs exposed to confirmed cases of COVID-19 the presence of symptoms, especially taste and smell alterations and fever, was associated with SARS-CoV-2 infection. The median time to clear the virus from nasopharynx was 23 days.


title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV2

text: Background The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5’ and 3’ untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. Methods To have an idea of the global changes in 5’ and 3’-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. Results We identified 28 unique variants in SARS-CoV2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5’-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3’UTR among most of the continents. Furthermore, we found that despite of the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. Conclusion Our results, shows for the first time in SARS-Cov2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future.


title: COVID-19: An Update on the Epidemiological, Genomic Origin, Phylogenetic study, India centric to Worldwide current status

text: The pandemic spread of novel coronavirus, (SARS-CoV-2) causing CoronaVirus Infectious Diseases (COVID-19) emerged into a global threat for human life causing serious death rates and economic crunch all over the globe. As on April 17, 2020 at 2:00am CEST, there include a total of 2,034,802 confirmed cases for Corona and 1,35,163 deaths worldwide have been reported which includes 212 countries, areas or territories reported by World Health Organization (WHO), in which USA tops 6,32,781 confirmed cases (28,221 deaths) followed by Italy 1,65,155 (21,647 deaths), Spain 1,77,633 (18,579 deaths) and China 84,149 (4,642 deaths). This study aims to compare the genomic nature of SARS-CoV-2 genome reported from Wuhan, China with two Indian isolate genome reported by ICMR-NIV, India. Further Phylogenetic studies performed with coronavirus infecting non-human species like Bats, Duck, and sparrow were compared with Indian and other country whole genome sequences of SARS-CoV2 using MegaX and traced out the association between the human coronavirus with the other species viral genome. In addition, epidemiological reports on COVID-19 among Worldwide and India centric data were compared between April 7, 2020 to April 17, 2020 global data and the number of active cases were increased dramatically in this 10 days period studied, highlighted in the current study.


title: COVID-19 Confinement and Health Risk Behaviors in Spain

text: The World Health Organization (WHO) has declared a world pandemic due to COVID-19. In response, most affected countries have enacted measures involving compulsory confinement and restrictions on free movement, which likely influence citizens' lifestyles. This study investigates changes in health risk behaviors (HRBs) with duration of confinement. An online cross-sectional survey served to collect data about the Spanish adult population regarding health behaviors during the first 3 weeks of confinement. A large sample of participants (N = 2,741) (51.8% women; mean age 34.2 years [SD 13.0]) from all Spanish regions completed the survey. Binomial logistic regressions adjusted for socioeconomic characteristics (i.e., gender, age, civil status, education, and occupation), body mass index (BMI), previous HRBs, and confinement context (i.e., solitude and exposure to COVID-19) were conducted to investigate associations between the number of weeks confined and a set of six HRBs (physical activity, alcohol consumption, fresh fruit and vegetable consumption, smoking, screen exposure, and sleep hours). When adjusted, we observed significantly lower odds of experiencing a higher number of HRBs than before confinement overall in a time-dependent fashion: OR 0.63; 95% CI: 0.49–0.81 for the second and OR 0.47; 95% CI: 0.36–0.61 for the third week of confinement. These results were equally consistent in all age and gender subgroup analyses. The present study indicates that changes toward a higher number of HRBs than before confinement, as well as the prevalence of each HRB except screen exposure, decreased during the first 3 weeks of COVID-19 confinement, and thus the Spanish adult population may have adapted to the new situational context by gradually improving their health behaviors.


title: Rapid Single Cell Evaluation of Human Disease and Disorder Targets Using REVEAL: SingleCell™

text: Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypothesis by querying extensive single-cell datasets. Large single-cell datasets like human cell atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics and vaccine targets; as the world struggles to cope with the on-going spread of COVID-19 infections. In this manuscript we describe, REVEAL: SingleCell which enables storage, retrieval and rapid query of single-cell datasets inclusive of millions of cells. The analytical database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypothesis. One such example includes identifying the most prevalent cell type annotation tag on returned cells. We used REVEAL: SingleCell to evaluate expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in <60 seconds. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic.


title: Studying the progress of COVID-19 outbreak in India using SIRD model

text: We explore a standard epidemiological model, known as the SIRD model, to study the COVID-19 infection in India, and a few other countries around the world. We use (a) the stable cumulative infection of various countries and (b) the number of infection versus the tests carried out to evaluate the model. The time-dependent infection rate is set in the model to obtain the best fit with the available data. The model is simulated aiming to project the probable features of the infection in India, various Indian states, and other countries. India imposed an early lockdown to contain the infection that can be treated by its healthcare system. We find that with the current infection rate and containment measures, the total active infection in India would be maximum at the end of June or beginning of July 2020. With proper containment measures in the infected zones and social distancing, the infection is expected to fall considerably from August. If the containment measures are relaxed before the arrival of the peak infection, more people from the susceptible population will fall sick as the infection is expected to see a three-fold rise at the peak. If the relaxation is given a month after the peak infection, a second peak with a moderate infection will follow. However, a gradual relaxation applied well ahead of peak infection, leads to a two-fold increase in the peak infection. The projection of the model is highly sensitive to the choice of the parameters and the available data. Our model provides a semi-quantitative overview of the progression of COVID-19 in India, with model projections reasonably replicating the current progress. However, since the pandemic is an ongoing dynamic phenomenon, the reported results are subjected to regular updates in consonance with the acquired real data.


title: Assembly of an integrated human lung cell atlas reveals that SARS-CoV-2 receptor is co-expressed with key elements of the kinin-kallikrein, renin-angiotensin and coagulation systems in alveolar cells

text: SARS-CoV-2, the pathogenic agent of COVID-19, employs angiotensin converting enzyme-2 (ACE2) as its cell entry receptor. Clinical data reveal that in severe COVID-19, SARS-CoV-2 infects the lung, leading to a frequently lethal triad of respiratory insufficiency, acute cardiovascular failure, and coagulopathy. Physiologically, ACE2 plays a role in the regulation of three systems that could potentially be involved in the pathogenesis of severe COVID-19: the kinin-kallikrein system, resulting in acute lung inflammatory edema; the renin-angiotensin system, promoting cardiovascular instability; and the coagulation system, leading to thromboembolism. Here we analyzed ~130,000 human lung single-cell transcriptomes and show that key elements of the kinin-kallikrein, renin-angiotensin and coagulation systems are co-expressed with ACE2 in alveolar cells, which could explain how changes in ACE2 promoted by SARS-CoV-2 cell entry result in the development of the three most severe clinical components of COVID-19.


title: Size Dependent Particle Removal Efficiency and Pressure Drop of a Dust Cleaning Material For Use as Facemask Filters for Protection during COVID-19

text: The COVID-19 pandemic has caused a severe demand for facemasks, and this has resulted in the use of those made from alternate media. As SARS-CoV-2 spreads primarily due to airborne droplets, it is critical to verify the filtration efficiency of these alternate media based facemasks. While several media are being tested and used, commercially available dust cleaners have shown reasonable filtration efficiency. This may also be due to the potential electrostatic charge on the surface which enhances capture of the fine particles. In this manuscript, we report the size dependent filtration efficiency studied systematically in a filter holder-based system as 47 mm punches; and test results on a mannequin that was 3D printed wearing a bandana mask that was placed in a chamber.


title: Open Access and Altmetrics in the pandemic age: Forescast analysis on COVID-19 literature

text: We present an analysis on the uptake of open access on COVID-19 related literature as well as the social media attention they gather when compared with non OA papers. We use a dataset of publications curated by Dimensions and analyze articles and preprints. Our sample includes 11,686 publications of which 67.5% are openly accessible. OA publications tend to receive the largest share of social media attention as measured by the Altmetric Attention Score. 37.6% of OA publications are bronze, which means toll journals are providing free access. MedRxiv contributes to 36.3% of documents in repositories but papers in BiorXiv exhibit on average higher AAS. We predict the growth of COVID-19 literature in the following 30 days estimating ARIMA models for the overall publications set, OA vs. non OA and by location of the document (repository vs. journal). We estimate that COVID-19 publications will double in the next 20 days, but non OA publications will grow at a higher rate than OA publications. We conclude by discussing the implications of such findings on the dissemination and communication of research findings to mitigate the coronavirus outbreak.


Toxicology Rounds: The Lowdown on Drugs to Treat COVID-19


title: Deep Learning-Based Cross-Machine Health Identification Method for Vacuum Pumps with Domain Adaptation

text: Abstract Intelligent data-driven machinery health identification has been attracting increasing attention in the manufacturing industries, due to reduced maintenance cost and enhanced operation safety. Despite the successful development, the main limitation of most existing methods lies in the assumption that the training and testing data are collected from the same distribution, i.e. the same machine under identical condition. However, this assumption is difficult to be met in the real industries, since the diagnostic model is generally expected to be applied on new machines. In order to address this issue, a deep learning-based cross-machine health identification method is proposed for industrial vacuum pumps, which are of great importance in the manufacturing industry but have received far less research attention in the literature. Generalized diagnostic features can be learnt using the proposed domain adaptation technique with maximum mean discrepancy metric. The health identification model learnt from the training machines can be well applied on new machines. Experiments on a real-world vacuum pump dataset validate the proposed method, which is promising for industrial applications.


title: Sample pooling on triplets to speed up SARS-CoV-2 diagnosis using CDC FDA EUA RT-qPCR kit.

text: The CDC designed "FDA Emergency Use Authorization" 2019-nCoV CDC RT-qPCR kit uses 3 different FAM probes for SARS-CoV-2 diagnosis so 3 reactions per sample are needed. We herein describe a sample pooling protocol: 3 RNA extractions are combined into a single PCR reaction. The sensitivity for this protocol is 100% as no shift on Ct values for N1 or N2 probes were observed. For a typical 96-well plate, triplet assay allows 96 samples processing, speeding up diagnosis.


title: Clinical features and outcomes of 2019 novel coronavirus-infected patients with high plasma BNP levels

text: Aims To explore clinical features and outcome of 2019 novel coronavirus(2019-nCoV)-infected patients with high BNP levels Methods and results Data were collected from patients medical records, and we defined high BNP according to the plasma BNP was above > 100 pg/mL. In total,34 patients with corona virus disease 2019(COVID-19)were included in the analysis. Ten patients had high plasma BNP level. The median age for these patients was 60.5 years (interquartile range, 40-80y), and 6/10 (60%) were men. Underlying comorbidities in some patients were coronary heart disease (n=2, 20%) ;hypertesion(n=3;30%);, heart failure (n=1,10%)and diabetes (n=2, 20%). Six (60%) patients had a history of Wuhan exposure. The most common symptoms at illness onset in patients were fever (n=7, 70%), cough (n=3, 30%), headache or fatigue(n=4,40%);. These patients had higher aspartate aminotransferase(AST), troponin I, C reactive protein and lower hemoglobin, and platelet count,compared with patients with normal BNP, respectively. Compared with patients with normal BNP, patients with high BNP were more likely to develop severe pneumonia, and receive tracheal cannula, invasive mechanical ventilation, continuous renal replacement therapy, extracorporeal membrane oxygenation, and be admitted to the intensive care unit. One patient with high BNP died during the study.


title: Successful Conservative Management of Acute Appendicitis in a Coronavirus Disease 2019 (COVID-19) Patient

text: Appendectomy is the gold standard of treatment for acute appendicitis; however, recent evidence suggests conservative management with intravenous antibiotics may provide similar outcomes and can be used as an alternative in selected patients. Performing appendectomy in acute appendicitis patients with 2019 novel Coronavirus Disease (COVID-19) is challenging, as it involves considerable operative risks for the patients and risks for health care professionals (HCPs) exposed to COVID-19. Medical management eliminates the morbidity and mortality associated with surgery but involves significant risks of treatment failures that, in turn, may lead to perforation, peritonitis, and death. We are reporting a case of a middle-aged man with multiple co-morbidities, who was diagnosed with COVID-19 and acute appendicitis. Our patient received intravenous antibiotics for seven days with a significant improvement in symptoms. Our case report illustrates the implementation of successful conservative treatment for acute appendicitis in COVID-19 patients.


title: A Mathematical Model for the COVID-19 Outbreak and Its Applications

text: A mathematical model based on nonlinear ordinary differential equations is proposed for quantitative description of the outbreak of the novel coronavirus pandemic The model possesses remarkable properties, such as as full integrability The comparison with the public data shows that exact solutions of the model (with the correctly specified parameters) lead to the results, which are in good agreement with the measured data in China and Austria Prediction of the total number of the COVID-19 cases is discussed and examples are presented using the measured data in Austria, France, and Poland Some generalizations of the model are suggested as well


title: Highs and lows

text: We must learn from ingenuity of space travel to solve problems close to home


title: Neutralizing Antibodies Responses to SARS-CoV-2 in COVID-19 Inpatients and Convalescent Patients

text: Background. COVID-19 is a pandemic with no specific antiviral treatments or vaccines. The urgent needs for exploring the neutralizing antibodies from patients with different clinical characteristics are emerging. Methods. A total of 117 blood samples were collected from 70 COVID-19 inpatients and convalescent patients. The presence of neutralizing antibody was determined with a modified cytopathogenic assay based on live SARS-CoV-2. The dynamics of neutralizing antibody levels at different with different clinical characteristics were analyzed. Results. The seropositivity rate reached up to 100.0% within 20 days since onset, and remained 100.0% till day 41-53. The total GMT was 1:163.7 (95% CI, 128.5 to 208.6), and the antibody level was highest during day 31-40 since onset, and then decreased slightly. Individual differences in changes of antibody levels were observed among 8 representative convalescent patients. In multivariate GEE analysis, patients at age of 31-60 and 61-84 had a higher antibody level than those at age of 16-30 (β=1.0518, P=0.0152; β=1.3718, P=0.0020). Patients with a worse clinical classification had a higher antibody titer (β=0.4639, P=0.0227). Conclusions. The neutralizing antibodies were detected even at the early stage of disease, and a significant response showed in convalescent patients. Moreover, changes on antibody levels ware individual specific.