title: A Holistic Approach to Identification of Covid-19 Patients from Chest X-Ray Images utilizing Transfer Based Learning

text: Novel coronavirus likewise called COVID-19 began in Wuhan, China in December 2019 and has now outspread over the world. Around 8 millions of individuals previously got influenced by novel coronavirus and it causes at any rate 500,000 deaths. There are just about 90,000 individuals contaminated by COVID-19 in Bangladesh too. As it is an exceptionally new pandemic infection, its diagnosis is challenging for the medical community. In regular cases, it is hard for lower incoming countries to test cases easily. RT-PCR test is the most generally utilized analysis framework for COVID-19 patient detection. However, by utilizing X-ray image based programmed recognition can diminish the expense and testing time. So according to handling this test, it is important to program and effective recognition to forestall transmission to others. In this paper, we attempt to distinguish COVID-19 patients by chest X-ray images. We execute different pre-trained deep neural system models, for example, Sequential, DenseNet121, ResNet152 and EfficientNetB4 to assess the most productive outcome. And aims to utilize transfer-based learning. We assess this outcome by AUC, where EfficientNetB4 has 0.997 AUC, ResNet50 has 0.967 AUC, DenseNet121 has 0.874 AUC and the Sequential model has 0.762 AUC individually. And EfficientNetB4 has achieved 98.86% accuracy.


title: Early Detection Of COVID-19 Using A Smartwatch

text: Wearable devices digitally measuring vital signs have been used for monitoring health and illness onset and have high potential for real-time monitoring and disease detection. As such they are potentially useful during public health crises, such as the current COVID-19 global pandemic. Using smartwatch data from 31 infected individuals identified from a cohort of over 5000 participants, we investigated the use of wearables for early, presymptomatic detection of COVID-19. From physiological and activity data, we first demonstrate that COVID-19 infections are associated with alterations in heart rate, steps and sleep in 80% of COVID-19 infection cases. Failure to detect these changes in the remaining patients often occurred in those with chronic respiratory/lung disease. Importantly the physiological alterations were detected prior to, or at, symptom onset in over 85% of the positive cases (21/24), in some cases nine or more days before symptoms. Through daily surveys we can track physiological changes with symptom onset and severity. Finally, we develop a method to detect onset of COVID-19 infection in real-time which detects 67% of infection cases at or before symptom onset. Our study provides a roadmap to a rapid and universal diagnostic method for the large-scale detection of respiratory viral infections in advance of symptoms, highlighting a useful approach for managing epidemics using digital tracking and health monitoring.


title: Current Understanding of COVID-19 Clinical Course and Investigational Treatments

text: Importance: Currently, there is no unified framework linking disease progression to established viral levels, clinical tests, inflammatory markers, and investigational treatment options. Objective: It may take many weeks or months to establish a standard treatment approach. Given the growing morbidity and mortality with respect to COVID-19, we present a treatment approach based on a thorough review of scholarly articles and clinical reports. Our focus is on staged progression, clinical algorithms, and individualized treatment. Evidence Review: We followed the protocol for a quality review article proposed by Heyn et. al.1 A literature search was conducted to find all relevant studies related to COVID-19. The search was conducted between April 1, 2020 and April 13, 2020 using the following electronic databases: PubMed (1809 to present), Google Scholar (1900 to present), MEDLINE (1946 to present), CINAHL (1937 to present), and Embase (1980 to present). Keywords used included COVID-19, 2019-nCov, SARS-CoV-2, SARS-CoV, and MERS-CoV, with terms such as efficacy, seroconversion, microbiology, pathophysiology, viral levels, inflammation, survivability, and treatment and pharmacology. No language restriction was placed on the search. Reference lists were manually scanned for additional studies. Findings: Of the articles found in the literature search, 70 were selected for inclusion in this study (67 cited in the body of the manuscript and 3 additional unique references in the Figures). The articles represent work from China, Japan, Taiwan, Vietnam, Rwanda, Israel, France, the United Kingdom, the Netherlands, Canada, and the United States. Most of the articles were cohort or case studies, but we also drew upon information found in guidelines from hospitals and clinics instructing their staff on procedures to follow. In addition, we based some decisions on data collected by agencies such as the CDC, FDA, IHME, ISDA, and Worldometer. None of the case studies or cohort studies used a large number of participants. The largest group of participants numbered less than 500 and some case studies had fewer than 30 patients. However, the review of the literature revealed the need for individualized treatment protocols due to the variability of patient clinical presentation and survivability. A number of factors appear to influence mortality: the stage at which the patient first presented for care, pre-existing health conditions, age, and the viral load the patient carried. Conclusion and Relevance: COVID-19 can be divided into three distinct Stages, beginning at the time of infection (Stage I), sometimes progressing to pulmonary involvement (Stage II, with or without hypoxemia) and less frequently to systemic inflammation (Stage III). In addition to modeling the stages of disease progression, we have also created a treatment algorithm which considers age, comorbidities, clinical presentation, and disease progression to suggest drug classes or treatment modalities. This paper presents the first evidence-based recommendations for individualized treatment for COVID-19.


title: How efficient are the lockdown measures taken for mitigating the Covid-19 epidemic?

text: Various lockdown measures have been taken in different countries to mitigate the Covid-19 pandemic. But, for citizens, it is not always simple to understand how these measures have been taken. Should they have been more (or less) restrictive? Should the lockdown period have been longer (or shorter)? What would have been the benefits of starting to confine the population earlier? To provide some elements of response to these questions, we propose a simple behavior model for the government decision-making operation. Although simple and obviously improvable, the proposed model has the merit to implement in a pragmatic and insightful way the tradeoff between health and macroeconomic aspects. For a given tradeoff between the assumed cost functions for the economic and health impacts, it is then possible to determine the best lockdown starting date, the best lockdown duration, and the optimal severity levels during and after lockdown. The numerical analysis is based on a standard SEIR model and performed for the case of France but the adopted approach can be applied to any country. Our analysis, based on the proposed model, shows that for France it would have been possible to have just a quarter of the actual number of people infected (over [March 1, August 31]), while simultaneously having a Gross Domestic Product loss about 30% smaller than the one expected with the current policy.


docid: qnpzmfdy

title: Analysis on diagnosis and treatment scheme of traditional Chinese medicine in treatment of COVID-19 in Chinese provinces and regions/ 全国各省区中医药治疗新型冠状病毒肺炎（COVID-19）的诊疗方案分析

text: Since December 2019, a novel coronavirus-infected pneumonia was first detected in Wuhan, such cases had been subsequently discovered in other cities. The disease caused by the novel coronavirus was officially named COVID -19 (coronavirus disease 2019) by the world health organization. National Health Commission of China and other provinces and cities have successively performed syndrome differentiation of COVID-19 and provided corresponding Chinese medicine treatment programs. In this epidemic, the disease is a “dampness toxin”. The best principle for treatment is early detection and early treatment. Both Chinese and Western medicine have their own advantages. The advantages could be complementary and could not be replaced each other. Therefore, we collected the Chinese medicine treatment programs for the treatment of COVID-19 comprehensively, conducted a systematic analysis, and especially analyzed the pharmacological basis of traditional Chinese medicine for the treatment of COVID-19, which provided a basis for the rationality of Chinese medicine prescription for the treatment of COVID-19, and provided a reference of updating the diagnosis and treatment plan for provinces and cities.


Guía sobre el uso de acupuntura y moxibustión para tratar COVID-19 (segunda edición)


title: Brief Report: Test-Retest Reliability of Explicit Auditory Processing Measures

text: In this brief report, we examined the test-retest reliability of our in-house explicit auditory processing measures in the context of 30 L1 and L2 English users. The participants took the same test battery which consisted of a total of four discrimination tasks (encoding acoustic details of formant, pitch, duration, and rise time) and two reproduction tasks (repeating novel melodic and rhythmic patterns) at Days 1 and 2. According to the results, the participants’ initial and second test scores demonstrated medium-to-large associations (r = .562-.907). The results suggest that the tests can tap into various dimensions of individuals’ auditory acuity and integration abilities.


docid: fxvvndic

title: Machine learning dimensionality reduction for heart rate n-variability (HRnV) based risk stratification of chest pain patients in the emergency department

text: Background: Chest pain is among the most common presenting complaints in the emergency department (ED). Swift and accurate risk stratification of chest pain patients in the ED may improve patient outcomes and reduce unnecessary costs. Traditional logistic regression with stepwise variable selection has been used to build risk prediction models for ED chest pain patients. In this study, we aimed to investigate if machine learning dimensionality reduction methods can achieve superior performance than the stepwise approach in deriving risk stratification models. Methods: A retrospective analysis was conducted on the data of patients >20 years old who presented to the ED of Singapore General Hospital with chest pain between September 2010 and July 2015. Variables used included demographics, medical history, laboratory findings, heart rate variability (HRV), and HRnV parameters calculated from five to six-minute electrocardiograms (ECGs). The primary outcome was 30-day major adverse cardiac events (MACE), which included death, acute myocardial infarction, and revascularization. Candidate variables identified using univariable analysis were then used to generate the stepwise logistic regression model and eight machine learning dimensionality reduction prediction models. A separate set of models was derived by excluding troponin. Receiver operating characteristic (ROC) and calibration analysis was used to compare model performance. Results: 795 patients were included in the analysis, of which 247 (31%) met the primary outcome of 30-day MACE. Patients with MACE were older and more likely to be male. All eight dimensionality reduction methods marginally but non-significantly outperformed stepwise variable selection; The multidimensional scaling algorithm performed the best with an area under the curve (AUC) of 0.901. All HRnV-based models generated in this study outperformed several existing clinical scores in ROC analysis. Conclusions: HRnV-based models using stepwise logistic regression performed better than existing chest pain scores for predicting MACE, with only marginal improvements using machine learning dimensionality reduction. Moreover, traditional stepwise approach benefits from model transparency and interpretability; in comparison, machine learning dimensionality reduction models are black boxes, making them difficult to explain in clinical practice.


title: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment

text: Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.


title: Coronavirus disease of 2019 (COVID-19) facts and figures: What every dermatologist should know in this hour of need

text: Coronavirus disease of 2019 (COVID-19) pandemic has affected India and world as a whole, like nothing in the recent history and we, dermatologists, are also affected directly or indirectly In this review, we have tried to address all COVID-19-related information we need to be aware of as a health-care professional We have discussed the relevant details of the disease: the agent, the symptomatology, common preventive measures, investigations, and management outline We have also discussed the implications of COVID-19 in dermatology practice and given a basic guideline for dermatology practice during the pandemic


docid: qujtxkxn

title: Clinical Outcomes and Plasma Concentrations of Baloxavir Marboxil and Favipiravir in COVID-19 Patients: an Exploratory Randomized, Controlled Trial

text: Background: Effective antiviral drugs for COVID-19 are still lacking. This study aims to evaluate the clinical outcomes and plasma concentrations of baloxavir marboxil and favipiravir in COVID-19 patients. Methods: Favipiravir and baloxavir acid were evaluated for their antiviral activity against SARS-CoV-2 in vitro before the trial initiation. We conducted an exploratory trial with 3 arms involving hospitalized adult patients with COVID-19. Patients were randomized assigned in a 1:1:1 ratio into baloxavir marboxil group, favipiravir group, and control group. The primary outcome was the percentage of subjects with viral negative by Day 14 and the time from randomization to clinical improvement. Virus load reduction, blood drug concentration and clinical presentation were also observed. The trial was registered with Chinese Clinical Trial Registry (ChiCTR 2000029544). Results: Baloxavir showed antiviral activity in vitro with the half-maximal effective concentration (EC50) of 5.48 M comparable to arbidol and lopinavir, but favipiravir did not demonstrate significant antiviral activity up to 100 M. Thirty patients were enrolled. The percentage of patients who turned viral negative after 14-day treatment was 70%, 77%, and 100% in the baloxavir, favipiravir, and control group respectively, with the medians of time from randomization to clinical improvement was 14, 14 and 15 days, respectively. One reason for the lack of virological effect and clinical benefits may be due to insufficient concentrations of these drugs relative to their antiviral activities. Conclusions: Our findings do not support that adding either baloxavir or favipiravir under the trial dosages to the existing standard treatment.


title: With $115 million, more than 80 Boston researchers will collaborate to tackle COVID-19

text: A $115 million collaboration to tackle the rapidly spreading viral disease COVID-19, led by heavy hitters of Boston science and funded by a Chinese property development company, kicked off today as the group’s leaders pledged to take on the virus on many fronts The project brings together researchers at many of the city’s top academic institutions, along with local biotechnology companies such as Moderna Those leading it hope they can quickly funnel money into studies that will build off a new repository of samples from infected people and community surveillance, materials that can be rapidly shared among scientists The project, they anticipate, should answer critical questions about how COVID-19 is spreading and how best to prevent and treat infections


title: Application of integrative medicine protocols in treatment of coronavirus disease 2019/ 中西医结合治疗新型冠状病毒肺炎的应用分析

text: Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered in Hubei, it has rapidly swept across the whole country and many overseas regions. At present, there are no specific drugs and vaccines for SARS-CoV-2 in modern medicine. Therefore, the therapy is mainly symptomatic for treatment. According to the instruction-spirit of “Following the development rules of traditional Chinese medicine (TCM), inheriting the essence and keeping the integrity and innovation” and “attaching equal importance to TCM and Western medicine” by President Xi Jin-ping, many local hospitals has established and improved the cooperation mechanism between traditional and modern medicine. And many protocols on the prevention & treatment have been published. By retrieving these protocols, opinions of academicians and scholars, and clinical therapies reported by medical research institutions, we summarized the main prevention and cure methods of COVID-19, and found that the clinical application of integrative medicine protocols have obvious advantages in improving patient symptoms, shortening the course of disease, delaying the progress of disease, and reducing mortality. The integrative medicine can play an active role in COVID-19’s prevention and treatment.


title: Increased risk for COVID-19 among Migrants from Latin-America, Caribbean, and Sub-Saharan Africa living in Spain

text: Background: There is scant information regarding risk for COVID-19 among migrants or ethnic minorities in Europe. Methods. Population-based cohort analysis of the cumulative incidence of PCR-confirmed COVID-19 cases until April 25 (2020) among 152018 residents at the city of Alcorcon (Spain) attended at the only public hospital serving this city. Crude incident rates for Spaniards and migrants from different areas of the world were estimated. Age and sex-adjusted relative risks for COVID19 were estimated by negative polynomial regression. Findings. PCR confirmed COVID-19 cumulative incidence was 6.81 cases per 1000 inhabitants among residents of Alcorcon. The crude incidence among migrants (n=20419) was higher than among Spaniards (n=131599): 8.81 and 6.51 and per 1000 inhabitants respectively (p<0.001). By regions of the world, crude cumulative COVID-19 incidences were Asia 2.1, European Union 2.4, Northern Africa 3.6, Russia & East Europe 4.4, Sub-Saharan Africa 11.2, Caribbean 18.3 and Latin-America 20.8 per 1000 inhabitants. By negative polynomial logistic regression, adjusted for age and sex, relative risks (RR) for COVID-19 were not significantly different from Spaniards for individuals from Europe, Asia or Northern Africa. In contrast, there was an increased risk for Sub-Saharan Africa (RR 3.66, 95% confidence interval (CI) 1.42-9.41, p=0.007), Caribbean (RR 6.35, 95% CI 3.83-10.55, p<0.001) and Latin-America (RR 6.92, 95% CI 4.49-10.67, p <0.001). Interpretation. There was a marked increased risk for COVID-19 among migrants from Sub-Saharan Africa, Caribbean and Latin-America residing in Spain. Our data suggest a heretofore unreported increased risk in these populations that may deserve special attention.


title: Early antibody response to SARS-CoV-2

text: Background. The role and significance of the immune response to SARS-CoV-2 infection is not yet well known. Methods. We therefore conducted a study on 46 symptomatic subjects with disease ascertained by laboratory tests to evaluate the presence of IgG and IgM antibodies in these subjects in relation to the time elapsed since the onset of symptoms. The analytical performance of the method used in the study (Maglumi 800, SNIBE, China) and the effect of two different serum and plasma matrices were also assessed. Results. IgG positivity was demonstrated in 100% of cases 15 days after the onset of the disease. IgM show lower concentrations and do not exceed 77% of cases after 15 days. The analytical performance of the method used was confirmed to be good in terms of imprecision, linearity, commutability in two blood sample matrices. Conclusion. The serological study through the search for specific IgG for SARS-CoV-2 results in our case series is sensitive and suitable for population research and can also play a role in diagnosis. The diagnostic performance of specific IgMs are lower.


docid: rvlbaxvw

title: Appendix E Precautions and breastfeeding recommendations for selected maternal infections

text: Unknown


Coronavirus SARS-COV-2: Announcement of the thematic issue of slovenian medical journal coronavirus SARS-COV-2/ Koronavirus SARS-CoV-2: Najava tematske številke zdravniškega vestnika koronavirus SARS-CoV-2


title: Effect of Velocity and Impact Angle on Residual Stress Generation in Cold Spray Process – A Molecular Dynamics Simulation Study

text: Abstract Cold Spray (CS) process is a solid-phase metal deposition technique capable of depositing micro to nanosized particles on a substrate without melting the particles. The CS process thus retains the original mechanical and chemical properties of the coating material. Residual stresses are an important factor affecting the quality, strength, and performance of the coated substrate in CS process. Currently, there is a lack of clear understanding of the residual stress generation in CS process and its control measures. Existing studies have not investigated the type III residual stress in CS process. This study attempts to investigate the effects of impact velocity and angle of impact on the Type III residual stress generation in CS process using molecular dynamics simulation technique. The study considers the impact of nanosized copper particles on copper substrate and the magnitude of the residual stresses is monitored. It is seen that the coated surface retains both tensile and compressive residual stresses. A higher angle impact shows higher compressive residual stresses, which are beneficial to industrial applications. Similarly, 400 m/s impact velocity showed the highest distribution of compressive residual stress on the body. The study results would be crucial in extending the industrial applications of the CS process.


title: Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2

text: Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last few months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.


title: A Comprehensive Analysis of COVID-19 Outbreak situation in India

text: The outbreak of COVID-19 in different parts of the world is a major concern for all the administrative units of respective countries. India is also facing this very tough task for controlling the virus outbreak and has managed its growth rate through some strict measures. This study presents the current situation of coronavirus spread in India along with the impact of various measures taken for it. With the help of data sources (till 7th-8th April 2020) from various state units of India and Ministry of Health and Family Welfare, Government of India, this study presents various trends and patterns. This study answers six different research ques-tions in a comprehensive manner. It has been reported that growth rate of infected cases has been controlled with the help of National Lockdown, however some uncontrolled mass level events had negatively impacted the infected cases. With the help of exponential and polyno-mial regression modelling, the predictions of up to 75000 cases have been done by the end of April 2020. It has also been seen that there are some prominent clusters and patient nodes in the network of patients which are the major influencers for COVID-19 spread. Also, death rate case predictions have been done through multi-class classification models with an accuracy of 75%. At the end, strategies for continuation for lockdown has been discussed and presented. It appears that only essential services should be open for the citizens of India and the national lockdown should be carried on for next 2-4 weeks. This study will be useful for the Government of India and various states of India, Administrative Units of India, Frontline health workforce of India, researchers and scientists. This study will also be favorable for the administrative units of other countries to consider various aspects related to the control of COVID-19 outspread in their respective regions.


title: Globally Coherent Weekly Periodicity in the Covid-19 Pandemic

text: After the major exponential phase, the Covid-19 pandemic is on a milder rate of increase globally, and past the peak in many countries. In this phase a marked systematic weekly periodicity in the Covid-19 attack has become clear, the study of which could be useful for the long term strategy to deal with the virus and the pandemic. The most important aspect of this strong weekly modulation is its global nature, phase-coherent over most of globe, independent of the geographical location, with the possible, but unconfirmed, exception of Russia and many countries in Asia and Africa, where the scale of the deaths from the pandemic relative to the population has been small so far. There could be a phase-difference of about a day between the modulations in the daily number of deaths and the daily reported cases.


title: No indications for overt innate immune suppression in critically ill COVID-19 patients

text: At the end of March 2020, there were in excess of 800.000 confirmed cases of coronavirus disease 2019 (COVID-19) worldwide. Several reports suggest that, in severe cases, COVID-19 may cause a hyperinflammatory 'cytokine storm'. However, unlike SARS-CoV infection, high levels of anti-inflammatory mediators have also been reported in COVID-19 patients. One study reported that 16% of COVID-19 patients who died developed secondary infection, which might indicate an immune-suppressed state. We explored kinetics of mHLA-DR expression, the most widely used marker of innate immune suppression in critically ill patients, in COVID-19 patients admitted to the ICU. Twenty-four confirmed COVID-19 patients were included, of which 75% was male and 79% had comorbidities. All patients were mechanically ventilated and exhibited large high levels of inflammatory parameters such as CRP and PCT. mHLA-DR expression levels were mostly within the normal range of 15000 - 45000 mAb/cell and showed no change over time. COVID-19 patients displayed notably higher mHLA-DR expression levels compared with bacterial septic shock patients. None of the COVID-19 patients developed a secondary infection. In conclusion, despite a pronounced inflammatory response, mHLA-DR expression kinetics indicate no overt innate immune suppression in COVID-19 patients. These data signify that innate immune suppression as a negative feedback mechanism following PAMP-induced inflammation appears not to be present in COVID-19.


title: Perceived versus proven SARS-CoV-2 specific immune responses in health care workers

text: Uncertain rates of asymptomatic infections have raised concerns about potentially high rates of thus far undiagnosed SARS-CoV-2 infections. Serological testing for SARS-CoV-2 specific IgG can be helpful in identification of asymptomatic infections. We report baseline results of the CVOID-19 Contact (CoCo) Study, which follows 217 frontline healthcare workers at a university hospital and performs weekly SARS-CoV-2 specific serology (IgA/IgG). The majority of participants had direct contact to patients with infectious respiratory diseases. Study participants estimated their personal likelihood of having had a SARS-CoV-2 infection with a mean of 20.9% (range 0 to 90%). In contrast, anti-SARS-CoV-2-IgG prevalence was in the range of 1-2% among health care workers. The CoCo Study is not fully representative for other hospitals and the sensitivity of anti-SARS-CoV-2 serology in low prevalence conditions may require further improvement. Taken together, low rates of SARS-CoV-2 specific IgG in healthcare workers in Northern Germany are in sharp contrast to the high personal risk perception. Regular anti-SARS-CoV-2 IgG testing of health-care workers may aid in monitoring the pandemic, assessing the quality of immune responses, directing resources for protective measures, and assuring CVID-19 care in the long run.


title: Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

text: Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread.


title: An Agent Based Modeling of COVID-19: Validation, Analysis, and Recommendations

text: The Coronavirus disease 2019 (COVID-19) has resulted in an ongoing pandemic worldwide. Countries have adopted Non-pharmaceutical Interventions (NPI) to slow down the spread. This study proposes an Agent Based Model that simulates the spread of COVID-19 among the inhabitants of a city. The Agent Based Model can be accommodated for any location by integrating parameters specific to the city. The simulation gives the number of daily confirmed cases. Considering each person as an agent susceptible to COVID-19, the model causes infected individuals to transmit the disease via various actions performed every hour. The model is validated by comparing the simulation to the real data of Ford county, Kansas, USA. Different interventions including contact tracing are applied on a scaled down version of New York city, USA and the parameters that lead to a controlled epidemic are determined. Our experiments suggest that contact tracing via smartphones with more than 60% of the population owning a smartphone combined with a city-wide lock-down results in the effective reproduction number (Rt) to fall below 1 within three weeks of intervention. In the case of 75% or more smartphone users, new infections are eliminated and the spread is contained within three months of intervention. Contact tracing accompanied with early lock-down can suppress the epidemic growth of COVID-19 completely with sufficient smartphone owners. In places where it is difficult to ensure a high percentage of smartphone ownership, tracing only emergency service providers during a lock-down can go a long way to contain the spread. No particular funding was available for this project.


title: Artificial intelligence finds drugs that could fight the new coronavirus

text: Two independent groups last week reported that they had used artificial intelligence in different ways to find possible treatments for the novel coronavirus, named 2019-nCoV On Feb 4, researchers from the AI drug discovery company BenevolentAI and Imperial College London reported that they had used AI software to find an already-approved drug that might limit the virus’s ability to infect people (Lancet 2020, DOI: 10 1016/S0140-6736(20)30304-4) On Feb 6, Insilico Medicine announced that its AI algorithms had designed new molecules that could stop the virus from replicating in people’s bodies The company says it submitted a paper to the bioRxiv server, but the preprint had not been posted there as of press time BenevolentAI’s algorithms connect molecular structure data to biomedical information about relevant receptors and diseases to find potential drug targets The group adapted its search to newly available information about 2019-nCoV and focused on the enzyme adaptor-associated protein kinase


title: Natural killer cell activation related to clinical outcome of COVID-19

text: Understanding innate immune responses in COVID-19 is important for deciphering mechanisms of host responses and interpreting disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections, but might also contribute to immune pathology. Here, using 28-color flow cytometry, we describe a state of strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients, a pattern mirrored in scRNA-seq signatures of lung NK cells. Unsupervised high-dimensional analysis identified distinct immunophenotypes that were linked to disease severity. Hallmarks of these immunophenotypes were high expression of perforin, NKG2C, and Ksp37, reflecting a high presence of adaptive NK cell expansions in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed in course of COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This provides a detailed map of the NK cell activation-landscape in COVID-19 disease.


title: Disproportionate COVID-19 Related Mortality Amongst African Americans in Four Southern States in the United States

text: Background African American have been severely affected by COVID-19 noted with the rising mortality rates within the African American community. Health disparities, health inequities and issues with systemic health access are some of the pre-existing issues African American were subjected to within the southern states in the United States. Second, social distancing is a critical non-pharmacological intervention to reduce the spread of COVID-19. However, social distancing was not practical and presented a challenge within the African American community, specifically, in the southern states. Objective This article assesses the effect of COVID-19 on African American in the southern states. Methodology This short communication queried the publicly available Department of Health statistics on COVID-19 related mortality and underlying health conditions in four southern states (Alabama [AL], Georgia [GA], Louisiana [LA] and Mississippi [MS]) with a high proportion of African American residents. Second, unacast COVID-19 toolkit was used to derive a social distancing (SD) grade for any given state, based on three different metrics: (i) percent change in average distance travelled (ii) percent change in non-essential visits and (iii) decrease in human encounters (compared to national baseline). Results Across the four states, on average, as many as 54% of COVID-19 related deaths are in the African American community, although this minority group comprises only 32% of the population cumulatively. This article finds that all four southern states received a social distancing grade of F. COVID-19 have demonstrated that adverse outcomes are higher in individuals with underlying health conditions such as diabetes, cardiovascular diseases, or pre-existing pulmonary compromise. Conclusion Recognizing that there is a great need for African American representation or diversity in the health workforce would be able to better address the health disparities. In addition, the lack of diversity in the healthcare system causes the morbidity and mortality rates to increase in the African American communities because it is not able to address its primary obligations within the African American communities in the southern states during COVID-19 pandemic. These primary obligations are to restore, protect, improve health and to suppress health disparities and inequalities of COVID-19 within in the African American communities. Keywords: COVID-19; African American; Mortality


docid: eecwjrdc

title: The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

text: SARS-CoV-2 emerged in late 2019, leading to the COVID-19 pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus we demonstrate that, in addition to human ACE2, the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the twenty-two different hosts we investigated, ACE2 proteins from dog, cat and rabbit were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the three genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Interestingly, while SARS-CoV-2 pseudoparticle entry was inefficient in cells bearing the ACE2 receptor from bats or birds the live virus was still able to enter these cells, albeit with markedly lower efficiency. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock and wildlife.


title: Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases

text: Objectives: Our objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by SARS-COV-2 virus, and provide an overview of the variation depending on the methodological approach. Design: Rapid scoping review. Literature review with fixed search terms, up to 1st April 2020. Central tendency and variation of the parameter estimates for infectious period in (a) asymptomatic (b) symptomatic cases from (i) virological studies (repeated testing), (ii) tracing studies (iii) modelling studies were gathered. Narrative review of viral dynamics. Information sources: Search strategies developed and the following searched: PubMed, Google Scholar, MedRxiv, BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was utilised, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, HRB open databases. Results: There was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5-9.5 days. Median pre-symptomatic infectious period across studies varied over <1-4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95%CI: 10.9-15.8), but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95%CI: 15.1-21.0); time to discharge was on average 4 days shorter than time-to-death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data. Conclusions: There are limitations of inferring infectiousness from repeated diagnosis, viral loads, and viral replication data alone, and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provides a preliminary evidence base to inform models of central tendency for key parameters, and variation for exploring parameter space and sensitivity analysis. Some current models may be underestimating infectious period.


Towards a Post-Covid-19 'New Normality?': Physical and Social Distancing, the Move to Online and Higher Education


title: A previously uncharacterized gene in SARS-CoV-2 and the origins of the COVID-19 pandemic

text: Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with the origins of pandemics, but are still widely overlooked. We identify ORF3c, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not more closely related pangolin-CoVs (Guangdong) or bat-CoVs (RaTG13 and RmYN02). We then document evidence of translation from ribosome profiling and conduct an evolutionary analysis at three levels: between-species (n=21 betacoronavirus genomes), between-host (n=3,978 SARS-CoV-2 consensus sequences), and within-host (401 deeply sequenced SARS-CoV-2 samples). ORF3c has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as ORF3b, an unrelated gene in other SARS-related betacoronaviruses, leading to confusion and unfounded functional inferences. Our results liken ORF3c to other viral accessory genes and stress the importance of studying OLGs.


title: Friction Stir Welding for Assembly of Copper Squirrel Cage Rotors for Electric Motors

text: Abstract The automotive industry is developing designs and manufacturing processes for new generations of electric motors intended for use in hybrid and electric vehicles. This paper focuses on solid-state welding to join copper end rings to copper spokes in the fabrication of copper rotors. Friction stir welding was explored to examine weldability of these copper components. Defect free welds were produced on 8-9.5 mm thick copper plates with copper spokes through slots at a travel speed of 225 mm/min and a tool speed rotation of 2250 rpm using lanthanated tungsten as the welding tool. The H13 and nimonic tool materials underperformed due to higher welding temperatures. The conditions were optimized by monitoring the tool and copper plate temperatures. Several tool geometries were investigated and the scrolled shoulder with tri-flat threaded pin performed the best. The strength and weld characteristics were sufficient for this application. Finally, this work puts forth major welding process for induction copper rotors.


title: MISTR: A conserved MItochondrial STress Response network revealed by signatures of evolutionary conflict

text: Host-pathogen conflicts leave genetic signatures of variation in homologous host genes. Using these “molecular scars” as a guide, we discovered a vertebrate-specific MItochondrial STress Response circuit (MISTR). MISTR proteins are associated with electron transport chain factors and activated by stress signals such as interferon-gamma and hypoxia. Upon stress, ultraconserved miRNAs downregulate MISTR1 followed by replacement with paralogs MISTR AntiViral (MISTRAV) or MISTR Hypoxia (MISTRH), depending on the insult. While cells lacking MISTR1 are more sensitive to apoptotic triggers, cells lacking MISTRAV or expressing the poxvirus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1 and MISTRAV indicate ancient and ongoing conflicts with pathogens. MISTR proteins are also found in plants, yeasts, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.


title: Corona Crisis and Inequality: Why Management Research Needs a Societal Turn

text: As the world struggles to deal with the COVID-19 pandemic, the stark inequalities in our societies have been laid bare, and the interplay between organizations and societies has also become evident yet again. This crisis underscores the need for management scholars to take a societal turn and examine how organizational practices interact with societal economic inequality. To illustrate this approach, we discuss organizational practices—corporate social responsibility, work design, recruitment and selection, and compensation management—that can contribute to the normalization, reinforcement, and reduction of economic inequalities in society. We conclude by calling on scholars of inequality, as well as of broader management research, to take a societal turn to enhance the relevance and impact of management research.


title: MALVIRUS: an integrated web application for viral variant calling

text: Motivation Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe. Results We present MALVIRUS, an easy-to-install and easy-to-use web application that assists users in (1) computing a variant catalog consisting in a set of population SNP loci from the population sequences and (2) efficiently calling variants of the catalog that are in the sample. Tests on Illumina and Nanopore samples prove the efficiency and the effectiveness of MALVIRUS in genotyping a SARS-CoV-2 strain sample with respect to GISAID data. Availability MALVIRUS is freely available at https://algolab.github.io/MALVIRUS/. Contact yuri.pirola@unimib.it Supplementary information Supplementary data are available at bioRxiv online.


title: Efficacy and safety of chloroquine or hydroxychloroquine in moderate type of COVID-19: a prospective open-label randomized controlled study

text: The outbreak of novel coronavirus disease 2019 (COVID-19) has become a pandemic. Drug repurposing may represent a rapid way to fill the urgent need for effective treatment. We evaluated the clinical utility of chloroquine and hydroxychloroquine in treating COVID-19. Forty-eight patients with moderate COVID-19 were randomized to oral treatment with chloroquine (1000 mg QD on Day 1, then 500 mg QD for 9 days; n=18), hydroxychloroquine (200 mg BID for 10 days; n=18), or control treatment (n=12). Adverse events were mild, except for one case of Grade 2 ALT elevation. Adverse events were more commonly observed in the chloroquine group (44.44%) and the hydroxychloroquine group (50.00%) than in the control group (16.67%). The chloroquine group achieved shorter time to clinical recovery (TTCR) than the control group (P=0.019). There was a trend toward reduced TTCR in the hydroxychloroquine group (P=0.049). The time to reach viral RNA negativity was significantly faster in the chloroquine group and the hydroxychloroquine group than in the control group (P=0.006 and P=0.010, respectively). The median numbers of days to reach RNA negativity in the chloroquine, hydroxychloroquine, and control groups was 2.5 (IQR: 2.0-3.8) days, 2.0 (IQR: 2.0-3.5) days, and 7.0 (IQR: 3.0-10.0) days, respectively. The chloroquine and hydroxychloroquine groups also showed trends toward improvement in the duration of hospitalization and findings on lung computerized tomography (CT). This study provides evidence that (hydroxy)chloroquine may be used effectively in treating moderate COVID-19 and supports larger trials.


title: Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India

text: The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected patients. Earlier reports have suggested that COVID-19 agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 target genes namely S gene, E gene, ORF1ab gene, RdRp gene and N gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks.


title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems

text: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 remains essential for tracking and containing the rapid spread of the virus. However, due to increased global demand, kits and proprietary reagents for RNA extraction are limited, which markedly reduce SARS-CoV-2 testing capabilities in many countries. Here, we explore the use of conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA purification as an alternative to commercial automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical oropharyngeal or nasopharyngeal swab specimens were extracted by AGPC and compared to the commercial platforms, the Maxwell(R) RSC 48 instrument for automated RNA extraction and the fully integrated diagnostic system, the Cobas(R)6800 apparatus. Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, we find that the AGPC method is easily scalable and implemented in conventional laboratories. Taken together, these data identify conventional AGPC-based RNA extraction as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2, when automated systems, kits and reagents are not readily available.


docid: bpvhtszb

title: Retrospective Methodology to Estimate Daily Infections from Deaths (REMEDID) in COVID-19: the Spain case study


title: Characteristics and outcomes of Acute Respiratory Distress Syndrome related to COVID-19 in Belgian and French Intensive Care Units according to antiviral strategies. The COVADIS multicenter observational study.

text: Background Limited data are available for antiviral therapy efficacy especially for the most severe patients under mechanical ventilation suffering from Covid-19 related Acute Respiratory Distress Syndrome (ARDS). Methods Observational multicenter cohort of patients with moderate to severe Covid-19 ARDS, comparing antiviral strategies (none, hydroxychloroquine (HCQ), lopinavir/ritonavir (L/R), others (combination or remdesivir). The primary end-point was the day-28 ventilator free days (VFD), patients which died before d28 were considered as having 0 VFD. The variable was dichotomized in patients still ventilated or dead at day 28 vs patients being extubated and alive at day 28 (VFD = or > 0). Results We analyzed 376 patients (80 with standard of care (SOC), 49 treated with L/R, 197 with HCQ, and 50 others). The median number of d28-VFD was 0 (IQR 0-13) and was different across the different groups (P=0.01), the SOC patients having the highest d28-VFD. A multivariate logistic regression including antiviral strategies, showed that age (OR 0.95 CI95%:0.93-0.98), male gender (OR 0.53 CI95%:0.31-0.93), Charlson score (OR 0.85 CI95%:0.73-0.99) and plateau pressure (OR 0.94 CI95%:0.88-0.99) were associated with having 0 d28-VFD whereas P/F ratio (OR 1.005 CI95%:1.001-1.010) was associated with having > or = 1 d28-VFD (ie. being extubated and alive). Acute kidney injury (AKI) was frequent (64%), its incidence was different across the patients groups (P=0.01). In a post-hoc logistic multivariate regression apart from demographics characteristics and comorbidities, the use of L/R (administered to 81 of 376 patients) was associated with occurrence of AKI (OR 2.07 CI95%:1.17-3.66) and need for renal replacement therapy (RRT). Conclusion In this observational study of moderate to severe Covid-19 ARDS patients, we did not observed a benefit of treating patients with any specific antiviral treatment. We observed an association between L/R treatment and occurrence of AKI and need for RRT.


title: Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-19)

text: A total of 565 Japanese citizens were evacuated from Wuhan, China to Japan. All passengers were screened for symptoms and also undertook reverse transcription polymerase chain reaction testing, identifying 5 asymptomatic and 7 symptomatic passengers testing positive for 2019-nCoV. We show that the screening result is suggestive of the asymptomatic ratio at 41.6%.


title: Higher virulence of COVID-19 in the air-polluted regions of eight severely affected countries

text: COVID-19 has spread in all continents in a span of just over three months, escalating into a pandemic that poses several humanitarian as well as scientific challenges. We here investigated the geographical character of the infection and correlate it with several annual satellite and ground indexes of air quality in China, Iran, Italy, Spain, France, Germany, U.K. and U.S.A. Adjusting for population size, we find more viral infections in those areas afflicted by high PM 2.5 and Nitrogen Dioxide values. Higher mortality was also correlated with relatively poor air quality. In Italy, the correspondence between the Po valley pollution and SARS-CoV-2 infections and induced mortality was the starkest, originating right in the most polluted European area. Air pollution appears to be for this disease a risk factor similar to smoking. This suggests the detrimental impact climate change will have on the trajectory of future respiratory epidemics.


title: Determinants of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey

text: In April 2020, a nationally representative sample of 4, 240 Canadians age 18 years and older were polled about COVID experience in March, early in the epidemic. We examined determinants of COVID symptoms, defined as fever plus difficulty breathing/shortness of breath, dry cough so severe that it disrupts sleep, and/or loss of sense of smell; and testing for SARS-CoV-2 by respondents and/or household members. About 8% of Canadians reported that they and/or one or more household members experienced COVID symptoms. Symptoms were more common in younger than older adults, and among visible minorities. Overall, 3% of respondents and/or household members had been tested for SARS-CoV-2. Being tested was associated with having COVID symptoms, being of Indigenous identity, and living in Quebec. Periodic nationally representative surveys, including high-risk older populations, of symptoms, as well as SARS-CoV-2 antibodies, are needed to understand the course of the Canadian epidemic and prepare for the future.


title: Unspecific post-mortem findings despite multiorgan 1 viral spread in COVID-19 patients

text: Background Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. Methods We evaluated whether some specific post-mortem features are observed in these patients and if these changes are related to the presence of the virus in different organs. Complete macroscopic and microscopic autopsies were performed on different organs in 17 COVID-19 non-survivors. Presence of SARS-CoV-2 was evaluated with immunohistochemistry (IHC) in lung samples and with real-time reverse-transcription polymerase chain reaction (RT-PCR) test in lung and other organs. Results Pulmonary findings revealed early-stage diffuse alveolar damage (DAD) in 15 out of 17 patients and microthrombi in small lung arteries in 11 patients. Late-stage DAD, atypical pneumocytes and/or acute pneumonia were also observed. Four lung infarcts, two acute myocardial infarctions and one ischemic enteritis were observed. There was no evidence of myocarditis, hepatitis or encephalitis. Kidney evaluation revealed the presence of hemosiderin in tubules or pigmented casts in most patients. Spongiosis and vascular congestion were the most frequently encountered brain lesions. No specific SARS-CoV-2 lesions were observed in any organ. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e. lung, heart, spleen, liver, colon, kidney and brain). Conclusions In conclusion, autopsies revealed a great heterogeneity of COVID-19-related organ injury and the remarkable absence of any specific viral lesions, even when RT-PCR identified the presence of the virus in many organs.


title: Pre-Procedural Surveillance Testing for SARS-CoV-2 in an Asymptomatic Population Shows Low Rates of Positivity

text: Introduction Seattle region hospitals have been severely impacted for several months by ongoing community spread of the novel coronavirus 2019 disease. (1,2) Although testing was initially focused on the diagnosis and treatment of symptomatic patients, this effort has now expanded to include surveillance of asymptomatic patients in order to protect health care workers and prevent nosocomial infections. There is an urgent need to understand best practices for the delivery of routine medical care during an ongoing outbreak. (3) Here we report the rates of SARS-CoV-2 infection in asymptomatic patients screened prior to admission or a surgical or aerosolizing procedure. Methods Beginning March 30, 2020, our hospital began screening all asymptomatic patients prior to needed surgeries and aerosolizing procedures (n=350). On April 13, 2020, we expanded this practice to universal surveillance screening of all patients prior to admission (n=349). Testing was performed on nasopharyngeal swabs using the Washington state emergency use authorized University of Washington CDC-based laboratory-developed test or FDA authorized DiaSorin Simplexa SARS-CoV-2, Hologic Panther Fusion SARS-CoV-2, or Roche cobas SARS-CoV-2 tests. This study was approved by the Institutional Review Board of University of Washington Medical Center (STUDY00009734). Informed consent was not required. Results For patients undergoing surgical or aerosolizing procedures, 3 of 350 patients (0.9%) were positive for SARS-CoV-2. For patients who were asymptomatic and tested at the time of admission, 3 of 349 patients (0.9%) were positive and 2 of 349 (0.6%) were inconclusive; inconclusive results were treated as low-level positives. For asymptomatic patients tested for any other reason (e.g. exposure risk), 12 of 157 patients (7.6%) were positive and 1 of 157 (0.6%) were inconclusive. Meanwhile, of the 473 inpatients in this period who had any symptom concerning for COVID-19, 68 of 473 patients (14.3%) were positive. There was a variety of ordering services and locations in all indication categories, with no particular predominating medical service or location. During this time period the outpatient prevalence of SARS-CoV-2 active infection in our region was 3-5% (manuscript in review). Discussion The application of universal surveillance testing for SARS-CoV-2 in patients prior to surgery or aerosolizing procedure shows that the positivity rate for SARS-CoV-2 is low (<1%) in asymptomatic patients without known exposure risk factors. The positivity rate for asymptomatic patients on admission screen was similar; both measures were notably lower than recently reported measurements during an outbreak in New York City that found a positivity rate of 13.7% in asymptomatic pregnant women. (4) The rate of sub-clinical infection likely varies with the scale of the community outbreak. Even in the context of a community-wide outbreak, our data show a low prevalence of COVID-19 infection in the urgent pre-procedural setting. These data reflect the prevalence of asymptomatic SARS-CoV-2 infection in a population of individuals who use medical services and provide an assessment of exposure risk to other patients and healthcare workers around the time of admission. The Greater Seattle Coronavirus Assessment Network (SCAN) also recently published results from the first 18 days of home-based testing and reported no positive tests in 1392 patients reporting no COVID-19-like illness. (5) Although other studies support a large proportion of asymptomatic infections, the data from this metropolitan outbreak do not support a similar pattern. Clinical providers, especially those involved in performing procedures that have a risk of aerosolization, are asking for methods to risk-assess patients prior to the procedure. Pre-procedure testing is one option to accomplish this goal. Importantly, in the midst of an outbreak, testing prior to procedures can decrease the use of PPE, identify appropriate precautions for patients, and reduce the risk of nosocomial infection.


docid: modtthxx

title: Blueprint for a Pop-up SARS-CoV-2 Testing Lab

text: The appearance and spread of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) led to the official declaration of a global pandemic, with states in the US implementing shelter in place orders at an unprecedented scale. SARS-CoV-2 has a robust person-to-person transmission rate and an asymptomatic period of two weeks or more, leading to widespread infection that has overwhelmed healthcare infrastructures around the globe. Effective public health measures require extensive, accurate, and rapid testing to determine infection rates. Here we describe the strategy we used to establish a CLIA-licensed clinical laboratory to perform a validated Laboratory-Developed Test (LDT) for SARS-CoV-2 in Berkeley, California and the surrounding Bay Area community. Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to aid others in setting up similar testing centers.


title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19

text: The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs that can help contain the outbreak. Enveloped viruses infect the host cell by cellular membrane fusion, a crucial mechanism required for virus replication. The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide initial evidence that inhibition of virus fusion may explain the antiviral action of imatinib. This finding is significant since pinpointing the mode of action allows evaluating the drug’s affinity to the SARS-CoV-2-specific target protein, and in turn, helps make inferences on the potency of the drug and evidence-based recommendations on its dosage. To this end, we provide evidence that imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 ± 0.9 µM, levels. We also show that imatinib inhibits other coronaviruses, SARS-CoV and MERS-CoV, possibly via fusion inhibition. Based on promising in vitro results, we propose the Abl kinase inhibitor (ATKI), imatinib, to be a viable repurposable drug candidate for further clinical validation against COVID-19.


Generation app: How do diff erent generations feel about sharing personal data in order to tackle Covid-19? We ask people in South Korea, Spain and Italy


title: Extrapolation of Infection Data for the CoVid-19 Virus in 21 Countries and States and Estimate of the Efficiency of Lock Down.

text: Predictions about the further development of the Corona pandemic are of great public interest but many approaches demand a large number of country specific parameters and are not easily transferable. A special interest of simulations on the pandemic is to trace the effect of politics for reducing the virus spread, since these measures have had an enormous impact on economy and daily life. Here a simple yet powerful algorithm is introduced for fitting the infection numbers by simple analytic functions. This way, the increase of the case numbers in periods with different regulations can be distinguished, and by extrapolating the fit functions, a forecast for the maximum numbers and time scales are possible. The effect of the restraints such as lock down are demonstrated by comparing the resulting infection history with the likely unconstrained virus spread, and it is shown that a delay of 1-4 weeks before imposing measures aiming at social distancing could have led to a complete infection of the respective populations. The approach is simply transferable to many different states. Here data from six E.U. countries, the UK, Russia, two Asian countries, the USA and ten states inside the USA with significant case numbers are analyzed, and striking qualitative similarities are found.


title: Lab-on-a-Chip Technologies for the Single Cell Level: Separation, Analysis, and Diagnostics

text: In the last three decades, microfluidics and its applications have been on an exponential rise, including approaches to isolate rare cells and diagnose diseases on the single-cell level. The techniques mentioned herein have already had significant impacts in our lives, from in-the-field diagnosis of disease and parasitic infections, through home fertility tests, to uncovering the interactions between SARS-CoV-2 and their host cells. This review gives an overview of the field in general and the most notable developments of the last five years, in three parts: 1. What can we detect? 2. Which detection technologies are used in which setting? 3. How do these techniques work? Finally, this review discusses potentials, shortfalls, and an outlook on future developments, especially in respect to the funding landscape and the field-application of these chips.


docid: wpdzdxoi

title: Early Trend of Imported COVID-19 Cases in South Korea

text: This study aimed to observe the initial trend of imported COVID-19 cases in South Korea since the beginning of the outbreak. All imported cases were classified into 5 regions (China, Asia, Europe, Africa, and America) according to travel history and potential exposure to the COVID-19. The list of countries for which confirmed cases had a travel history (single visit, multiple visits) and presented, were used to estimate the potential “exposure countries” of confirmed cases. For better understanding of the overall imported cases, time differences (day) among 3 major steps (symptom onset, entry to South Korea, laboratory confirmation) were measured based on available data. From the first importation of a COVID-19 case on January 20(th), a total of 171 imported cases have been officially reported in South Korea as of March 23(rd) 2020. The overall trend of importation has significantly changed during this period. Importation of confirmed cases were initially from China, and subsequently from other Asian countries. After that, importation from Europe rapidly increased, with importation from America also increasing. One hundred fifteen (81%) were confirmed within 7 days of symptom onset. One Hundred forty three (84.1%) imported cases were confirmed within a week after entry into South Korea. One hundred seven imported cases (75.9%) developed symptoms within 5 days before or after, entry to South Korea. Streamlined processes of detection, subsequent testing, isolation, and treatment by public health authority, was key in minimizing the risk of secondary transmission.


docid: bjvgezux

title: A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence

text: Suppressing SARS-CoV-2, the causative agent of COVID-19, requires that infected individuals are rapidly identified and isolated, on an ongoing basis. However, regular testing of every individual is expensive. We present an approach to pooled testing, based on the geometry of a hypercube, which enables fast, cost-effective identification of infected people when the prevalence of the virus is low. Field trials of this approach are now under way in Rwanda.


title: Dynamics and Prediction of the COVID-19 Epidemics in the US:a Compartmental Model with Deep Learning Enhancement

text: Compartmental models dominate epidemic modeling. Estimations of transmission parameters between compartments are typically done through stochastic parameterization processes that depend upon detailed statistics on transmission characteristics, which are economically and resource-wide expensive to collect. We apply deep learning techniques as a lower data dependency alternative to estimate transmission parameters of a customized compartmental model, for the purposes of projecting further development of the US COVID-19 epidemics. The deep learning-enhanced compartment model predicts that the basic reproduction rate (R_0) will become less than one around June 18-19, 2020, and that the US Infected population will peak on June 17-18, 2020 at around 1.36 million individual cases. The model also predicts that the number of accumulative confirmed cases will cross the 2 million mark around June 11, 2020. It also projects that the infection transmission parameter will drop to virtually zero as early as July 8, 2020, implying that the total number of confirmed cases will likely become stabilized around that time frame (predicted at 2.23-2.24 million).


title: Robust Estimation of Infection Fatality Rates during the Early Phase of a Pandemic

text: During a pandemic, robust estimation of case fatality rates (CFRs) is essential to plan and control suppression and mitigation strategies. At present, estimates for the CFR of COVID-19 caused by SARS-CoV-2 infection vary considerably. Expert consensus of 0.1-1% covers in practical terms a range from normal seasonable Influenza to Spanish Influenza. In the following, I deduce a formula for an adjusted Infection Fatality Rate (IFR) to assess mortality in a period following a positive test adjusted for selection bias. Official datasets on cases and deaths were combined with data sets on number of tests. After data curation and quality control, a total of IFR (n=819) was calculated for 21 countries for periods of up to 26 days between registration of a case and death. Estimates for IRFs increased with length of period, but levelled off at >9days with a median for all 21 countries of 0.11 (95%-CI: 0.073-0.15). An epidemiologically derived IFR of 0.040 % (95%-CI: 0.029%-0.055%) was determined for Iceland and was very close to the calculated IFR of 0.057% (95%-CI: 0.042-0.078), but 2.7-6-fold lower than CFRs. IFRs, but not CFRs, were positively associated with increased proportions of elderly in age-cohorts (n=21, spearman's ρ =.73, p =.02). Real-time data on molecular and serological testing may further displace classical diagnosis of disease and its related death. I will critically discuss, why, how and under which conditions the IFR, provides a more solid early estimate of the global burden of a pandemic than the CFR.


title: Rising evidence of COVID-19 transmission potential to and between animals: do we need to be concerned?

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)--the virus that causes coronavirus disease (COVID-19)--has been detected in domestic dogs and cats, raising concerns of transmission from, to, or between these animals. There is currently no indication that feline- or canine-to-human transmission can occur, though there is rising evidence of the reverse. To explore the extent of animal-related transmission, we aggregated 17 case reports on confirmed SARS-CoV-2 infections in animals as of 15 May 2020. All but two animals fully recovered and had only mild respiratory or digestive symptoms. Using data from probable cat-to-cat transmission in Wuhan, China, we estimated the basic reproduction number R0 under this scenario at 1.09 (95% confidence interval: 1.05, 1.13). This value is much lower than the R0 reported for humans and close to one, indicating that the sustained transmission between cats is unlikely to occur. Our results support the view that the pet owners and other persons with COVID-19 in close contact with animals should be cautious of the way they interact with them.


title: Convalescent plasma treatment of severe COVID-19: A matched control study

text: Background Since December 2019, Coronavirus Disease 2019 (COVID-19) has become a global pandemic, causing mass morbidity and mortality. Prior studies in other respiratory infections suggest that convalescent plasma transfusion may offer benefit to some patients. Here, the outcomes of thirty-nine hospitalized patients with severe to life-threatening COVID-19 who received convalescent plasma transfusion were compared against a cohort of retrospectively matched controls. Methods Plasma recipients were selected based on supplemental oxygen needs at the time of enrollment and the time elapsed since the onset of symptoms. Recipients were transfused with convalescent plasma from donors with a SARS-CoV-2 (severe acute respiratory disease coronavirus 2) anti-spike antibody titer of [≥]1:320 dilution. Matched control patients were retrospectively identified within the electronic health record database. Supplemental oxygen requirements and survival were compared between plasma recipients and controls. Results Convalescent plasma recipients were more likely than control patients to remain the same or have improvements in their supplemental oxygen requirements by post-transfusion day 14, with an odds ratio of 0.86 (95% CI: 0.75~0.98; p=0.028). Plasma recipients also demonstrated improved survival, compared to control patients (log-rank test: p=0.039). In a covariates-adjusted Cox model, convalescent plasma transfusion improved survival for non-intubated patients (hazard ratio 0.19 (95% CI: 0.05 ~0.72); p=0.015), but not for intubated patients (1.24 (0.33~4.67); p=0.752). Conclusions Convalescent plasma transfusion is a potentially efficacious treatment option for patients hospitalized with COVID-19; however, these data suggest that non-intubated patients may benefit more than those requiring mechanical ventilation.


title: Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection

text: Higher mortality of COVID19 patients with comorbidity is the formidable challenge faced by the health care system. In response to the present crisis, understanding the molecular basis of comorbidity is essential to accelerate the development of potential drugs. To address this, we have measured the genetic association between COVID19 and various lung disorders and observed a remarkable resemblance. 141 lung disorders directly or indirectly linked to COVID19 result in a high-density disease-disease association network that shows a small-world property. The clustering of many lung diseases with COVID19 demonstrates a greater complexity and severity of SARS-CoV-2 infection. Furthermore, our results show that the functional protein-protein interaction modules involved RNA and protein metabolism, substantially hijacked by SARS-CoV-2, are connected to several lung disorders. Therefore we recommend targeting the components of these modules to inhibit the viral growth and improve the clinical conditions in comorbidity.


title: rAre graphene and graphene-derived products capable of preventing COVID-19 infection?

text: The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) causes the new coronavirus disease 2019 (COVID-19). This disease is a severe respiratory tract infection that spread rapidly around the world. In this pandemic situation, the researchers' effort is to understand the targets of the virus, mechanism of their cause, and transmission from animal to human and vice-versa. Therefore, to support COVID-19 research and development, we have proposed approaches based on graphene and graphene-derived nanomaterials against COVID-19.


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Singapore and Covid-19: in the forefront of response efforts?


title: Empirical Model of Spring 2020 Decrease in Daily Confirmed COVID-19 Cases in King County, Washington

text: Projections of the near future of daily case incidence of COVID-19 in King County are valuable for informing public policy. Projections made with the latest data may be better for some purposes than projections based on older data freezes of more reliable data. Incidence-count half-life is a better statistic for many purposes than reproductive rate (R). Currently, an empirical fit to King County data predicts a half-life of 24.5 days (95% CI: 21.2 - 28.8), corresponding to an R of about 0.8. Under this model, the number of cases per day in King County is extrapolated to be 40 cases per day on May 24 and 20 cases per day on June 18, 2020.


title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro

text: COVID-19 has become a global pandemic that threatens millions of people worldwide. There is an urgent call for developing effective drugs against the virus (SARS-CoV-2) causing this disease. The main protease of SARS-CoV-2, 3C-like protease (3CLpro), is highly conserved across coronaviruses and is essential for the maturation process of viral polyprotein. Scutellariae radix (Huangqin in Chinese), the root of Scutellaria baicalensis has been widely used in traditional Chinese medicine to treat viral infection related symptoms. The extracts of S. baicalensis have exhibited broad spectrum antiviral activities. We studied the anti-SARS-CoV-2 activity of S. baicalensis and its ingredient compounds. We found that the ethanol extract of S. baicalensis inhibits SARS-CoV-2 3CLpro activity in vitro and the replication of SARS-CoV-2 in Vero cells with an EC50 of 0.74 μg/ml. Among the major components of S. baicalensis, baicalein strongly inhibits SARS-CoV-2 3CLpro activity with an IC50 of 0.39 μM. We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. Our study demonstrates that the extract of S. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors.


docid: ocwhnmig

title: Trials of drugs to prevent coronavirus infection begin in health care workers

text: When malaria researcher Nicholas White saw coronavirus infections picking up around the world 2 months ago, he immediately thought of the impact they could have on poorer countries “In fragile health care systems, if you start knocking out a few nurses and doctors, the whole thing can collapse,” says White, who is based at Mahidol University in Bangkok “So we realized that the priority would be to protect them ” White and his colleagues at the Mahidol Oxford Tropical Medicine Research Unit wondered whether widely available drugs could help They have designed a trial in which 40,000 doctors and nurses in Asia, Africa, and Europe will prophylactically receive chloroquine or hydroxychloroquine, two old drugs against malaria White hopes the trial will start this month, but its launch has been “incredibly difficult because of bureaucratic processes,” he says


title: Dramatic reduction of psychiatric emergency consultations during lockdown linked to COVID-19 in Paris and suburbs

text: Background The COVID-19 pandemic and associated lockdown may have psychiatric consequences and increase the number of psychiatric emergency consultations. Methods Three psychiatric centers in Paris and its suburbs took part in the study. We compared the number of total psychiatric emergency consultations during the 4 first weeks of the lockdown in France to the corresponding 4 weeks in 2019. We also compared the number of consultations during these 4-week time periods in 2020 and 2019 across different diagnostic categories. Findings In the 4 first weeks of the lockdown in France, 553 emergency psychiatry consultations were carried out, compared to 1224 consultations during the corresponding period of 2019, representing a 54.8 % decrease. This decrease was evident across all psychiatric disorders, including anxiety (number of consultations in 2020 representing 36.1 % of 2019), mood (41.1 %), and psychotic disorders (57.3 %). The number of suicide attempts also decreased (number of suicide attempts in 2020 representing 42.6 % of 2019). In comparison to 2019, the proportion of total consultations for anxiety disorders also decreased (16.6 % vs. 20.8 %), whilst the proportion of total consultations increased for psychotic disorders (31.1 % vs. 24.1 %). Conclusions The total number of psychiatric emergency consultations during lockdown dramatically decreased. The psychological consequences of lockdown may be delayed, indicating that psychiatric services should be prepared for a secondary increase in emergency presentations.


title: COVID-19 social distancing: A snippet view of the autistic social world

text: In this Current Issues article, I will use National Health Service guidelines on hand hygiene and social distancing measures (which the UK government introduced in March, 2020, to combat the COVID-19 coronavirus) to give readers an insight into the restricted social life of an autistic person, using auto/biography to explore my personal experience of social isolation and being a 'vulnerable adult' I am an Autistic, newly qualified sociologist and I will be using my positionality as a vantage point, as the public adjust to my 'normal' I acknowledge the element of 'choice' in autistic individuals' self-isolation but focus here on the social restrictions imposed on us from outside (social isolation) I call for social change, once the social distancing measures are lifted These changes might occur at the individual level (e g being a friend) but will still broaden our social world


title: Traumatic Times

text: Discusses how businesses are impacted by traumatic events and pandemics such as the current Coronavirus (COVID-19) As I write this in late March, we are early in the coronavirus (COVID-19) pandemic It is like nothing any of us have experienced before, except perhaps the very few who may have lived through the flu pandemic of 1918-1920 The COVID-19 crisis is like a combination of all the worst we've seen There is social trauma as we isolate ourselves, lose some individual liberties, and try to work from home We don't know when society will return to normal and, when it does, how it will have changed


title: Demographic science aids in understanding the spread and fatality rates of COVID-19

text: Governments around the world must rapidly mobilize and make difficult policy decisions to mitigate the COVID-19 pandemic. Because deaths have been concentrated at older ages, we highlight the important role of demography, particularly how the age structure of a population may help explain differences in fatality rates across countries and how transmission unfolds. We examine the role of age structure in deaths thus far in Italy and South Korea and illustrate how the pandemic could unfold in populations with similar population sizes but different age structures, showing a dramatically higher burden of mortality in countries with older versus younger populations. This powerful interaction of demography and current age-specific mortality for COVID-19 suggests that social distancing and other policies to slow transmission should consider both the age composition of local and national contexts as well as the social connectedness of older and younger generations. We also call for countries to provide case and fatality data disaggregated by age and sex to improve real-time targeted nowcasting.


docid: mgvrbfzd

title: Screening of SARS-CoV-2 among homeless people, asylum seekers and other people living in precarious conditions in Marseille, France, March April 2020.

text: Surveillance of SARS-CoV-2 infection among sheltered homeless and other vulnerable people might provide the information needed to prevent its spread within accommodation centres. In March-April, we enrolled 411 homeless individuals, 77 asylum-seekers, 58 people living in precarious conditions, and 152 employees working in these accommodation centres and collected nasal samples. SARS-CoV-2 carriage was assessed by quantitative PCR. Overall, 49 (7.0%) people were positive for SARS-CoV-2, including 37 homeless individuals (of 411, 9.0%), 12 employees (of 152, 7.9%). SARS-CoV-2 positivity correlated with symptoms, although 51% of positive patients did not report respiratory symptoms or fever. Among homeless people, being young (18-34 years) (OR: 3.83 [1.47-10.0], p=0.006) and being housed in one specific shelter (OR: 9.13 [4.09-20.37], p<0.0001) were independent factors associated with the SARS-CoV-2 positivity rates (11.4% and 20.6%, respectively). The survey reveals the role of collective housing in relation to viral transmission within centres.


Pandemic-related pregnancy stress and anxiety among women pregnant during the COVID-19 pandemic


Simultaneous Treatment of COVID-19 With Serine Protease Inhibitor Camostat and/or Cathepsin L Inhibitor?


docid: azlajqbe

title: Urgent Measures for the Containment of the Coronavirus (Covid-19) Epidemic in the Neurorehabilitation/Rehabilitation Departments in the Phase of Maximum Expansion of the Epidemic

text: COVID-19 has rapidly become a pandemic emergency, distressing health systems in each affected country. COVID-19 determines the need for healthcare in a large number of people in an extremely short time and, like a tsunami wave, overruns emergency, infectious diseases, and pneumology departments as well as intensive care units, choking healthcare services. Rehabilitation services are also affected by this epidemic which forces radical changes both in the organization and in the operating methods. In the absence of reference literature on this issue, this report aims to provide a background documentation to support physicians and healthcare personnel involved in neurorehabilitation and rehabilitation care.


title: A territory-wide study of early COVID-19 outbreak in Hong Kong community: A clinical, epidemiological and phylogenomic investigation

text: Background: Initial cases of coronavirus disease 2019 (COVID-19) reported in Hong Kong were mostly imported cases from Mainland China. However, most cases reported in February 2020 were local infections with unknown source, indicating local community transmissions. This study aimed to report the clinical, epidemiological and phylogenomic characteristics of the local cases of COVID-19 in our community. Methods: We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53.8% of the cases in Hong Kong by the end of February 2020. We used both Nanopore and Illumina platforms to perform whole-genome sequencing (WGS) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from these patients. Phylogenetic relatedness among these local cases and their placement in the global phylogeny were examined. The evolutionary rate and divergence time of transmission were also determined. Findings: Of these 50 patients, only three (6.0%) had visited Wuhan while 43 (86.0%) did not have recent travel records. The average interval from symptom onset to hospital admission was 8.5 days. The most common signs and symptoms on admission were cough (74.0%) and fever (58.0%). Radiographic abnormality was found in 46 (92.0%) patients. Three (6.0%) patients required ICU admission. Phylogenetic analysis concurred with epidemiological investigation that 42 (84.0%) cases could be grouped into six transmission clusters. Forty-four (88.0%) cases harboured a common mutation Orf3a G251V. Global phylogeny of SARS-CoV-2 revealed that most (88.0%) cases in Hong Kong were clustered in two subclades with the strains from other countries. The estimated time to the most recent common ancestor (tMRCA) of COVID-2019 outbreak in Hong Kong was December 24, 2019 with an evolutionary rate of 3.04x10-3 substitutions per site per year. The reproduction number value was 1.84 as of February 28, 2020 in Hong Kong. Interpretation: We provided a territory-wide overview of COVID-19 in Hong Kong, which has borders connecting to Mainland China. Transmission in closed settings especially during family and religious gatherings is a hallmark of the recently reported cases. The reproduction number value indicated an ongoing outbreak in the community. Social distancing and vigilant epidemiological control are crucial to the containment of COVID-19 transmission


title: COVID-Net: A deep learning based and interpretable predication model for the county-wise trajectories of COVID-19 in the United States

text: The confirmed cases of novel coronavirus disease (COVID-19) have been reported in the United States since late January 2020. There were over 4.8 million confirmed cases and about 320,000 deaths as of May 19, 2020 in the world. We examined the characteristics of the confirmed cases and deaths of COVID-19 in all affected counties of the United States. We proposed a COVID-Net combining the architecture of both Long Short Term Memory (LSTM) and Gated Recurrent Unit (GRU) by using the trajectories of COVID-19 during different periods until May 19, 2020, as the training data. The validation of the COVID-Net was performed by predicting the numbers of confirmed cases and deaths in subsequent 3-day, 5-day, and 7-day periods. The COVID-Net produced relatively smaller Mean Relative Errors (MREs) for the 10 counties with the most severe epidemic as of May 19, 2020. On average, MREs were 0.01 for the number of confirmed cases in all validation periods, and 0.01, 0.01, and 0.03 for the number of deaths in the 3-day, 5-day, and 7-day periods, respectively. The COVID-Net incorporated five risk factors of COVID-19 and was used to predict the trajectories of COVID-19 in Hudson County, New Jersey and New York County, New York until June 28, 2020. The risk factors include the percentage of the population with access to exercise opportunities, average daily PM2.5, population size, preventable hospitalization rate, and violent crime rate. The expected number of cumulative confirmed cases and deaths depends on the dynamics of these five risk factors.


Reasons to decline an invitation to peer review during the coronavirus (Covid-19) outbreak-are there implications for journal policy?


title: The prevalence and influencing factors for anxiety in medical workers fighting COVID-19 in China: A cross-sectional survey

text: Abstract: Background: The COVID-19 outbreak caused by the SARS-Cov-2 virus has been sustained in China since December 2019, and could become a pandemic if we do not contain it. The mental health of frontline medical staff is a concern. In this study, we aimed to identify the influencing factors on medical worker anxiety in China during the COVID-19 outbreak. Methods: We conducted a cross-sectional study to estimate the prevalence of anxiety among medical staff from 10th February 2020 to 20th February 2020 in China using the Zung Self-rating Anxiety Scale (SAS) to assess anxiety, using the criteria of normal (≤49), mild (50-59), moderate (60-70) and severe anxiety (≥70). We used multivariable linear regression to determine the factors (e.g., having direct contact treating infected patients, being a medical staff worker from Hubei province, being a suspect case) for anxiety. We also used adjusted models to confirm independent factors for anxiety after adjusting for gender, age, education and marital status. Results: Of 512 medical staff from China, 164 healthcare workers (32.03%) had had direct contact by treating infected patients. The prevalence of anxiety was 12.5%, with 53 workers suffering from mild (10.35%), seven workers from moderate (1.36%) and four workers from severe anxiety (0.78%). After adjusting for sociodemographic characteristics (gender, age, education and marital status), medical staff who had had direct contact treating infected patients saw higher anxiety scores than those who had not had direct contact (βvalue=2.33, CI: 0.65 -4.00; p=0.0068). Similar things were observed in medical staff from Hubei province, compared with those from other parts of China (βvalue=3.67, CI: 1.44 -5.89; p=0.0013). The most important variable was suspect cases with high anxiety scores, compared to non-suspect cases (βvalue=4.44, CI: 1.55 -7.33; p=0.0028). Conclusion: Our results highlight that government authorities should make early detection of the high risk of anxiety among medical staff a priority, and implement appropriate psychological intervention programs, to prevent medical staff from developing psychological disorders that could potentially exert an adverse effect on combating the COVID-19 epidemic.


title: Chloroquine, hydroxychloroquine and COVID-19

text: The media have featured the antimalarials chloroquine (CQ) and hydroxychloroquine (HCQ) to treat coronavirus (COVID-19). Political leaders have touted their use and recommended availability to the public. These anti-inflammatory agents have substantial human toxicity with a narrow therapeutic window. CQ and HCQ poisoning cause myocardial depression and profound hypotension due to vasodilation. Bradycardia and ventricular escape rhythms arise from impaired myocardial automaticity and conductivity due to sodium and potassium channel blockade. With cardiotoxicity, ECGs may show widened QRS, atrioventricular heart block and QT interval prolongation. CQ may also cause seizures, often refractory to standard treatment. Of concern is pediatric poisoning, where 1–2 pills of CQ or HCQ can cause serious and potentially fatal toxicity in a toddler. The treatment of CQ/HCQ poisoning includes high-dose intravenous diazepam postulated to have positive ionotropic and antidysrhythmic properties that may antagonize the cardiotoxic effects of CQ. Infusions of epinephrine titrated to treat unstable hypotension, as well as potassium for severe hypokalemia may be required. Current scientific evidence does not support treatment or prophylactic use of these agents for COVID-19 disease. Regulatory and public health authorities recognize that CQ/HCQ may offer little clinical benefit and only add risk requiring further investigation before wider public distribution.