title: System Dynamics Modeling of Within-Host Viral Kinetics of Coronavirus (SARS CoV-2)

text: Mathematical models are being used extensively in the study of SARS-CoV-2 transmission dynamics, becoming an essential tool for decision making concerning disease control. It is now required to understand the mechanisms involved in the interaction between the virus and the immune response effector cells, both innate and adaptive, in order to support lines of research related to the use of drugs, production of protective antibodies and of course, vaccines against SARS-CoV-2. The present study, using a system dynamic approach, hypothesizes over the conditions that characterize the fraction of the population which get infected by SARS-CoV-2 as the asymptomatic patients, the mild symptomatic, acute symptomatic, and also super-spreaders, in terms of innate immune response, the initial virus load, the virus burden with shedding events, and the cytokine levels.


title: Safe handling considerations in a coronavirus outbreak (Covid-19). how to prepare a surgical unit?/ Consideraciones para el manejo seguro en brote de enfermedad por coronavirus (Covid-19). ¿cómo preparar una unidad quirúrgica?

text: While the world is facing a pandemic caused by the virus 2019-nCoV, critical hospital areas like the surgical unit must be ready to prevent contamination of the environment and the healthcare provider. The main purpose of this article is to review the current recommendations for using personal protection equipment, introduce devices that can prove useful for the practice of anesthesia and to explain the modifications and adaptations that must be made to both human and material resources in the surgical unit.


docid: ahtlroiq

title: Six Scenarios for non-medical interventions in the SARS-CoV-2 epidemic

text: We investigate six scenarios spanning main parts of the decision space of non-medical interventions against the CoV-2 epidemic in Germany. Based on the notion of interventions-lifting we classify and evaluate the scenarios by five attributes (indicators): amount of interventions-lifting, death numbers, Public Health Care capacity, population immunity, peak dates of infections. For quantitative reasoning we use a simulated modified SEIR-model calibrated with actual data. We identify margins for intervention-liftings wrt. 13.05.2020 and discuss the relation to the effective reproduction number with a 6d-generation time . We show that, in order to constrain death numbers comparable to a strong Influenza epidemic, there is only a small corridor of 16% of possible liftings, with an additional 4% margin contributed by automated contact tracing. We show also that there is a much broader corridor of 50%+18%, though not overloading critical Public Health Care capacity, implying high death numbers.


title: Implementation of An Online COVID-19 Epidemic Calculator for Tracking the Spread of the Coronavirus in Singapore and Other Countries

text: This paper describes the methods underlying the development of an online COVID-19 Epidemic Calculator for tracking COVID-19 growth parameters. From publicly available infection case data, the calculator is used to estimate the effective reproduction number, doubling time, final epidemic size, and death toll. As a case study, we analyzed the results for Singapore during the 'Circuit breaker' period from April 7, 2020 to the end of May 2020. The calculator shows that the stringent measures imposed have an immediate effect of rapidly slowing down the spread of the coronavirus. After about two weeks, the effective reproduction number reduced to 1.0. Since then, the number has been fluctuating around 1.0. The COVID-19 Epidemic Calculator is available in the form of an online Google Sheet and the results are presented as Tableau Public dashboards at www.cv19.one. By making the calculator readily accessible online, the public can have a tool to meaningfully assess the effectiveness of measures to control the pandemic.


docid: mwttkclk

title: Angiotensin II Receptor Blockers and Angiotensin-Converting Enzyme Inhibitors Usage is Associated with Improved Inflammatory Status and Clinical Outcomes in COVID-19 Patients With Hypertension

text: With the capability of inducing elevated expression of ACE2, the cellular receptor for SARS-CoV-2, angiotensin II receptor blockers or angiotensin-converting enzyme inhibitors (ARBs/ACEIs) treatment may have a controversial role in both facilitating virus infection and reducing pathogenic inflammation. We aimed to evaluate the correlation of ARBs/ACEIs usage with the pathogenesis of COVID-19 in a retrospective, single-center study. 126 COVID-19 patients with preexisting hypertension at Hubei Provincial Hospital of Traditional Chinese Medicine (HPHTCM) in Wuhan from January 5 to February 22, 2020 were retrospectively allocated to ARBs/ACEIs group (n=43) and non-ARBs/ACEIs group (n=83) according to their antihypertensive medication. 125 age- and sex-matched COVID-19 patients without hypertension were randomly selected as non-hypertension controls. In addition, the medication history of 1942 hypertension patients that were admitted to HPHTCM from November 1 to December 31, 2019 before COVID-19 outbreak were also reviewed for external comparison. Epidemiological, demographic, clinical and laboratory data were collected, analyzed and compared between these groups. The frequency of ARBs/ACEIs usage in hypertension patients with or without COVID-19 were comparable. Among COVID-19 patients with hypertension, those received either ARBs/ACEIs or non-ARBs/ACEIs had comparable blood pressure. However, ARBs/ACEIs group had significantly lower concentrations of CRP (p=0.049) and procalcitonin (PCT, p=0.008). Furthermore, much lower proportion of critical patients (9.3% vs 22.9%; p=0.061), and a lower death rate (4.7% vs 13.3%; p=0.216) were observed in ARBs/ACEIs group than non-ARBs/ACEIs group, although these differences failed to reach statistical significance. Our findings thus support the use of ARBs/ACEIs in COVID-19 patients with preexisting hypertension.


title: COVID-19 clinical characteristics, and sex-specific risk of mortality: Systematic Review and Meta-analysis

text: Objectives: The rapidly evolving coronavirus disease 2019 (COVID-19), was declared a pandemic by the World Health Organization on March 11, 2020. It was first detected in the city of Wuhan in China and has spread globally resulting in substantial health and economic crisis in many countries. Observational studies have partially identified the different aspects of this disease. Up to this date, no comprehensive systematic review for the clinical, laboratory, epidemiologic and mortality findings has been published. We conducted this systematic review and meta-analysis for a better understanding of COVID-19. Methods: We reviewed the scientific literature published from January 1, 2019 to March 3, 2020. Statistical analyses were performed with STATA (version 14, IC; Stata Corporation, College Station, TX, USA). The pooled frequency with 95% confidence intervals (CI) was assessed using random effect model. Publication bias was assessed and p <0.05 was considered a statistically significant publication bias. Results: Out of 1102 studies, 32 satisfied the inclusion criteria. A total of 4789 patients with a mean age of 49 years were evaluated. Fever (83.0%, CI 77.5 to 87.6), cough (65.2%, CI 58.6 to 71.2) and myalgia/fatigue (34.7, CI 26.0 to 44.4) were the most common symptoms. The most prevalent comorbidities were hypertension (18.5 %, CI 12.7 to 24.4) and Cardiovascular disease (14.9 %, CI 6.0 to 23.8). Among the laboratory abnormalities, elevated C-Reactive Protein (CRP) (72.0% (CI 54.3 to 84.6) and lymphopenia (50.1%, CI 38.0 to 62.4) were the most common findings. Bilateral ground-glass opacities (66.0%, CI 51.1 to 78.0) was the most common CT-Scan presentation. Pooled mortality rate was 6.6%, with males having significantly higher mortality compared to females (OR 3.4; 95% CI 1.2 to 9.1, P = 0.01). Conclusion: COVID-19 commonly presented with a progressive course of cough and fever with more than half of hospitalized patients showing leukopenia or a high CRP on their laboratory findings. Mortality associated with COVID19 was higher than that reported in studies in China with Males having a 3-fold higher risk of mortality in COVID19 compared to females.


title: Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients

text: Background: In 2020 the current outbreak of Coronavirus Disease 2019(COVID-19) has constituted a global pandemic. But the question about the immune mechanism of patients with COVID-19 is unclear and cause particular concern to the world. Here, we launched a follow-up analysis of antibodies against SARS-CoV-2 of 192 COVID-19 patients, aiming to depict a kinetics profile of antibodies against SARS-CoV-2 and explore the related factors of antibodies expression against SARS-CoV-2 in COVID-19 patient. Methods: A total of 192 COVID-19 patients enrolled in the designated hospital of Guangzhou , Guangzhou Eighth People's Hospital, from January to February 2020 were selected as the study cohort. A cohort of 130 COVID-19 suspects who had been excluded from SARS-CoV-2 infected by negative RT-PCR result and 209 healthy people were enrolled in this study. Detection of IgM and IgG against SARS-CoV-2 were performed by Chemiluminescence immunoassay in different groups . Results: It has been found that the seroconversion time of IgM against SARS-CoV-2 in most patients was 5-10 days after the symptoms onset , and then rose rapidly, reaching a peak around 2 to 3 weeks, and the median peak concentration was 2.705 AU / mL. The peak of IgM maintained within one week, and then enters the descending channel. IgG seroconverted later than or synchronously with IgM, reaching peaks around 3 to 4 weeks.The median peak concentration was 33.998AU / ml,which was higher than that of IgM . IgM titers begins to gradually decrease after reaching the peak in the 4th week, after the 8th week, a majority of IgM in patient's serum started to turn negative. On the contrary, titers of IgG began to decline slightly after the fifth week, and more than 90% of results of patients were positive after 8 weeks. Additionally, the concentration of antibodies positively correlated with the severity of the disease and the duration of virus exist in host. Conclusion: We depict a kinetics profile of antibodies against SARS-CoV-2 in COVID-19 patients and found out that the levels of antibodies were related to the disease severity,age, gender and virus clearance or continuous proliferation of COVID-19 patients.


title: Prepared and highly committed despite the risk of COVID-19 infection: A cross-sectional survey of primary care physicians' concerns and coping strategies in Singapore

text: BACKGROUND Primary care physicians (PCPs) play a crucial role as first points-of-contact between suspected cases and the healthcare system in the current Coronavirus Disease 2019 (COVID-19) pandemic. An overlooked angle is the potential psychosocial impact on PCPs as they place themselves at increased risk of infection. This study examines PCPs' concerns, impact on personal lives and work, and level of pandemic preparedness in the context of COVID-19 in Singapore. We also examine factors and coping strategies that PCPs have used to manage stress during the outbreak. METHODS 216 PCPs actively practicing in either a public or private clinic were convenience sampled from three primary care organizations in Singapore. Participants completed an online questionnaire consisting of items on work- and non-work-related concerns, impact on personal and work life, perceived pandemic preparedness, stress-reduction factors, and personal coping strategies related to COVID-19. RESULTS A total of 158 questionnaires were usable for analyses. PCPs perceived themselves to be at high risk of COVID-19 infection, and a source of risk and concern to loved ones. PCPs reported acceptance of these risks and the need to care for COVID-19 patients. Overall perceived pandemic preparedness was extremely high. PCPs prioritized availability of personal protective equipment, strict infection prevention guidelines, accessible information about COVID-19, and well-being of their colleagues and family as the most effective stress management factors. CONCLUSIONS Primary care will continue to be crucial in outbreak management efforts. Healthcare organizations should continue to support PCPs by managing their psychosocial and professional needs.


title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing.

text: Effective interventions are mandatory to control the transmission and spread of SARS-CoV-2, a highly contagious virus causing devastating effects worldwide. Cost-effective approaches are pivotal tools required to increase the detection rates and escalate further in massive surveillance programs, especially in countries with limited resources that most of the efforts have focused on symptomatic cases only. Here, we compared the performance of the RT-qPCR using an intercalating dye with the probe-based assay. Then, we tested and compared these two RT-qPCR chemistries in different pooling systems: after RNA extraction (post-RNA extraction) and before RNA extraction (pre-RNA extraction) optimizing by pool size and template volume. We evaluated these approaches in 610 clinical samples. Our results show that the dye-based technique has a high analytical sensitivity similar to the probe-based detection assay used worldwide. Further, this assay may also be applicable in testing by pool systems post-RNA extraction up to 20 samples. However, the most efficient system for massive surveillance, the pre-RNA extraction pooling approach, was obtained with the probe-based assay in test up to 10 samples adding 13.5 uL of RNA template. The low cost and the potential use in pre-RNA extraction pool systems, place of this assays as a valuable resource for scalable sampling to larger populations. Implementing a pool system for population sampling results in an important savings of laboratory resources and time, which are two key factors during an epidemic outbreak. Using the pooling approaches evaluated here, we are confident that it can be used as a valid alternative assay for the detection of SARS-CoV-2 in human samples.


title: Comprehensive genome analysis of 6,000 USA SARS-CoV-2 isolates reveals haplotype signatures and localized transmission patterns by state and by country

text: Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. This points to the effectiveness of existing travel restriction policies and public health measures in controlling the transmission of SARS-CoV-2.


title: Population-wide evolution of SARS-CoV-2 immunity tracked by a ternary immunoassay

text: Serological assays can detect anti-SARS-CoV-2 (SARS2) antibodies, but their sensitivity often comes at the expense of specificity. Here we used a Ternary Automated Blood Im-munoassay (TRABI) to assess the IgG response against SARS2 in 3,815 prepandemic plasma samples and 126 virologically and/or clinically confirmed COVID-19 samples. Posterior probabilities were calculated from 3x8 measurements of logarithmically diluted samples against the ectodomain and the receptor-binding domain of the spike protein and the nucleoprotein. We then performed 429,624 assays on 17,901 blood samples from patients of the University Hospital Zurich and from healthy blood donors. We found se-ropositivity in 44 of 8,591 patients and in 26 of 5,388 blood donors from December 2019 to May 2020. Western blotting confirmed seropositivity in COVID samples but in none of the prepandemic samples. Solution-equilibrium measurements revealed immunodominant antibodies with nanomolar affinity in COVID samples, whereas prepandemic plasma showed lower affinities despite similar titers for individual SARS2 antigens. Hence, TRABI identifies seropositive individuals in large unselected cohorts, discriminates be-tween SARS2 immunity and low-affinity crossreactivity, and is therefore suitable for large-scale nationwide screening campaigns.


The most effective interventions


title: Generic probabilistic modelling and non-homogeneity issues for the UK epidemic of COVID-19

text: Coronavirus COVID-19 spreads through the population mostly based on social contact. To gauge the potential for widespread contagion, to cope with associated uncertainty and to inform its mitigation, more accurate and robust modelling is centrally important for policy making. We provide a flexible modelling approach that increases the accuracy with which insights can be made. We use this to analyse different scenarios relevant to the COVID-19 situation in the UK. We present a stochastic model that captures the inherently probabilistic nature of contagion between population members. The computational nature of our model means that spatial constraints (e.g., communities and regions), the susceptibility of different age groups and other factors such as medical pre-histories can be incorporated with ease. We analyse different possible scenarios of the COVID-19 situation in the UK. Our model is robust to small changes in the parameters and is flexible in being able to deal with different scenarios. This approach goes beyond the convention of representing the spread of an epidemic through a fixed cycle of susceptibility, infection and recovery (SIR). It is important to emphasise that standard SIR-type models, unlike our model, are not flexible enough and are also not stochastic and hence should be used with extreme caution. Our model allows both heterogeneity and inherent uncertainty to be incorporated. Due to the scarcity of verified data, we draw insights by calibrating our model using parameters from other relevant sources, including agreement on average (mean field) with parameters in SIR-based models. We use the model to assess parameter sensitivity for a number of key variables that characterise the COVID-19 epidemic. We also test several control parameters with respect to their influence on the severity of the outbreak. Our analysis shows that due to inclusion of spatial heterogeneity in the population and the asynchronous timing of the epidemic across different areas, the severity of the epidemic might be lower than expected from other models. We find that one of the most crucial control parameters that may significantly reduce the severity of the epidemic is the degree of separation of vulnerable people and people aged 70 years and over, but note also that isolation of other groups has an effect on the severity of the epidemic. It is important to remember that models are there to advise and not to replace reality, and that any action should be coordinated and approved by public health experts with experience in dealing with epidemics. The computational approach makes it possible for further extensive scenario-based analysis to be undertaken. This and a comprehensive study of sensitivity of the model to different parameters defining COVID-19 and its development will be the subject of our forthcoming paper. In that paper, we shall also extend the model where we will consider different probabilistic scenarios for infected people with mild and severe cases.


title: Accounting for underreporting in mathematical modelling of transmission and control of COVID-19 in Iran

text: BACKGROUND: Iran has been the hardest hit country by the outbreak of SARS-CoV-2 in the Middle East with 74,877 confirmed cases and 4,683 deaths as of 15 April 2020. With a relatively high case fatality ratio and limited testing capacity, the number of confirmed cases reported is suspected to suffer from significant under-reporting. Therefore, understanding the transmission dynamics of COVID-19 and assessing the effectiveness of the interventions that have taken place in Iran while accounting for the uncertain level of underreporting is of critical importance. We use a mathematical epidemic model utilizing official confirmed data and estimates of underreporting to understand how transmission in Iran has been changing between February and April 2020. METHODS: We developed a compartmental transmission model to estimate the effective reproduction number and its fluctuations since the beginning of the outbreak in Iran. We associate the variations in the effective reproduction number with a timeline of interventions and national events. The estimation method also accounts for the underreporting due to low case ascertainment by estimating the percentage of symptomatic cases using delay adjusted case fatality ratio based on the distribution of the delay from hospitalization to death. FINDINGS: Our estimates of the effective reproduction number ranged from 0.66 to 1.73 between February and April 2020, with a median of 1.16. We estimate a reduction in the effective reproduction number during this period, from 1.73 (95% CI 1.60-1.87) on 1 March 2020 to 0.69 (95% CI 0.68-0.70) on 15 April 2020, due to various non-pharmaceutical interventions including school closures, a ban on public gatherings including sports and religious events, and full or partial closure of non-essential businesses. Based on these estimates and given that a near complete containment is no longer feasible, it is likely that the outbreak may continue until the end of the 2020 if the current level of physical distancing and interventions continue and no effective vaccination or therapeutic are developed and made widely available. INTERPRETATION: The series of non-pharmaceutical interventions and the public compliance that took place in Iran are found to be effective in slowing down the speed of the spread of COVID-19 within the studied time period. However, we argue that if the impact of underreporting is overlooked, the estimated transmission and control dynamics could mislead the public health decisions, policy makers, and general public especially in the earlier stages of the outbreak. FUNDING: Nil.


title: Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections

text: Background: A novel coronavirus disease 2019 (COVID-19) broke out in Wuhan of Hubei province and had spread throughout the world since December 2019. Because the clinically diagnosed cases in Hubei province were reported for the first time on February 13, 2020, a very high peak of new cases in China was observed. The reason why so many clinically diagnosed cases appeared was not clear. Methods: All data of new cases in China were acquired from WHO situation reports. Linear fitting was used to infer the ability to detect COVID-19 infections. Primer-BLAST and nucleotide blast were applied to check the specificity of primers. Expression data of human mRNA in different tissues was obtained from Human Protein Atlas. Finding: Based on the data and analysis of changes of new laboratory-confirmed cases and new clinically diagnosed cases, it was inferred that there were many false-negative results in all clinically diagnosed cases in Hubei province. There were eight non-specific primers in dozens of primers used in clinical or research detection of COVID-19. Among them, a pair of primer for the ORF1ab regions of SARS-CoV-2 genome, which widely applied to detect SARS-CoV-2 virus in China, well matched some human mRNAs such as Cathepsin C transcripts. Compared to other transcripts, Cathepsin C mRNA had a high abundance in tonsil, lung and small intestine. Interpretation: Some non-specific RT-PCR primers could cause the serious interference during RT-PCR amplification so as to increase the risk of false-negative diagnoses for COVID-19 infections. Funding Key Research Project of the Higher Education of Henan Province


title: Infoveillance to Analyze Covid19 Impact on Central America Population

text: Infoveillance is an application within the Infodemiology field with the aim of monitoring public health and create public policies. Latin American countries have a different context about economics and health , so Infoveillance can be a useful tool to monitor and improve the decisions and be more strategical during the COVID-19 pandemic . The aim of this paper is to illustrate how data generated through Twitter can be used to help the implementation of strategies to address pandemic emergence in countries with Spanish as a native language in Central America by using a Text Mining Approach with Twitter as a data source in the capital of those countries.


title: COVID-19 detection from chest X-Ray images using Deep Learning and Convolutional Neural Networks

text: The COVID-19 pandemic in 2020 has highlighted the need to pull all available resources towards the mitigation of the devastating effects of such "Black Swan" events. Towards that end, we investigated the option to employ technology in order to assist the diagnosis of patients infected by the virus. As such, several state-of-the-art pre-trained convolutional neural networks were evaluated as of their ability to detect infected patients from chest X-Ray images. A dataset was created as a mix of publicly available X-ray images from patients with confirmed COVID-19 disease, common bacterial pneumonia and healthy individuals. To mitigate the small number of samples, we employed transfer learning, which transfers knowledge extracted by pre-trained models to the model to be trained. The experimental results demonstrate that the classification performance can reach an accuracy of 95% for the best two models.


title: Impact of COVID-19 pandemic on severity of illness and resources required during intensive care in the greater New York City area

text: Objective: Describe the changes in patient population, bed occupancy, severity of illness and ventilator requirements across a large health system in the greater New York City area during the pandemic response in comparison with the 2019 baseline. Design: Observational, descriptive study of ICUs monitored by a tele-ICU system across Northwell Health. Inclusion criteria: All patients admitted to Northwell Health tele-ICUs during 2019 and between March 23, 2020 and April 6, 2020. Exposure: A data extract was developed to collect data every hour for each ICU bed in the Northwell tele-critical care program as a quality reporting initiative to understand ICU capacity and resource utilization. A similar extract was developed for each hour of 2019. Main Outcomes and Measures: Average of any given hour during the pre-COVID-19 and pandemic periods for the following metrics: proportion of beds occupied, proportion of ventilated patients, severity of illness (measured by the ICU Discharge Readiness Score (DRS)), and length of stay (LOS). Results: Hourly analysis of data from 186 ICU beds from 14 ICUs and 9 hospitals were included, representing 10,714 patients in 2019 and 465 patients between March 23 and April 6, 2020. Average hourly occupancy increased from 64% to 78%, while the proportion of patients invasively ventilated increased from 33.9% to 84.2%. Median DRS (severity of illness score) increased from 1.08 (IQR: 0.24-6.98) to 39.38 (IQR: 12.00-71.28). Proportion of patients with Hispanic ethnicity doubled (7.8% to 16.6%; p<0.01) and proportion of female patients decreased from 46.3% to 32.9% (p<0.01). Conclusions and Relevance: In addition to the expected increase in ICU occupancy and ventilator requirements, this large group of ICUs in midst of the COVID-19 epidemic are faced with managing a cohort of ICU patients with a dramatically higher severity of illness than their typical census.


2021 olympic games Tokyo: Safety issues and protection against COVID-19 transmission


title: Dynamics of RT-qPCR SARS-CoV-2 Detection Rates Prior to and After Symptom Onset

text: Effective RT-qPCR testing for SARS-CoV-2 is essential for treatment, surveillance and control of the COVID-19 pandemic. A recent meta-analysis suggested that testing prior to the onset of symptoms is likely to miss the majority of infected individuals. These findings cast severe doubts on the effectiveness of mass screening efforts intended to detect SARS-CoV-2 prior to the onset of symptoms and decrease community transmissions from pre-/asymptomatic individuals. However, alternative analyses and additional data described herein refine these estimates and suggest that many SARS-CoV-2 infections could potentially be detected prior to symptom onset.


title: Persistence of Positive SARS‐CoV‐2 RT‐PCR Test Result for 24 Days in a Hospitalized Asymptomatic Carrier

text: BACKGROUND: Several countries imposed a mandatory 14‐day period of quarantine on individuals arriving from countries considered high‐risk for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. However, it is not clear how long asymptomatic patients infected with SARS‐CoV‐2 can be an asymptomatic carrier. CASE PRESENTATION: We experienced a case of an asymptomatic female patient infected with SARS‐CoV‐2 with abnormal chest CT findings. She did not develop a fever during hospitalized isolation. She remained reverse transcriptase‐polymerase chain reaction (RT‐PCR) positive for 24 days. CONCLUSION: An asymptomatic patient diagnosed with SARS‐CoV‐2 infection remained RT‐PCR positive for 24 days although she was quarantined in an isolation hospital. This finding suggests that an asymptomatic patient diagnosed with SARS‐CoV‐2 infection with abnormal chest CT findings can be an asymptomatic carrier for greater than 3 weeks.


title: Pandemic Impacts on Library Consortia and Their Sustainability

text: Library consortia are planning on how their funding, programs, and services may need to change with the societal tumult caused by the 2020 Covid-19 pandemic. Most consortia in North America are either state agencies or non-profit corporations which may have different approaches and options available for solving substantial budget shortfalls. Changes may need to take place in staffing, programs, and services. Some consortia may have financial portfolios which may help on filling-in budget holes. Other consortia have applied for, and received, funds from the Paycheck Protection Program (PPP) to help with staffing. Many library consortia will not see a quick recovery but may have long-term consequences as their member libraries and parent organizations try to recover.


title: Vir taps Samsung for coronavirus candidate

text: In a deal worth up to $362 million, Vir Biotechnology has tapped Samsung Biologics to provide commercial-scale production of a monoclonal antibody against the novel coronavirus Vir hopes to begin Phase II clinical trials in the next 3–5 months “We are taking proactive steps to reserve large-scale manufacturing capacity to be ready to move quickly with any of our antibody candidates that prove to be clinically safe and effective,” says Vir CEO George Scangos Vir has a similar production deal with WuXi Biologics


title: Is it Just About Physical Health? An Internet-Based Cross-Sectional Study Exploring the Psychological Impacts of COVID-19 Pandemic on University Students in Jordan Using Kessler Psychological Distress Scale

text: Background Since the spread of COVID-19 on a global scale, most of efforts at the local, national, and international levels were directed primarily to mitigate the spread of the disease. However, the psychological impacts of COVID-19 on global mental health were not thoroughly investigated yet, and studies that report the mental health risks of COVID-19 are still scarce. Objectives This study aimed to assess the level of psychological distress among university students in Jordan during the COVID-19 pandemic and the associated national measures. Methods A cross-sectional study was conducted using an online self-administered questionnaire, The survey comprised of questions about (i) sociodemographic information, (ii) the 10-item Kessler Psychological Distress Scale (K10), (iii) coping activities , and (iv) the students most serious concern during the COVID-19 pandemic. Results A total of 381 completed questionnaires were included in the analysis. Female participants slightly predominated the sample (n=199, 52.2%). The respondents aged 18-38 years (mean 22.6 years, SD: 3.16). The total K10 distress scores had a mean of 34.2 (SD:9.4). However, the mean of total K10 distress scores had no significant association with gender (P=0.57). Age was negatively associated with total K10 distress scores (P=0.0013). Concerning severity, most of the respondents were regarded as having severe psychological distress (n=265, 69.5%), and females were found to have a statistically significant higher percentage in mild and severe psychological distress (P= 0.035), (P=0.016); respectively. 209 students (54.9%) reported that they had no motivation for distance learning. There was a statistically significant inverse relationship between severe psychological distress and motivation for distance learning (P<0.0001). The most common coping strategy among students was Spending more time on social media (n=269, 70.6%). Besides, 49 students (12.9%) reported the use of medications to cope with COVID-10 related distress, and 209 students (54.9%) reported distance learning was their most serious concern. Conclusion The COVID-19 control measures resulted in a severe disruption of various human life activities, and this could impact the mental health of individuals, including students. A nationwide psychological support program should be incorporated into Jordan response strategy in combating the COVID-19, considering students and other vulnerable groups in Jordan. Keywords: COVID-19, Jordan, University, Students, Psychological, Pandemic, Impacts, Kessler.


title: Development of a fluorescence based, high-throughput SARS-CoV-2 3CLpro reporter assay

text: In late 2019 a human coronavirus, now known as SARS-CoV-2, emerged, likely from a zoonotic reservoir. This virus causes COVID-19 disease, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CLpro. 3CLpro is an attractive target for antiviral therapeutics as it is essential for processing newly translated viral proteins, and the viral lifecycle cannot be completed without protease activity. In this work, we present a new assay to identify inhibitors of the SARS-CoV-2 main protease, 3CLpro. Our reporter is based on a GFP-derived protein that only fluoresces after cleavage by 3CLpro. This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level-2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread. IMPORTANCE The COVID-19 pandemic has already led to more than 400,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level-2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic.


title: Trust-by-Design: Evaluating Issues and Perceptions within Clinical Passporting

text: A substantial administrative burden is placed on healthcare professionals as they manage and progress through their careers. Identity verification, pre-employment screening and appraisals: the bureaucracy associated with each of these processes takes precious time out of a healthcare professional's day. Time that could have been spent focused on patient care. In the midst of the COVID-19 crisis, it is more important than ever to optimize these professionals' time. This paper presents the synthesis of a design workshop held at the Royal College of Physicians of Edinburgh (RCPE) and subsequent interviews with healthcare professionals. The main research question posed is whether these processes can be re-imagined using digital technologies, specifically Self-Sovereign Identity? A key contribution in the paper is the development of a set of user-led requirements and design principles for identity systems used within healthcare. These are then contrasted with the design principles found in the literature. The results of this study confirm the need and potential of professionalising identity and credential management throughout a healthcare professional's career.


title: Biodefense: Principles and Pathogens Michael S. Bronze

text: Unknown


title: Tracking the spread of novel coronavirus (2019-nCoV) based on big data

text: The novel coronavirus (2019-nCoV) appeared in Wuhan in late 2019 have infected 34,598 people, and killed 723 among them until 8th February 2020. The new virus has spread to at least 316 cities (until 1st February 2020) in China. We used the traffic flow data from Baidu Map, and number of air passengers who left Wuhan from 1st January to 26th January, to quantify the potential infectious people. We developed multiple linear models with local population and air passengers as predicted variables to explain the variance of confirmed cases in every city across China. We found the contribution of air passengers from Wuhan was decreasing gradually, but the effect of local population was increasing, indicating the trend of local transmission. However, the increase of local transmission is slow during the early stage of novel coronavirus, due to the super strict control measures carried out by government agents and communities.


title: Unfractionated heparin potently inhibits the binding of SARS-CoV-2 spike protein to a human cell line

text: The SARS-CoV-2 spike protein is known to bind to the receptor, ACE2, on the surface of target cells. The spike protein is processed by membrane proteases, including TMPRSS2, and is either internalised or fuses directly with the cell, leading to infection. We identified a human cell line that expresses both ACE2 and TMPRSS2, the RT4 urinary bladder transitional carcinoma, and used it to develop a proxy assay for viral interactions with host cells. A tagged recombinant form of the spike protein, containing both the S1 and S2 domains, binds strongly to RT4 cells as determined by flow cytometry. Binding is temperature dependent and increases sharply at 37°C, suggesting that processing of the spike protein is likely to be important in the interaction. As the spike protein has previously been shown to bind heparin, a soluble glycosaminoglycan, we used a flow cytometry assay to determine the effect of heparin on spike protein binding to RT4 cells. Unfractionated heparin inhibited spike protein binding with an IC50 value of <0.05U/ml whereas two low molecular weight heparins were much less effective. This suggests that heparin, particularly unfractionated forms, could be considered to reduce clinical manifestations of COVID-19 by inhibiting continuing viral infection. Despite the sensitivity to heparin, we found no evidence that host cell glycosaminoglycans such as heparan and chondroitin sulphates play a major role in spike protein attachment.


title: Severe acute respiratory syndrome-coronavirus 2 and novel coronavirus disease 2019: An extraordinary pandemic

text: COVID-19 has emerged as one of the most significant illnesses of the current century. It is caused by severe acute respiratory syndrome coronavirus 2. The world was initially viewing it as a localized outbreak in Wuhan city of China; however, it started spreading quickly to other parts of the world. Globally, half-hearted containment measures and a false sense of safety against this novel coronavirus led to the dissemination of disease. Currently, no effective therapy or vaccine is available to manage this illness. After learning a huge lesson, global efforts would hopefully lead to effective control of this pandemic.


title: Characteristics of scientific articles on COVID-19 published during the initial three months of the pandemic: a meta-epidemiological study

text: Importance: The COVID-19 pandemic has been characterized by an unprecedented amount of published scientific articles. Objective: To assess the characteristics of articles published during the first 3 months of the COVID-19 pandemic and to compare it with articles published during 2009 H1N1 swine influenza pandemic. Data sources: Articles on COVID-19 and on H1N1 swine influenza indexed in PubMed (Medline) during the first 3 months of these pandemics. Study selection: Any article published in the respective study periods that included any terminology related to COVID-19 or H1N1 in the title, abstract or full-text was eligible for inclusion. Articles that did not present an English abstract, as well as correspondence to previous research and erratum were excluded. Data Extraction and Synthesis: Two operators conducted the selection of articles and data extraction procedures independently. The article is reported following STROBE guidelines for observational studies. Main Outcomes and Measures: Prevalence of primary and secondary articles. Prevalence of reporting of limitations in the abstracts. Results: Of the 2482 articles retrieved, 1165 were included. Approximately half of them were secondary articles (575, 49.4%). Common primary articles were: human medical research (340, 59.1%), in silico studies (182, 31.7%) and in vitro studies (26, 4.5%). Of the human medical research, the vast majority were observational studies and cases series, followed by single case reports and one randomized controlled trial. Secondary articles were mainly reviews, viewpoints and editorials (373, 63.2%). The second largest category was guidelines or guidance articles, including 193 articles (32.7%), of which 169 were indications for specific departments, patients or procedures. Limitations were reported in 42 out of 1165 abstracts (3.6%), with 10 abstracts reporting actual methodological limitations. In a similar timeframe in 2009 there were 223 articles published on the H1N1 pandemic. As compared to that pandemic, during COVID-19 there were higher chances to publish reviews and guidance articles and lower chances to publish in vitro and animal research studies. Conclusions and Relevance: As compared to the most recent pandemic, there is an overwhelming amount of information published on COVID-19. However, the majority of the articles published do not add significant information, possibly diluting the original information published. Also, only a negligible number of published articles reports limitations in the abstracts, hindering a rapid interpretation of their shortcomings.


title: COVID-19 related mortality and spread of disease in long-term care: first findings from a living systematic review of emerging evidence

text: Background: Policy responses to mitigate the impact of the COVID-19 pandemic on long-term care (LTC) require robust and timely evidence on mortality and spread of the disease in these settings. The aim of this living systematic review is to synthesise early international evidence on mortality rates and incidence of COVID-19 among people who use and provide LTC. Methods: We report the initial findings of a living systematic review (CRD42020183557), including studies identified through database searches up to 29 May 2020. We searched seven databases (MEDLINE; Embase; CINAHL Plus; Web of Science; Global Health; WHO COVID-19 Research Database; medRxiv) to identify all studies reporting primary data on COVID-19 related mortality and incidence of disease among LTC users and staff. We excluded studies not focusing on LTC. Included primary studies were critically appraised and results on number of deaths and COVID-19 related mortality rates, case fatality rates, and excess deaths (co-primary outcomes), as well as incidence of disease, hospitalisations, and ICU admissions were synthesised narratively. We further included official figures on number of deaths in LTC. Findings: A total of 30 study reports for 27 unique primary studies or outbreak reports were included. Outbreak investigations in LTC facilities found COVID-19 incidence rates of between 0.0% and 71.7% among residents and between 1.5% and 64.0% among staff. Mortality rates varied from 0.0% to 9.9% of all residents at outbreak facilities, with case fatality rates between 0.0% and 33.7%. In included studies, no LTC staff members had died. LTC residents accounted for between 0% (Hong Kong) and 82% (Canada) of COVID-related deaths, according to official figures. Interpretation: Long-term care users have been particularly vulnerable to the COVID-19 pandemic. However, we found wide variation in spread of disease and mortality rates between outbreaks at individual LTC facilities. Further research into the factors determining successful prevention and containment of COVID-19 outbreaks is needed to protect long-term care users and staff.


docid: sxsrzdac

title: Occupational dermatology in times of COVID-19: What needs to be done now and after the crisis/ Berufsdermatologie in Zeiten von COVID-19: Was jetzt und nach der Krise zu tun ist


title: Strong Correlation Between Prevalence of Severe Vitamin D Deficiency and Population Mortality Rate from COVID-19 in Europe

text: Background: SARS-CoV-2 virus causes a very wide range of COVID-19 disease severity in humans: from completely asymptomatic to fatal, and the reasons behind it are often not understood. There is some data that Vitamin D may have protective effect, so authors decided to analyze European country-wide data to determine if Vitamin D levels are associated with COVID-19 population death rate. Methods: To retrieve the Vitamin D levels data, authors analyzed the Vitamin D European population data compiled by 2019 ECTS Statement on Vitamin D Status published in the European Journal of Endocrinology. For the data set to used for analysis, only recently published data, that included general adult population of both genders ages 40-65 or wider, and must have included the prevalence of Vitamin D deficiency. Results: There were 10 countries data sets that fit the criteria and were analyzed. Severe Vitamin D deficiency was defined as 25(OH)D less than 25 nmol/L (10 ng/dL). Pearson correlation analysis between death rate per million from COVID-19 and prevalence of severe Vitamin D deficiency shows a strong correlation with r = 0.76, p = 0.01, indicating significant correlation. Correlation remained significant, even after adjusting for age structure of the population. Additionally, over time, correlation strengthened, and r coefficient asymptoticaly increased. Conclusions: Authors recommend universal screening for Vitamin D deficiency, and further investigation of Vitamin D supplementation in randomized control studies, which may lead to possible treatment or prevention of COVID-19.


title: Diaper need is associated with risk for food insecurity in a statewide sample of WIC participants

text: Diaper need is a form of material hardship that acutely affects families with young children, is not currently addressed by US antipoverty programs, and has received little public or scientific attention. This study examined the association between diaper need and risk for food insecurity in a statewide sample of participants in the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC). Families enrolled in Vermont WIC in August 2019 were invited to an online survey. Generalized linear models were used to estimate the relationship between risk for food insecurity measured by the Hunger Vital Sign tool and diaper need, with and without adjustment for household factors. Follow-up questions asked those with diaper need what they do when they run out of diapers and those without diaper need how they access enough diapers. Complete data were available for 501 households. Over half (52.3%) were at risk for food insecurity and nearly one-third (32.5%) reported diaper need. The odds of experiencing risk for food insecurity were 3.852 (95% CI=2.557, 5.803) times greater for families with diaper need than for families that had enough diapers. The association persisted with adjustment for location, age of respondent, number of children in diapers, and length of time participating in WIC (adjusted OR=4.036, 95% CI=2.645, 6.160). Strategies to avoid running out of diapers included borrowing, stretching supplies, switching to cloth or underwear, and buying on credit. It is possible that public health interventions that address diaper need may reduce food insecurity in households with children.


title: A Coronavirus Disease 2019 (COVID-19) Patient with Multifocal Pneumonia Treated with Hydroxychloroquine

text: After an outbreak in December 2019 in Wuhan, Hubei Province of China, coronavirus disease 2019 (COVID-19) has rapidly become a pandemic. The 2019 novel coronavirus (2019 nCov), now called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes a wide spectrum of illness and patients with underlying comorbidities have a high mortality. Here we present a 49-year-old male patient with comorbid conditions who presented with fever, cough, myalgia and shortness of breath for five days with likely exposure to a COVID-19 contact. A computed tomography scan of the thorax revealed multifocal bilateral ground-glass lung opacities with areas of subpleural sparing. He tested positive for SARS-CoV-2 by nucleic acid amplification. Hydroxychloroquine therapy was started, and the patient responded favorably with improvement of symptoms. Early diagnosis and self-isolation or quarantine remain key to stemming the tide of the contagion as there is a real risk of the healthcare system being overwhelmed.


title: Kinetics of the humoral immune response to SARS-CoV-2: comparative analytical performance of seven commercial serology tests

text: Background SARS-CoV-2 serology tests are clinically useful to document a prior SARS-CoV-2 infection in patients with no or inconclusive PCR results and suspected COVID-19 disease or sequelae. Data are urgently needed to select the assays with optimal sensitivity at acceptable specificity. Methods A comparative analysis of analytical sensitivity was performed of seven commercial SARS-CoV-2 serology assays on 171 sera from 135 subjects with PCR-confirmed SARS-CoV-2 infection, composed of 71 patients hospitalized for COVID-19 pneumonia and 64 healthcare workers with paucisymptomatic infections. The kinetics of IgA/IgM/IgG seroconversion to viral N- and S-protein epitopes were studied from 0 to 54 days after symptom onset. Specificity was verified on 57 pre-pandemic samples. Results Wantai SARS-COV-2 Ab ELISA and Orient Gene COVID-19 IgG/IgM Rapid Test achieved a superior overall sensitivity. Elecsys Anti-SARS-CoV-2 assay, EUROIMMUN Anti-SARS-CoV-2 combined IgG/IgA and EUROIMMUN Anti-SARS-CoV-2-NCP(IgG) also showed acceptable sensitivity (>95%) versus the consensus result of all assays from 10 days post symptom onset. Optimal specificity (>98%) was achieved only by Wantai SARS-COV-2 Ab ELISA, Elecsys Anti-SARS-CoV-2 assay and Innovita 2019-nCoV Ab rapid test. LIAISON SARS-CoV-2 S1/S2 IgG showed a significantly lower sensitivity as compared to all other assays. Lack of seroconversion by any test was seen in 1.4% of hospitalized and 4.7% of paucisymptomatic infections. Within 10 days from symptom onset, only the Wantai SARS-COV-2 Ab ELISA has acceptable sensitivity. Conclusions Wantai SARS-COV-2 Ab ELISA and Elecsys Anti-SARS-CoV-2 assays are suitable for sensitive and specific screening of a SARS-CoV-2 infection from 10 days after symptom onset.


title: Distinct Inductions of and Responses to Type I and Type III Interferons Promote Infections in Two SARS-CoV-2 Isolates

text: The recent emerging coronavirus, SARS-CoV-2, has been rapidly and widely spread and causing an ongoing viral pneumonia outbreak worldwide. It has been observed that SARS-CoV-2 patients show a rather long and asymptomatic incubation time. We characterized the abilities to induce and to response to IFNβ/IFNλ1 of two or our clinical isolates, SARS-CoV-2/NTU01/TWN/human/2020 and SARS-CoV-2/NTU02/TWN/human/2020, which exhibit only two amino acid differences over the ∼30kb viral genome. We found that both isolates may infect Huh7, A549 and Calu-3 cells, yet the RIG-I-like receptor-dependent antiviral signaling was poorly induced in these cells in the early infections. Unexpectedly, we found that the intracellular vRNA levels of these isolates were sustained upon to type I/III IFN treatments, and this phenotype was more pronounced in the Taiwan/NTU01/2020 isolate. The type I/III IFN responses are antiviral but partially proviral in the case of SARS-CoV-2 infections. Poor induction and response to innate immunity may contribute to destitute neutralization index of the antibody produced, and indeed we found that the patient serum could not efficiently neutralize SARS-CoV-2 virions. With better understandings of the interplay between SARS-CoV-2 and the host antiviral innate immunity, our report may provide new insights for the regimen of therapies for SARS-CoV-2 infected patients.


title: Ethnics and economics in COVID-19: Meta-regression of data from countries in the New York metropolitan area

text: Ethnics and economics may affect prevalence and case fatality of Coronavirus disease 2019 (COVID-19). To determine whether COVID-19 prevalence and fatality are modulated by ethnics and economics, meta-regression of data from the countries in the New York metropolitan area were herein conducted. We selected 31 countries in the New York metropolitan area. 1) Prevalence and case-fatality rates of confirmed COVID-19 cases on May 20, 2020 and 2) income and poverty estimates were obtained in each country. We performed random-effects meta-regression using OpenMetaAnalys. The covariates included 1) black (%), 2) Hispanic or Latino (%), 3) poverty rates (%), and 4) median household income ($). Statistically significant (P < .05) covariates in the univariable model were together entered into the multivariable model. A slope (coefficient) of the univariable meta-regression line for COVID-19 prevalence was not significant for household income (P = .639), whereas the coefficient was significantly positive for black (coefficient, 0.021; P = .015), Hispanic/Latino (0.033; P < .001), and poverty (0.039; P = .02), which indicated that COVID-19 prevalence increased significantly as black, Hispanic/Latino, and poverty increased. The multivariable model revealed that the slope was significantly positive for only Hispanic/Latino (P < .001). The coefficient in the univariable model for COVID-19 fatality, however, was not significant for all the covariate. In conclusion, black, Hispanic/Latino, and poverty (not household income), especially Hispanic/Latino independently, may be associated with COVID-19 prevalence. There may be no association of black, Hispanic/Latino, poverty, and household income with COVID-19 fatality.


title: Transmission routes of Covid-19 virus in the Diamond Princess Cruise ship

text: Background: An outbreak of COVID-19 occurred on the Diamond Princess cruise ship in January and February 2020. We analysed information about cases to infer transmission dynamics and potential modes of transmission. Methods: We collected the daily number of 197 symptomatic cases, and that of the 146 passenger cases in two categories, i.e. those who stayed and did not stay in the same stateroom. We retrieved the quarantine details and the ship's 14-day itinerary. We searched the websites of national/local health authority along the cruise routes and local news using Google for locally confirmed cases associated with the ship. We obtained the design of air conditioning and sewage treatment of the ship from literature. We back-calculated the dates of infection from the epidemic curve and compared with the start of on-board quarantine. Results: Major infections started on Jan 28 and completed by Feb 6 for passengers except those who stayed in the same stateroom with infected individual(s). No other confirmed cases were identified among the disembarked people in Hong Kong except an 80 years old passenger. No confirmed cases were reported in three other stopovers between Jan 27-31 associated with disembarked passengers or visitors from the ship, however two Okinawa taxi drivers became confirmed cases in association with driving the ship passengers. Infection among passengers after Feb 6 was limited to those who stayed in the same stateroom with an infected passenger. Infections in crew members peaked on Feb 7, suggesting significant transmission among crew members after quarantine on Feb 5. Conclusions: We infer that the ship central air conditioning system did not play a role, i.e. the long-range airborne route was absent in the outbreak. Most transmission appears to have occurred through close contact and fomites.


title: VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data

text: The possibility that RNA transcripts from clinical samples contain plenty of virus RNAs has not been pursued actively so far. We here developed a new tool for analyzing virus-transcribed mRNAs, not virus copy numbers, in the data of conventional and single-cell RNA-sequencing of human cells. Our pipeline, named VIRTUS (VIRal Transcript Usage Sensor), was able to detect 763 viruses including herpesviruses, retroviruses, and even SARS-CoV-2 (COVID-19), and quantify their transcripts in the sequence data. This tool thus enabled simultaneously detecting infected cells, the composition of multiple viruses within the cell, and the endogenous host gene expression profile of the cell. This bioinformatics method would be instrumental in addressing the possible effects of covertly infecting viruses on certain diseases and developing new treatments to target such viruses. Availability and implementation VIRTUS is implemented using Common Workflow Language and Docker under a CC-NC license. VIRTUS is freely available at https://github.com/yyoshiaki/VIRTUS. Supplementary information Supplementary data are available at Bioinformatics online.


Adipositas begünstigt einen schweren COVID-19-Verlauf


title: Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients

text: Coronavirus disease 2019 (COVID-19) has caused over 220,000 deaths so far and is still an ongoing global health problem. However, the immunopathological changes of key types of immune cells during and after virus infection remain unclear. Here, we enriched CD3+ and CD19+ lymphocytes from peripheral blood mononuclear cells of COVID-19 patients (severe patients and recovered patients at early or late stages) and healthy people (SARS-CoV-2 negative) and revealed transcriptional profiles and changes in these lymphocytes by comprehensive single-cell transcriptome and V(D)J recombination analyses. We found that although the T lymphocytes were decreased in the blood of patients with virus infection, the remaining T cells still highly expressed inflammatory genes and persisted for a while after recovery in patients. We also observed the potential transition from effector CD8 T cells to central memory T cells in recovered patients at the late stage. Among B lymphocytes, we analyzed the expansion trajectory of a subtype of plasma cells in severe COVID-19 patients and traced the source as atypical memory B cells (AMBCs). Additional BCR and TCR analyses revealed a high level of clonal expansion in patients with severe COVID-19, especially of B lymphocytes, and the clonally expanded B cells highly expressed genes related to inflammatory responses and lymphocyte activation. V-J gene usage and clonal types of higher frequency in COVID-19 patients were also summarized. Taken together, our results provide crucial insights into the immune response against patients with severe COVID-19 and recovered patients and valuable information for the development of vaccines and therapeutic strategies.


title: Clinical Features and Predictors for Patients with Severe SARS-CoV-2 Pneumonia: a retrospective multicenter cohort study

text: Objectives: This study was performed to investigate clinical features of patients with severe SARS-CoV-2 pneumonia and identify risk factors for converting to severe cases in those who had mild to moderate diseases. Methods: In this retrospective, multicenter cohort study, patients with mild to moderate SARS-CoV-2 pneumonia were included. Demographic data, symptoms, laboratory values, and clinical outcomes were collected. Data were compared between non-severe and severe patients. Results: 58 patients were included in the final analysis. Compared with non-severe cases, severe patients with SARS-CoV-2 pneumonia had a longer: time to clinical recovery (p=0.0011), duration of viral shedding (p=0.0183), and hospital stay ( p=0.0211). Multivariate logistic regression indicated that lymphocyte count was significantly associated with the rate of converting to severe cases (odds ratio 1.28, 95%CI 1.06-1.54, per 0.1*10 9/L reduced; p=0.007), while using of low-to-moderate doses of systematic corticosteroids was associated with reduced likelihood of converting to a severe case (odds ratio 0.14, 95%CI 0.02-0.80; p=0.0275). Conclusions: The low peripheral blood lymphocyte count was an independent risk factor for SARS-CoV-2 pneumonia patients converting to severe cases. This finding may help clinicians more accurately predict prognosis, and triage priorities to improve clinical outcomes.


title: Pediatric COVID-19 in Southern California: clinical features and viral genetic diversity

text: Clinical presentation of COVID-19 in children remains under investigation. In this manuscript, we present a summary of clinical findings from the first 23 cases of COVID-19 in children at Children's Hospital Los Angeles. Considering the paucity of genomics data for circulating SARS-CoV-2 isolates in Southern California, we also present an overview of the viral genetic diversity in isolates obtained from these patients and compare them to isolates from other parts of the United States and globally. Our study presents much needed clinical and viral genomics data pertaining to COVID-19 in children.


title: Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses

text: The ongoing novel coronavirus pneumonia COVID-19 outbreak in Wuhan, China, has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Combining the advantages of target amplification and long-read, real-time nanopore sequencing, we developed nanopore target sequencing (NTS) to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. NTS is thus suitable for contemporary COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses or pathogens.


title: Fetal tissue ban blocks study of potential coronavirus therapies

text: The Trump administration’s 2019 ban on the use of human fetal tissue by scientists at the National Institutes of Health (NIH) is preventing a leading researcher from using special mice to test potential therapies for coronavirus disease 2019 (COVID-19), The Washington Post reports According to the Post, Kim Hasenkrug, an immunologist at NIH’s Rocky Mountain Laboratories, has spent nearly 1 month appealing to the Trump administration to grant him an exemption to the administration’s strict policy Federal restrictions imposed in June 2019 ban NIH scientists from using human fetal tissue donated after elective abortions


title: Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France.

text: An indirect immunofluorescent assay was developed in order to assess the serological status of 888 RT-PCR-confirmed COVID-19 patients (1,302 serum samples) and controls in Marseille, France. Incorporating an inactivated clinical SARS CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre [≥] 1:200; 98.6% for IgM titre [≥] 1:200; and 96.3% for IgG titre [≥] 1:100 after testing a series of negative controls as well as 150 serums collected from patients with non-SARS-CoV-2 Coronavirus infection, non-Coronavirus pneumonia and infections known to elicit false-positive serology. Seroprevalence was then measured at 3% before a five-day evolution up to 47% after more than 15 days of evolution. We observed that the seroprevalence as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that serotherapy may not be a therapeutic option in patients with severe COVID-19 infection. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels.


title: Chronic treatment with hydroxychloroquine and SARS-CoV-2 infection.

text: Background: Hydroxychloroquine sulphate (HCQ) is being scrutinized for repositioning in the treatment and prevention of SARS-Cov-2 infection. This antimalarial drug is also chronically used to treat patients with autoimmune diseases. Methods: By analyzing the Portuguese anonymized data on private and public based medical prescriptions we have identified all cases chronically receiving HCQ for the management of diseases such as systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. Additionally, we have detected all laboratory confirmed cases of SARS-CoV-2 infection and all laboratory confirmed negative cases in the Portuguese population (mandatorily registered in a centrally managed database). Cross linking the two sets of data has allowed us to compare the proportion of HCQ chronic treatment (at least 2 grams per month) in laboratory confirmed cases of SARS-CoV-2 infection with laboratory confirmed negative cases. Results: Out of 26,815 SARS-CoV-2 positive patients, 77 (0.29%) were chronically treated with HCQ, while 1,215 (0.36%) out of 333,489 negative patients were receiving it chronically (P=0.04). After adjustment for age, sex, and chronic treatment with corticosteroids and/or immunosuppressants, the odds ratio of SARS-CoV-2 infection for chronic treatment with HCQ has been 0.51 (0.37-0.70). Conclusions: Our data suggest that chronic treatment with HCQ confer protection against SARS-CoV-2 infection.


title: Early transmission dynamics of COVID-19 in Chile: From sub-exponential ascending growth dynamics to a stationary disease wave, March-April, 2020

text: The COVID-19 pandemic reached Latin America in February 2020, with the first case in Chile identified on March 3rd, 2020. Since then Chile has accumulated a total of 14365 cases as of April 28th, 2020. We estimate the reproduction number during the early transmission phase in Chile and study the effectiveness of control interventions by conducting short-term forecasts based on early transmission dynamics of COVID-19. The incidence curve displays sub-exponential growth dynamics with the scaling of growth parameter, p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number estimated at 1.6 (95% CI: 1.5, 1.6). The sub-epidemic model indicates a stationary wave of stable epidemic size. Our current findings point to sustained transmission of SARS-CoV-2 in Chile. While the social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing efforts to control the epidemic.


title: Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats

text: Objective Patients with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibit not only respiratory symptoms but also symptoms of chemo-sensitive disorders and kidney failure. Cellular entry of SARS-CoV-2 depends on the binding of its spike protein to a cellular receptor named angiotensin-converting enzyme 2 (ACE2), and the subsequent spike protein-priming by host cell proteases, including transmembrane protease serine 2 (TMPRSS2). Thus, high expression of ACE2 and TMPRSS2 are considered to enhance the invading capacity of SARS-CoV-2. Methods To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry. Results Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. These results coincide with the reported clinical symptoms of COVID-19, such as the loss of taste, loss of olfaction, respiratory dysfunction, and acute nephropathy. Conclusions A wide range of organs have been speculated to be affected by SARS-CoV-2 depending on the expression levels of ACE2 and TMPRSS2. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. This study might provide potential clues for further investigation of the pathogenesis of COVID-19. Level of Evidence NA


title: Epidemiological model for the inhomogeneous spatial spreading of COVID-19 and other diseases

text: We suggest a mathematical model for the spread of an infectious disease in human population, with particular attention to the COVID-19. Common epidemiological models, e.g., the well-known susceptible-exposed-infectious-recovered (SEIR) model, implicitly assume fast mixing of the population relative to the local infection rate, similar to the regime applicable to many chemical reactions. However, in human populations, especially under different levels of quarantine conditions, this assumption is likely to fail. We develop a continuous spatial model that includes five different populations, in which the infectious population is split into latent (or pre-symptomatic) and symptomatic. Based on nearest-neighbor infection kinetics, we arrive into a ``reaction-diffusion'' model. Our model accounts for front propagation of the infectious population domains under partial quarantine conditions, which is present on top of the common local infection process. Importantly, we also account for the variable geographic density of the population, that can strongly enhance or suppress infection spreading. Our results demonstrate how infected domains spread outward from epicenters/hotspots, leading to different regimes of sub-exponential (quasi linear or power-law) growth. Moreover, we show how weakly infected regions surrounding a densely populated area can cause rapid migration of the infection towards the center of the populated area. Predicted heat-maps show remarkable similarity to recently media released heat-maps. We further demonstrate how localized strong quarantine conditions can prevent the spreading of the disease from an epicenter/hotspot, significantly reducing the number of infected people. Application of our model in different countries, using actual demographic data and infectious disease parameters, can provide a useful predictive tool for the authorities, in particular, for planning strong lockdown measures in localizes areas.


docid: zvsiltsn

title: COVID-19 restrictions and increased risk of overdose for street-based people with opioid dependence in South Africa


title: Psychological impact of infectious disease outbreaks on pregnant women: Rapid evidence review

text: Infectious disease outbreaks can be distressing for everyone, especially so for those deemed to be particularly vulnerable, such as pregnant women who have been named a high-risk group in the current COVID-19 pandemic. This rapid review aimed to summarise existing literature on the psychological impact of infectious disease outbreaks on women who were pregnant at the time of the outbreak. In April 2020 five databases were searched for relevant literature and main findings were extracted. Thirteen papers were included in the review. The following themes were identified: negative emotional states; living with uncertainty; concerns about infection; concerns about and uptake of prophylaxis or treatment; disrupted routines; non-pharmaceutical protective behaviours; social support; demands from others; financial and occupational concerns; disrupted expectations of birth, prenatal care and postnatal care, and; sources of information. Results showed that pregnant women have unique needs during infectious disease outbreaks and could benefit from: up-to-date, consistent information and guidance; appropriate support and advice from healthcare professionals, particularly with regards to the risks and benefits of prophylaxis and treatment; virtual support groups, and; designating locations or staff specifically for pregnant women.


title: A simple model to fit the time evolution of the daily death rate of Covid-19 in European Union countries

text: We suggest a minimal model to describe the evolution of daily deaths due to Covid-19 in the European Union (EU) and UK, without any epidemiological hypothesis. Assuming current lockdown conditions were to remain in place, as of May 3rd 2020, this ad hoc fitting model is forecasting a total of 204,586 deaths in the EU. We could currently be at 2/3 of the total casualty count, and reach an overall death rate of one over 2500 people.


title: Death, Demography and the Denominator:New Influenza-18 Mortality Estimates for Ireland

text: Using the Irish experience of the Spanish flu, we demonstrate that pandemic mortality statistics are sensitive to the demographic composition of a country. We build a new demographic database for Ireland's 32 counties with vital statistics on births, ageing, migration and deaths. We then show how age-at-death statistics in 1918 and 1919 should be reinterpreted in light of these data. Our new estimates suggest the very young were most impacted by the flu. New studies of the economic impact of Influenza-18 must better control for demographic factors if they are to yield useful policy-relevant results. Covid-19 mortality statistics must go through a similar procedure so policymakers can better target their public health interventions.


title: Strategies of RT-PCR-based assay design and surveillance of SARS-CoV-2/ СТРАТЕГИИ ДИЗАЙНА РТ-ПЦР-СИСТЕМ И ОРГАНИЗАЦИЯ МОНИТОРИНГА SARS-COV-2

text: High population density in the cities with bustling transportation systems and a thriving tourism industry can promote the global spread of a viral infection in a matter of days. The novel SARS-CoV-2 coronavirus has already infected over 2,000,000 people worldwide and caused upwards of 156,000 deaths. One of the factors driving the rapid unfolding of the pandemic is the absence of diagnostic tests for SARS-CoV-2 detection. Molecular techniques allow SARS-CoV-2 RNA to be quickly detected in clinical samples, aiding the differential diagnosis in severely ill patients and facilitating identification of asymptomatic carriers or presymptomatic individuals. Real-time PCR with fluorescent hybridization is the most available, highly sensitive and specific technique for SARS-CoV-2 RNA detection in biological samples. More RT-PCR assay kits are needed for mass screening, which will help to identify infected individuals and contain the current outbreak of COVID-19 in Russia.


title: Decontamination of face masks and filtering facepiece respirators via ultraviolet germicidal irradiation, hydrogen peroxide vaporisation, and use of dry heat inactivates an infectious SARS-CoV-2 surrogate virus.

text: Background: In the context of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the supply of personal protective equipment remains under severe strain. To address this issue, re-use of surgical face masks and filtering facepiece respirators has been recommended; prior decontamination is paramount to their re-use. Aim: We aim to provide information on the effects of three decontamination procedures on porcine respiratory coronavirus (PRCV)-contaminated masks and respirators, presenting a stable model for infectious coronavirus decontamination of these typically single-use-only products. Methods: Surgical masks and filtering facepiece respirator coupons and straps were inoculated with infectious PRCV and submitted to three decontamination treatments, UV irradiation, H2O2 vaporisation, and dry heat treatment. Viruses were recovered from sample materials and viral titres were measured in swine testicle cells. Findings: UV irradiation, H2O2 vaporisation and dry heat reduced infectious PRCV by more than three orders of magnitude on mask and respirator coupons and rendered it undetectable in all decontamination assays. Conclusion: This is the first description of stable disinfection of face masks and filtering facepiece respirators contaminated with an infectious SARS-CoV-2 surrogate using UV irradiation, H2O2 vaporisation and dry heat treatment. The three methods permit demonstration of a loss of infectivity by more than three orders of magnitude of an infectious coronavirus in line with the FDA policy regarding face masks and respirators. It presents advantages of uncomplicated manipulation and utilisation in a BSL2 facility, therefore being easily adaptable to other respirator and mask types.


title: Prioritization of Proton Patients in the COVID-19 Pandemic: Recommendations from The New York Proton Center

text: It has been well documented from the early days of the 2019 novel coronavirus (COVID-19) pandemic that patients with a diagnosis of cancer are not only at higher risks of contracting a COVID-19 infection but also at higher risks of suffering severe, and possibly fatal, outcomes from the infection. Given that the United States has the greatest number of positive coronavirus cases, it is likely that many, if not all, radiation oncology clinics will be faced with the challenge of safely balancing a patient's risk of contracting COVID-19, while under active radiation treatment, against their risk of cancer progression if treatment is delayed. To address this challenge, the New York Proton Center established an internal algorithm that considers treatment-related, tumor-related, and patient-related characteristics. Despite having suffered staff shortages due to illness, this algorithm has allowed the center to maintain patient treatment volumes while keeping the rate of COVID-19 infection low.


title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019

text: This review will briefly examine the clinical presentation and important immunology of viral pneumonia with a focus on severe acute respiratory syndrome coronavirus 2 (coronavirus disease 2019). DATA SOURCES, STUDY SELECTION, DATA EXTRACTION, AND DATA SYNTHESIS: The most relevant, original and review literature were assessed for inclusion in this review. Sources included the Centers for Disease Control and Prevention, World Health Organization, and PubMed. CONCLUSIONS: Pneumonia is a leading cause of hospitalization and death worldwide, with viral etiologies being very common. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Symptoms of viral pneumonia include common respiratory tract infection symptoms of cough, fever, and shortness of breath. Immunologic changes include up-regulation of airway pro-inflammatory cytokines and pathogen- and damage-associated molecular patterns contributing to cytokine and genomic changes. Coronavirus disease 2019 clinical presentation is typical of viral pneumonia with an increased prevalence of early pulmonary infiltrates and lymphopenia. Principles of early coronavirus disease 2019 management and isolation as well as potential therapeutic approaches to the emerging pandemic are discussed.


title: National and state wise estimate of time varying reproduction number for COVID-19 in India during the nationwide lockdown.

text: To understand the effect of nationwide lockdown on transmissibilty of SARS-CoV-2 in India, time varying reproduction number during the first weeks of April, 2020 was estimated. The time varying reproduction number was estimated using EpiEstim package in R programming language. The reproduction number has come down significantly during the lockdown period both at national level and in most states but it was not reduced to less than 1. This calls for urgent need for more effective control measures in addition to lockdown to stop the epidemic spread of the virus.


title: Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals

text: Objectives: We aimed to identify key demographic risk factors for hospital attendance with COVID-19 infection. Design: Community survey Setting: The COVID Symptom Tracker mobile application co-developed by physicians and scientists at Kings College London, Massachusetts General Hospital, Boston and Zoe Global Limited was launched in the UK and US on 24th and 29th March 2020 respectively. It captured self-reported information related to COVID-19 symptoms and testing. Participants: 2,618,948 users of the COVID Symptom Tracker App. UK (95.7%) and US (4.3%) population. Data cut-off for this analysis was 21st April 2020. Main outcome measures: Visit to hospital and for those who attended hospital, the need for respiratory support in three subgroups (i) self-reported COVID-19 infection with classical symptoms (SR-COVID-19), (ii) self-reported positive COVID-19 test results (T-COVID-19), and (iii) imputed/predicted COVID-19 infection based on symptomatology (I-COVID-19). Multivariate logistic regressions for each outcome and each subgroup were adjusted for age and gender, with sensitivity analyses adjusted for comorbidities. Classical symptoms were defined as high fever and persistent cough for several days. Results: Older age and all comorbidities tested were found to be associated with increased odds of requiring hospital care for COVID-19. Obesity (BMI >30) predicted hospital care in all models, with odds ratios (OR) varying from 1.20 [1.11; 1.31] to 1.40 [1.23; 1.60] across population groups. Pre-existing lung disease and diabetes were consistently found to be associated with hospital visit with a maximum OR of 1.79 [1.64,1.95] and 1.72 [1.27; 2.31]) respectively. Findings were similar when assessing the need for respiratory support, for which age and male gender played an additional role. Conclusions: Being older, obese, diabetic or suffering from pre-existing lung, heart or renal disease placed participants at increased risk of visiting hospital with COVID-19. It is of utmost importance for governments and the scientific and medical communities to work together to find evidence-based means of protecting those deemed most vulnerable from COVID-19. Trial registration: The App Ethics have been approved by KCL ethics Committee REMAS ID 18210, review reference LRS-19/20-18210


title: SARS-CoV-2 qRT-PCR Ct value distribution in Japan and possible utility of rapid antigen testing kit

text: The exact pathology of COVID-19 remains mostly unclear, and accurate epidemiological understanding and rapid testing are crucial to overcome this disease. Several types of nucleic acid tests (NAT) have been used in Japan, but information about the viral RNA load, determined by Ct values, of the patients is limited due to the small number of patients tested in each clinical institution and lack of standardization of the testing kits. We have been performing the qRT-PCR tests established by NIID, and the mean Ct value distribution of 62 cases, which are deemed (first-visit) patients, among the total of 88 positive cases tested in a 4-day window of early April, was 24.9 with SD=5.45. Recently approved antigen testing kits were also used in the same samples (62 positives) along with 100 negative cases, and it revealed the positive predictive value of 80.6% and negative predictive value of 100%, with an overall agreement rate of 92.6%. These results indicate that a certain number of patients with lower Ct values, existed in Japan when SARS-CoV-2 virus started to spread. The newly approved rapid antigen testing kit will be a useful tool to identify such populations rapidly.


title: AI334 and AQ806 antibodies recognize the spike S protein from SARS-CoV-2 by ELISA

text: We tested 10 recombinant antibodies directed against the spike S protein from SARS-CoV-1. Among them, antibodies AI334 and AQ806 detect by ELISA the spike S protein from SARS-CoV-2.


title: A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys

text: Coronavirus infection spreads in clusters and therefore early identification of these clusters is critical for slowing down the spread of the virus. Here, we propose that daily population-wide surveys that assess the development of symptoms caused by the virus could serve as a strategic and valuable tool for identifying such clusters to inform epidemiologists, public health officials, and policy makers. We show preliminary results from a survey of over 38,000 Israelis and call for an international consortium to extend this concept in order to develop predictive models. We expect such data to allow: Faster detection of spreading zones and patients; Obtaining a current snapshot of the number of people in each area who have developed symptoms; Predicting future spreading zones several days before an outbreak occurs; Evaluating the effectiveness of the various social distancing measures taken, and their contribution to reduce the number of symptomatic people. Such information can provide a valuable tool for decision makers to decide which areas need strengthening of social distancing measures and which areas can be relieved. Researchers from the U.S, Spain, and Italy have adopted our approach and we are collaborating to further improve it. We call with urgency for other countries to join this international consortium, and to share methods and data collected from these daily, simple, one-minute surveys.


title: Prevalence of SARS-CoV-2 Antibodies Among Healthcare Workers at a Tertiary Academic Hospital in New York City

text: Background: SARS-CoV-2 antibody testing is important for understanding immunity prevalence, and may have implications for healthcare workers (HCW) during the SARS-CoV-2 pandemic. Methods: We conducted immunologic testing of healthcare workers to determine the prevalence of SARS-CoV-2 IgG in this population. HCW were advised to wait at least two weeks from time of symptom onset or suspected exposure before undergoing testing. All participants were self-reported asymptomatic for at least three days at the time of testing. Results: Two hundred eighty-five samples were collected from March 24, 2020 to April 4, 2020. The average age of participants was 38 years (range 18-84), and 54% were male. Thirty-three percept tested IgG positive, 3% tested weakly positive, and 64% tested negative. Neither age nor sex was associated with antibody development. Conclusion: Thirty-six percent of HCW had IgG antibodies to SARS-CoV-2, reflecting the high exposure of inpatient and ambulatory frontline staff to this viral illness, most of whom had minimal symptoms and were working in the weeks preceding testing. While we continue to recommend standard protective precautions per CDC guidelines for all HCW, HCW with SARS-CoV-2 IgG may become our safest frontline providers as we learn if our IgG antibodies confer immunity. Knowing IgG antibody status may ease concerns regarding personal risk as this pandemic continues.


title: On the Generation of Medical Dialogues for COVID-19

text: Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets - CovidDialog - (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog datasets. Experiments demonstrate that these approaches are promising in generating meaningful medical dialogue about COVID-19. But more advanced approaches are needed to build a fully useful dialogue system that can offer accurate COVID-related consultations. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue


docid: fcmzdcuh

title: Clinical characteristics of 82 death cases with COVID-19

text: Background A recently developing pneumonia caused by SARS-CoV-2 was originated in Wuhan, China, and has quickly spread across the world. We reported the clinical characteristics of 82 death cases with COVID-19 in a single center. Methods Clinical data on 82 death cases laboratory-confirmed as SARS-CoV-2 infection were obtained from a Wuhan local hospital′s electronic medical records according to previously designed standardized data collection forms. Findings All patients were local residents of Wuhan, and the great proportion of them were diagnosed as severe illness when admitted. Most of the death cases were male (65.9%). More than half of dead patients were older than 60 years (80.5%) and the median age was 72.5 years. The bulk of death cases had comorbidity (76.8%), including hypertension (56.1%), heart disease (20.7%), diabetes (18.3%), cerebrovascular disease (12.2%), and cancer (7.3%). Respiratory failure remained the leading cause of death (69.5%), following by sepsis syndrome/MOF (28.0%), cardiac failure (14.6%), hemorrhage (6.1%), and renal failure (3.7%). Furthermore, respiratory, cardiac, hemorrhage, hepatic, and renal damage were found in 100%, 89%, 80.5%, 78.0%, and 31.7% of patients, respectively. On the admission, lymphopenia (89.2%), neutrophilia (74.3%), and thrombocytopenia (24.3%) were usually observed. Most patients had a high neutrophil-to-lymphocyte ratio of >5 (94.5%), high systemic immune-inflammation index of >500 (89.2%), increased C-reactive protein level (100%), lactate dehydrogenase (93.2%), and D-dimer (97.1%). A high level of IL-6 (>10 pg/ml) was observed in all detected patients. Median time from initial symptom to death was 15 days (IQR 11-20), and a significant association between aspartate aminotransferase (p=0.002), alanine aminotransferase (p=0.037) and time from initial symptom to death were interestingly observed. Conclusion Older males with comorbidities are more likely to develop severe disease, even die from SARS-CoV-2 infection. Respiratory failure is the main cause of COVID-19, but either virus itself or cytokine release storm mediated damage to other organ including cardiac, renal, hepatic, and hemorrhage should be taken seriously as well.


title: The All of Us Research Program: data quality, utility, and diversity

text: Importance: The All of Us Research Program hypothesizes that accruing one million or more diverse participants engaged in a longitudinal research cohort will advance precision medicine and ultimately improve human health. Launched nationally in 2018, to date All of Us has recruited more than 345,000 participants. All of Us plans to open beta access to researchers in May 2020. Objective: To demonstrate the quality, utility, and diversity of the All of Us Research Programs initial data release and beta launch of the cloud-based analysis platform, the cloud-based Researcher Workbench. Evidence: We analyzed the initial All of Us data release, comprising surveys, physical measurements (PM), and electronic health record (EHR) data, to characterize All of Us participants including self-reported descriptors of diversity. Data depth, density, and quality were evaluated using medication sequencing analyses for depression and type 2 diabetes. Replication of known oncologic associations with smoking exposure ascertained by EHR and survey data and calculation of population-based atherosclerotic cardiovascular disease risk scores demonstrated the utility of data and platform capability. Findings: The beta launch of the All of Us Researcher Workbench contains data on 224,143 participants. Seventy-seven percent of this cohort were identified as Underrepresented in Biomedical Research (UBR) including over forty-eight percent self-reporting non-White race. Medication usage patterns in common diseases depression and type 2 diabetes replicated prior findings previously reported in the literature and showed differences based on race. Oncologic associations with smoking were replicated and effect sizes compared for EHR and survey exposures finding general agreement. A cardiovascular disease score was calculated utilizing multiple data elements curated across sources. The cloud-based architecture built in the Researcher Workbench provided secure access and powerful computational resources at a low cost. All analyses have been made available for replication and reuse by registered researchers. Conclusions and Relevance: The All of Us Research Programs initial release of cohort data contains longitudinal and multidimensional data on diverse participants that replicate known associations. This dataset and the cloud-based Researcher Workbench advance the mission of All of Us to make data widely and securely available to researchers to improve human health and advance precision medicine.


title: Fractal analysis of muscle activity patterns during locomotion: pitfalls and how to avoid them

text: Time-dependent physiological data, such as electromyogram (EMG) recordings from multiple muscles, is often difficult to interpret objectively. Here, we used EMG data gathered during mouse locomotion to investigate the effects of calculation parameters and data quality on two metrics for fractal analysis: the Higuchi’s fractal dimension (HFD) and the Hurst exponent (H). A curve is fractal if it repeats itself at every scale or, in other words, if its shape remains unchanged when zooming in the curve at every zoom level. Many linear and nonlinear analysis methods are available, each of them aiming at the explanation of different data features. In recent years, fractal analysis has become a powerful nonlinear tool to extract information from physiological data not visible to the naked eye. It can present, however, some dangerous pitfalls that can lead to misleading interpretations. To calculate the HFD and the H, we have extracted muscle synergies from normal and mechanically perturbed treadmill locomotion from the hindlimb of adult mice. Then, we used one set per condition (normal and perturbed walking) of the obtained time-dependent coefficients to create surrogate data with different fluctuations over the original mean signal. Our analysis shows that HFD and H are exceptionally sensitive to the presence or absence of perturbations to locomotion. However, both metrics suffer from variations in their value depending on the parameters used for calculations and the presence of quasi-periodic elements in the time series. We discuss those issues giving some simple suggestions to reduce the chance of misinterpreting the outcomes. New & Noteworthy Despite the lack of consensus on how to perform fractal analysis of physiological time series, many studies rely on this technique. Here, we shed light on the potential pitfalls of using the Higuchi’s fractal dimension and the Hurst exponent. We expose and suggest how to solve the drawbacks of such methods when applied to data from normal and perturbed locomotion by combining in vivo recordings and computational approaches.