title: Bibliometric Analysis of COVID-19 in the Context of Migration Health: A Study Protocol

text: Introduction: Human mobility has been pivotal to the spread of COVID-19 through travel and migration.To mitigate the spread, most countries have imposed strict travel restrictions that have severely affected both the wellbeing and livelihoods of many migrant and mobile populations (both internally and internationally), particularly those from impoverished communities, those affected by humanitarian crises, including populations displaced and/or living in camps and camp-like settings. The need to include migrants (both regular and irregular or undocumented) in national strategic response plans for disease prevention and control has been increasingly recognized. Better understanding of the existing scientific evidence in migration health is crucial in designing effective response measures. In this paper, we present a protocol for a bibliometric analysis of scientific publications on COVID-19 and migration health. Expected study findings aim to provide valuable information to support evidence mapping on COVID-19 and migration health, particularly the identification of important research gaps. Methods and analysis: Using Elseviers Scopus abstract and citation database, a comprehensive search strategy will be applied to map scientific publications on COVID-19 and migration health. The current analysis will focus on research published from 1 January 2020 to 4 May 2020. The search query on migration health will largely focus on migration, migrant and human mobility-related terms. Three reviewers will screen publications for eligibility. The extracted bibliographic information will be analysed to determine the dominant research themes, country coverage and migrant groups. Collaboration networks will be analysed using VosViewer, a network analysis software. A deep dive on dominant research themes or migrant health-related topics will be done by creating visualization network maps of keywords from the retrieved publications.


title: A cell phone data driven time use analysis of the COVID-19 epidemic

text: Transmission of the SAR-COV-2 virus that causes COVID-19 is largely driven by human behavior and person-to-person contact. By staying home, people reduce the probability of contacting an infectious individual, becoming infected, and passing on the virus. One of the most promising sources of data on time use is smartphone location data. We develop a time use driven proportional mixing SEIR model that naturally incorporates time spent at home measured using smartphone location data and allows people of different health statuses to behave differently. We simulate epidemics in almost every county in the United States. The model suggests that Americans' behavioral shifts have reduced cases in 55%-86% of counties and for 71%-91% of the population, depending on modeling assumptions. Resuming pre-epidemic behavior would lead to a rapid rise in cases in most counties. Spatial patterns of bending and flattening the curve are robust to modeling assumptions. Depending on epidemic history, county demographics, and behavior within a county, returning those with acquired immunity (assuming it exists) to regular schedules generally helps reduce cumulative COVID-19 cases. The model robustly identifies which counties would experience the greatest share of case reduction relative to continued distancing behavior. The model occasionally mischaracterizes epidemic patterns in counties tightly connected to larger counties that are experiencing large epidemics. Understanding these patterns is critical for prioritizing testing resources and back-to-work planning for the United States.


title: The success of public health measures in Europe during the COVID-19 pandemic

text: SARS-CoV-2, a serious threat to sustainable development prospects, is spreading within countries at varying speeds, among other things depending on their population density, behavioural responses, cultural factors, personal hygiene practices and habits. This has led to significant variation in countries' policy responses aimed at stemming the proliferation of the virus. Using crisp-set qualitative comparative analysis, we conducted a comparative study at the European level to study the performance of different combinations of COVID-19 containment measures along with the response speeds. A set of configurations for two different scenarios (above-and below-median death rates) helps to illustrate how specific containment measures in each examined European country are related to the number of deaths. The main observation arising from the analysis is that the speed of response along with the decision to suspend international flights might determine the epidemic outbreak's impact on fatality. The results also imply that several different combinations of containment measures are associated with death rates across Europe. The outcome of this analysis can assist in identifying which set of containment measures in the event of an epidemic outbreak is beneficial/detrimental.


title: Impact of Social Distancing Measures on COVID-19 Healthcare Demand in Central Texas

text: A novel coronavirus (SARS-CoV-2) emerged in Wuhan, China in late 2019 and rapidly spread worldwide. In the absence of effective antiviral drugs and vaccines, well-targeted social distancing measures are essential for mitigating the COVID-19 pandemic, reducing strain on local health systems, and preventing mortality. Here, we provide a quantitative assessment of the efficacy of social distancing to slow COVID-19 transmission and reduce hospital surge, depending on the timing and extent of the measures imposed for a metropolitan region and its health care systems. We built a granular mathematical model of COVID-19 transmission that incorporated age-specific and risk-stratified heterogeneity, estimates for the transmission, and severity of COVID-19 using current best evidence. We performed thousands of stochastic simulations of COVID-19 transmission in the Austin-Round Rock Metropolitan Area to project the impact of school closures coupled with social distancing measures that were estimated to reduce non-household contacts by 0%, 25%, 50%, 75% or 90%. We compare early versus late implementation and estimate the number of COVID-19 hospitalizations, ICU patients, ventilator needs and deaths through mid-August, 2020. We queried local emergency services and hospital systems to estimate total hospital bed, ICU, and ventilator capacity for the region. We expected COVID-19 hospital beds and ICU requirements would surpass local capacity by mid-May if no intervention was taken. Assuming a four-day epidemic doubling time, school closures alone would be expected to reduce peak hospitalizations by only 18% and cumulative deaths by less than 3%. Immediate social distancing measures that reduced non-household contacts by over 75%, such as stay-at-home orders and closing of non-essential businesses, would be required to ensure that COVID-19 cases do not overwhelm local hospital surge capacity. Peak ICU bed demand prior to mid August 2020 would be expected to be reduced from 2,121 (95% CI: 2,018-2,208) with no intervention to 698 (95% CI: 204-1,100) with 75% social distancing and 136 (95% CI: 38-308) with 90% social distancing; current ICU bed capacity was estimated at 680. A two-week delay in implementation of such measures is projected to accelerate a local ICU bed shortage by four weeks. School closures alone hardly impact the epidemic curve. Immediate social distancing measures that reduce non-household contacts by over 75% were required to ensure that COVID-19 cases do not overwhelm local hospital surge capacity. These findings helped inform the Stay Home-Work Safe order enacted by the city of Austin, Texas on March 24, 2020 as a means of mitigating the emerging COVID-19 epidemic.


title: Assignment of coronavirus spike protein site-specific glycosylation using GlycReSoft

text: Widely-available LC-MS instruments and methods allow users to acquire glycoproteomics data. Complex glycans, however, add a dimension of complexity to the data analysis workflow. In a sense, complex glycans are post-translationally modified post-translational modifications, reflecting a series of biosynthetic reactions in the secretory pathway that are spatially and temporally regulated. One problem is that complex glycan is micro-heterogeneous, multiplying the complexity of the proteome. Another is that glycopeptide glycans undergo dissociation during tandem MS that must be considered for tandem MS interpretation algorithms and quantitative tools. Fortunately, there are a number of algorithmic tools available for analysis of glycoproteomics LC-MS data. We summarize the principles for glycopeptide data analysis and show use of our GlycReSoft tool to analyze SARS-CoV-2 spike protein site-specific glycosylation.


title: De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein

text: The emergence of SARS-CoV-2 is responsible for the pandemic of respiratory disease known as COVID-19, which emerged in the city of Wuhan, Hubei province, China in late 2019. Both vaccines and targeted therapeutics for treatment of this disease are currently lacking. Viral entry requires binding of the viral spike receptor binding domain (RBD) with the human angiotensin converting enzyme (hACE2). In an earlier paper1, we report on the specific residue interactions underpinning this event. Here we report on the de novo computational design of high affinity antibody variable regions through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike protein using the software tool OptMAVEn-2.02. Subsequently, we carry out computational affinity maturation of the designed prototype variable regions through point mutations for improved binding with the target epitope. Immunogenicity was restricted by preferring designs that match sequences from a 9-mer library of “human antibodies” based on H-score (human string content, HSC)3. We generated 106 different designs and report in detail on the top five that trade-off the greatest affinity for the spike RBD epitope (quantified using the Rosetta binding energies) with low H-scores. By grafting the designed Heavy (VH) and Light (VL) chain variable regions onto a human framework (Fc), high-affinity and potentially neutralizing full-length monoclonal antibodies (mAb) can be constructed. Having a potent antibody that can recognize the viral spike protein with high affinity would be enabling for both the design of sensitive SARS-CoV-2 detection devices and for their deployment as therapeutic antibodies.


title: Refractory Acute Respiratory Distress Syndrome Secondary to COVID-19 Successfully Extubated to Average Volume-assured Pressure Support Non-invasive Ventilator

text: Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by the highly infectious novel SARS-CoV-2 coronavirus spread by droplet transmission. Consequently, the use of respiratory devices that may potentially promote aerosolization like non-invasive positive pressure ventilation (NIPPV) for diseases such as obstructive sleep apnea (OSA), advanced chronic obstructive lung disease, pulmonary hypertension (PH), and neuromuscular respiratory disease has been called into question. We present a case of a patient with history of OSA and PH convalescing from refractory acute respiratory distress syndrome (ARDS) secondary to COVID-19 who was successfully extubated to average volume-assured pressure support (AVAPS). A 74-year-old male with medical history notable for OSA on NIPPV, PH, and hypertension presented with respiratory failure secondary to COVID-19 confirmed on polymerase chain reaction (PCR) test. His respiratory status worsened leading to ARDS requiring intubation. He was initially extubated to high flow nasal cannula (HFNC) due to hospital policy to avoid NIPPV due to concerns of viral dissemination. He did not tolerate HFNC and required re-intubation for prolonged period. He was then medically optimized for a second attempt and extubated two days later to AVAPS with an anti-viral filter and negative pressure room with a goal of optimizing his critical illness myopathy and pre-existing OSA and PH. He tolerated extubation well, and over the next five days was weaned from alternating AVAPS/HFNC to eventually requiring two liters nasal cannula in the day and AVAPS mode at night. This case highlights a potential therapeutic option for patients with severe respiratory failure secondary to COVID-19. This patient’s pre-existing comorbidities of OSA and PH markedly increased his risk for extubation failure on HFNC. The use of AVAPS after his second extubation attempt helped ensure ventilation and oxygenation non-invasively. COVID-19 can lead to prolonged dependence on mechanical ventilation. This pandemic has the potential to create medical resource scarcities, especially in rural areas where ventilators and trained personnel are already in short supply. By using AVAPS mode, this patient was able to rehabilitate his myopathy and participate in intermittent weaning of HFNC to ultimately simple nasal cannula. AVAPS is useful tool to facilitate extubation, as it allows non-invasive support of respiratory dynamics, particularly in those with co-morbidities such as OSA and PH. Further, larger scale studies are needed to determine its exact role during the COVID-19 pandemic.


title: Face mask designs following novel Coronavirus

text: Doctors need to wear complete protective equipment when large numbers of patients flood into the emergency room. Taiwan has so far managed to prevent a large scale community outbreak, city forces wearing face masks on public transportation, and keep social distancing to stem the virus from spreading. The protective device may be contaminated and must be replaced. In the situation of limited resources, how to take care of the physiological needs of the doctor without increasing the chance of contamination during replacement is a consideration. By reducing the chance of contamination during removal and storage, the previous designs were analyzed and improved. We proposed three improved designs to reduce the contact. Design-A features a mask with a water channel that allows the user to remain hydrated without removing the cover. Design-B has a folding pattern that hides the outer surface. Design-C combines the mask with the brim of a cap which form an extended air-intake area. Through understanding the problem, related product began distribute on the market, Design-D extend the mask usages period with less contact.


Before that, during and after that... ... will be the attributes of a new time calculation of our generation/ Davor, während und danach…


title: The Viral Infection and Respiratory Illness Universal Study (VIRUS): An International Registry of Coronavirus 2019-Related Critical Illness

text: The coronavirus disease 2019 pandemic has disproportionally strained intensive care services worldwide. Large areas of uncertainly regarding epidemiology, physiology, practice patterns, and resource demands for patients with coronavirus disease 2019 require rapid collection and dissemination of data. We describe the conception and implementation of an intensive care database rapidly developed and designed to meet data analytic needs in response to the coronavirus disease 2019 pandemic—the multicenter, international Society of Critical Care Medicine Discovery Network Viral Infection and Respiratory Illness Universal Study. DESIGN: Prospective cohort study and disease registry. SETTING: Multinational cohort of ICUs. PATIENTS: Critically ill patients with a diagnosis of coronavirus disease 2019. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Within 2 weeks of conception of the Society of Critical Care Medicine Discovery Network Viral Infection and Respiratory Illness Universal Study, study leadership was convened, registry case report forms were designed, electronic data entry set up, and more than 250 centers had submitted the protocol for institutional review board approval, with more than 100 cases entered. CONCLUSIONS: The Society of Critical Care Medicine Discovery Network Viral Infection and Respiratory Illness Universal Study provides an example of a rapidly deployed, international, pandemic registry that seeks to provide near real-time analytics and information regarding intensive care treatments and outcomes for patients with coronavirus disease 2019.


title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

text: Peculiar among human RNA viruses, coronaviruses have large genomes containing accessory genes that are not required for replication. Numerous mutations within the SARS-CoV-2 genome have been described but few deletions in the accessory genes of SARS-CoV-2 have been reported. Here, we report two large deletions in ORF7a, both of which produce new open reading frames (ORFs) through the fusion of the N-terminus of ORF7a and a downstream ORF.


title: Could masks curtail the post-lockdown resurgence of COVID-19 in the US?

text: The community lockdown measures implemented in the United States, during late March to end of May of 2020, resulted in a significant reduction in the community transmission of the COVID-19 pandemic throughout the country. However, a number of US states are currently experiencing an alarming post-lockdown resurgence of the pandemic, triggering the fear for a possible severe second wave of the pandemic in some US jurisdictions. We designed a mathematical model for addressing the key question of whether or not the universal use of face masks can halt or curtail such resurgence (and possibly avert a second wave, without having to undergo another cycle of major community lockdown) in the states of Arizona, Florida, New York and the entire US. The model was parametrized and fitted using cumulative mortality data from the four jurisdictions. Our study highlights the importance of early implementation of the community lockdown measures. In particular, a sizable reduction in the burden of the pandemic would have been recorded in each of the four jurisdictions if the community lockdown measures were implemented a week or two earlier. These reductions are greatly augmented if the early implementation of the lockdown measures is complemented with a public face masks use strategy. It is shown that the pandemic would have been almost completely suppressed from significantly taking off if the lockdown measures were implemented two weeks earlier, and if a sizable percentage of the residents of the four jurisdictions wore face masks during the respective lockdown periods. If the level of lifting of community lockdown is high (which entails allowing for greater community contacts and re-opening of businesses and social activities, in comparison to what was allowed during the community lockdown period), the states of Arizona and Florida will record a devastating second wave of the pandemic by the end of 2020, while the state of New York and the entire US will record milder second waves. If the level of lifting for the community lockdown was mild (i.e., only allowing very limited community contacts and business activities, in comparison to the lockdown period), only the state of Florida will experience a second wave. The severity of the projected second wave depends on the level of lifting of the community lockdown. For instance, the projected second wave for Arizona and Florida, associated with moderate and high level of lifting of lockdown, will be more severe than their respective first wave. For high level of lifting of lockdown measures, the increased use of face masks after the lockdown period greatly reduces the burden of the pandemic. In particular, for this high lifting scenario, none of the four jurisdictions will experience a second wave if half of their residents wear face masks consistently after their respective lockdown period). A testing strategy that increases the maximum detection rate of asymptomatic infected individuals (followed by contact tracing and self-isolation of the detected cases) greatly reduces the burden of the pandemic in all four jurisdictions, particularly if also combined with universal face mask use strategy. Universal use of face masks in public, with at least moderate level of compliance, could halt the post-lockdown resurgence of COVID-19, in addition to averting the potential for (or severity of) a second wave of the pandemic in each of the four jurisdictions.


title: Prevalence and clinical features of 2019 novel coronavirus disease (COVID-19) in the Fever Clinic of a teaching hospital in Beijing: a single-center, retrospective study

text: Background With the spread of COVID-19 from Wuhan, Hubei Province to other areas of the country, medical staff in Fever Clinics faced the challenge of identifying suspected cases among patients with respiratory infections manifested with fever. We aimed to describe the prevalence and clinical features of COVID-19 as compared to pneumonias of other etiologies in a Fever Clinic in Beijing. Methods In this single-center, retrospective study, 342 cases of pneumonia were diagnosed in Fever Clinic in Peking University Third Hospital between January 21 to February 15, 2020. From these patients, 88 were reviewed by panel discussion as possible or probable cases of COVID-19, and received 2019-nCoV detection by RT-PCR. COVID-19 was confirmed by positive 2019-nCoV in 19 cases, and by epidemiological, clinical and CT features in 2 cases (the COVID-19 Group, n=21), while the remaining 67 cases served as the non-COVID-19 group. Demographic and epidemiological data, symptoms, laboratory and lung CT findings were collected, and compared between the two groups. Findings The prevalence of COVID-19 in all pneumonia patients during the study period was 6.14% (21/342). Compared with the non-COVID-19 group, more patients with COVID-19 had an identified epidemiological history (90.5% versus 32.8%, P<0.001). The COVID-19 group had lower WBC [5.19×10^9/L (±1.47) versus 7.21×10^9/L (±2.94), P<0.001] and neutrophil counts [3.39×10^9/L (±1.48) versus 5.38×10^9/L (±2.85), P<0.001] in peripheral blood. However, the percentage and count of lymphocytes were not different. On lung CT scans, involvement of 4 or more lobes was more common in the COVID-19 group (45% versus 16.4%, P=0.008). Interpretation In the period of COVID-19 epidemic outside Hubei Province, the prevalence of COVID-19 in patients with pneumonia visiting to our Fever Clinic in Beijing was 6.14%. Epidemiological evidence was important for prompt case finding, and lower blood WBC and neutrophil counts may be useful for differentiation from pneumonia of other etiologies.


title: COVID-19: Predictive Mathematical Models for the Number of Deaths in South Korea, Italy, Spain, France, UK, Germany, and USA

text: We have recently introduced two novel mathematical models for characterizing the dynamics of the cumulative number of individuals in a given country reported to be infected with COVID-19. Here we show that these models can also be used for determining the time-evolution of the associated number of deaths. In particular, using data up to around the time that the rate of deaths reaches a maximum, these models provide estimates for the time that a plateau will be reached signifying that the epidemic is approaching its end, as well as for the cumulative number of deaths at that time. The plateau is defined to occur when the rate of deaths is 5% of the maximum rate. Results are presented for South Korea, Italy, Spain, France, UK, Germany, and USA. The number of COVID-19 deaths in other counties can be analyzed similarly.


title: Modelling oral adrenal cortisol support

text: A simplified mathematical model of oral hydrocortisone delivery in adrenal insufficiency is described; the model is based on three components (gastric hydrocortisone, free serum cortisol and bound serum cortisol) and is formulated in terms of linear kinetics, taking into account the dynamics of glucocorticoid-protein binding. Motivated by the need to optimise cortisol replacement in the situations of COVID-19 infection, the model is fitted to recently-published data on 50 mg dosing and earlier data on 10 mg dosing. The fitted model is used to predict typical responses to standard dosing regimes, which involve a larger dose in the morning and 1 or 2 smaller doses later in the day, and the same regimes with doses doubled. In all cases there is a circadian-like response, with early morning nadir. The model is also used to consider an alternative dosing strategy based on four equal and equally-spaced doses of 10, 20 or 30 mg per 24 h, resulting in a more even response resembling a response to sustained inflammatory stress.


title: HSV Forms an HCMV-like Viral Assembly Center in Neuronal Cells

text: Herpes simplex virus (HSV) is a neuroinvasive virus that has been used as a model organism for studying common properties of all herpesviruses. HSV induces host organelle rearrangement and forms dispersed assembly compartments in epithelial cells, which complicates the study of HSV assembly. In this study, we show that HSV forms a visually distinct unitary cytoplasmic viral assembly center (cVAC) in both cancerous and primary neuronal cells that concentrates viral structural proteins and is the site of capsid envelopment. The HSV cVAC also concentrates host membranes that are important for viral assembly, such as Golgi- and recycling endosome-derived membranes. Lastly, we show that HSV cVAC formation and/or maintenance depends on an intact microtubule network and a viral tegument protein, pUL51. Our observations suggest that the neuronal cVAC is a uniquely useful model to study common herpesvirus assembly pathways, and cell-specific pathways for membrane reorganization. Summary This study shows that HSV forms a viral assembly center in neuronal cells by reorganization of host membranes. This system is a novel and powerful tool to study herpesvirus assembly pathways and host cell membrane dynamics.


title: Statins and the COVID-19 main protease: in silico evidence on direct interaction

text: INTRODUCTION: No proven drug and no immunisation are yet available for COVID-19 disease. The SARS-CoV-2 main protease (Mpro), a key coronavirus enzyme, which is a potential drug target, has been successfully crystallised. There is evidence suggesting that statins exert anti-viral activity and may block the infectivity of enveloped viruses. The aim of this study was to assess whether statins are potential COVID-19 Mpro inhibitors, using a molecular docking study. MATERIAL AND METHODS: Molecular docking was performed using AutoDock/Vina, a computational docking program. SARS-CoV-2 Mpro was docked with all statins, while antiviral and antiretroviral drugs – favipiravir, nelfinavir, and lopinavir – were used as standards for comparison. RESULTS: The binding energies obtained from the docking of 6LU7 with native ligand favipiravir, nelfinavir, lopinavir, simvastatin, rosuvastatin, pravastatin, pitavastatin, lovastatin, fluvastatin, and atorvastatin were –6.8, –5.8, –7.9, –7.9, –7.0, –7.7, –6.6, –8.2, –7.4, –7.7, and –6.8 kcal/mol, respectively. The number of hydrogen bonds between statins and amino acid residues of Mpro were 7, 4, and 3 for rosuvastatin, pravastatin, and atorvastatin, respectively, while other statins had two hydrogen bonds. CONCLUSIONS: These results indicate, based upon the binding energy of pitavastatin, rosuvastatin, lovastatin, and fluvastatin, that statins could be efficient SARS-CoV-2 Mpro inhibitors. This is supported by the fact that the effects of some statins, especially pitavastatin, have a binding energy that is even greater than that of protease or polymerase inhibitors. However, further research is necessary to investigate their potential use as drugs for COVID-19.


title: Statistical methods for estimating cure fraction of COVID-19 patients in India

text: The human race is under the COVID-19 pandemic menace since beginning of the year 2020. Even though the disease is easily transmissible, a massive fraction of the affected people are recovering. Most of the recovered patients will not experience death due to COVID-19, even if they observed for a long period. They can be treated as long term survivors (cured population) in the context of lifetime data analysis. In this article, we present some statistical methods to estimate the cure fraction of the COVID-19 patients in India. Proportional hazards mixture cure model is used to estimate the cure fraction and the effect of covariates gender and age on lifetime. The data available on website https://api.cvoid19india.org is used in this study. We can see that, the cure fraction of the COVID-19 patients in India is more than 90%, which is indeed an optimistic information.


title: Performance and impact of disposable and reusable respirators for healthcare workers during pandemic respiratory disease: a rapid evidence review.

text: Objectives In the context of the Covid-19 pandemic, to identify the range of filtering respirators that can be used in patient care and synthesise evidence to guide the selection and use of different respirator types. Design Comparative analysis of international standards for filtering respirators and rapid review of their performance and impact in healthcare. Data sources Websites of international standards organisations, Medline and EMBASE (final search 11th May 2020), with hand-searching of references and citations. Study selection Guided by the SPIDER tool, we included studies whose sample was healthcare workers (including students). The phenomenon of interest was respirators, including disposable and reusable types. Study designs including cross-sectional, observational cohort, simulation, interview and focus group. Evaluation approaches included test of respirator performance, test of clinician performance or adherence, self-reported comfort and impact, and perceptions of use. Research types included quantitative, qualitative and mixed methods. We excluded studies comparing the effectiveness of respirators with other forms of protective equipment. Data extraction, analysis and synthesis Two reviewers extracted data using a template. Suitability for inclusion in the analysis was judged by two reviewers. We synthesised standards by tabulating data according to key criteria. For the empirical studies, we coded data thematically followed by narrative synthesis. Results We included relevant standards from 8 authorities across Europe, North and South America, Asia and Australasia. 39 research studies met our inclusion criteria. There were no instances of comparable publications suitable for quantitative comparison. There were four main findings. First, international standards for respirators apply across workplace settings and are broadly comparable across jurisdictions. Second, effective and safe respirator use depends on proper fitting and fit-testing. Third, all respirator types carry a burden to the user of discomfort and interference with communication which may limit their safe use over long periods; studies suggest that they have little impact on specific clinical skills in the short term but there is limited evidence on the impact of prolonged wearing. Finally, some clinical activities, particularly chest compressions, reduce the performance of filtering facepiece respirators. Conclusion A wide range of respirator types and models is available for use in patient care during respiratory pandemics. Careful consideration of performance and impact of respirators is needed to maximise protection of healthcare workers and minimise disruption to the delivery of care.


title: Characteristics of patients with COVID-19 during epidemic ongoing outbreak in Wuhan, China

text: Background Since Dec 2019, SARS-CoV-2 has caused about fifty thousand patients and over two thousand deaths in Wuhan, China. We reported characteristics of patients with COVID-19 during epidemic ongoing outbreak in Wuhan. Methods Data of COVID-19 patients with clinical outcome in a designated hospital in Wuhan, were retrospectively collected from electronic medical records. Characteristics were compared between patients who died or recovered, and between patients with different disease severity. Results By Feb 25, 2020, 403 patients were enrolled, 100 died and 303 recovered. Most of non-survivors tended to be males, old aged, or with chronic diseases. Duration from illness onset to admission was 9 (7-12) days. Patients with severe or critical illness had more days from onset to admission compared to those with ordinary illness. Lymphopenia, anemia, hypoproteinemia, and abnormal serum sodium were presented in 52.6%, 54.6%, 69.8%, and 21.8% cases, respectively. Patients who died or with severe/critical illness showed increased white blood cell and neutrophil count, serum total bilirubin, creatinine, hypersensitive troponin I, D-dimer, procalcitonin, and C-reactive protein, and decreased red blood cell, lymphocyte, platelet count, and serum albumin on admission compared to those who recovered or with ordinary illness. Complications of acute organ injury and secondary infection were common in patients with COVID-19, especially in non-survivors. Conclusions Multiple homeostasis disturbances were common in patients with severe or critical illness at admission. Early support should be provided, especially for old men with chronic disease, which is vital to control disease progression and reduce mortality of COVID-19 during epidemic ongoing outbreak.


title: IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

text: Background Metagenomic next generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource limited environments. Findings We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics which are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences, and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. Conclusion The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.


title: Modeling COVID-19: Forecasting and analyzing the dynamics of the outbreak in Hubei and Turkey

text: As the pandemic of Coronavirus Disease 2019 (COVID-19) rages throughout the world, accurate modeling of the dynamics thereof is essential. However, since the availability and quality of data varies dramatically from region to region, accurate modeling directly from a global perspective is difficult, if not altogether impossible. Nevertheless, via local data collected by certain regions, it is possible to develop accurate local prediction tools, which may be coupled to develop global models. In this study, we analyze the dynamics of local outbreaks of COVID-19 via a coupled system of ordinary differential equations (ODEs). Utilizing the large amount of data available from the ebbing outbreak in Hubei, China as a testbed, we estimate the basic reproductive number, R0 of COVID-19 and predict the total cases, total deaths, and other features of the Hubei outbreak with a high level of accuracy. Through numerical experiments, we observe the effects of quarantine, social distancing, and COVID-19 testing on the dynamics of the outbreak. Using knowledge gleaned from the Hubei outbreak, we apply our model to analyze the dynamics of outbreak in Turkey. We provide forecasts for the peak of the outbreak and the total number of cases/deaths in Turkey, for varying levels of social distancing, quarantine, and COVID-19 testing.


title: A review on clinical application of high frequency traditional Chinese medicine in treatment of coronavirus pneumonia 2019/ 临床使用治疗新型冠状病毒肺炎中药复方中高频数中药抗病毒研究概述

text: Since December 2019, there has been a sharp increase in the number of confirmed cases of pneumonia caused by the novel coronavirus (SARS-CoV-2) in China, which has caused great concern around the world. In face of severe epidemic, no specific drugs have been found in clinical practice. However, some Chinese medicine compounds have shown obvious clinical efficacy, and it is feasible to find and develop natural drugs for the treatment of novel coronavirus pneumonia from these compounds. In this paper, based on the recommends of new type of coronavirus infection pneumonia diagnosis and treatment scheme (trial version 6), the use frequency of Chinese herbal medicines was calculated. The antiviral reports of high frequency Chinese herbal medicines were reviewed, in order to provide the reference for screening the active components against SARS-CoV-2 from traditional Chinese medicine.


title: Assessment of small pulmonary blood vessels in COVID-19 patients using HRCT

text: Background Mounting evidence supports the role of pulmonary hemodynamic alternations in the pathogenesis of COVID-19. Previous studies have demonstrated that changes in pulmonary blood volumes measured on CT are associated with histopathological markers of pulmonary vascular pruning, suggesting that quantitative HRCT analysis may eventually be useful in the assessment pulmonary vascular dysfunction more broadly. Methods Building upon previous work, automated HRCT measures of small blood vessel volume and pulmonary vascular density were developed. Scans from 103 COVID-19 patients and 108 healthy volunteers were analyzed and their results compared, with comparisons made both on lobar and global levels. Results Compared to healthy volunteers, COVID-19 patients showed significant reduction in BV5 (pulmonary blood volume contained in blood vessels of <5 mm2) expressed as BV5/(Total pulmonary blood volume) (p<0.0001), and significant increases in BV5_10 and BV 10 (pulmonary blood volumes contained in vessels between 5 and 10 mm2 and above 10 mm2, respectively) (p<0.0001). These changes were consistent across lobes. Conclusions COVID-19 patients display striking anomalies in the distribution of blood volume within the pulmonary vascular tree, consistent with increased pulmonary vasculature resistance in the pulmonary vessels below the resolution of HRCT.


title: Burden and prevalence of prognostic factors for severe covid-19 disease in Sweden

text: Objectives: Describe the burden and prevalence of prognostic factors of severe COVID-19 disease at national and county level in Sweden. Design: Cross sectional study Setting: Sweden Participants: 9,624,428 individuals living in Sweden on 31st December 2014 and alive on 1st January 2016 Main outcome measures: Burden and prevalence of prognostic factors for severe COVID-19 based on the guidelines from the World Health Organization and European Centre for Disease Prevention and Control, which are age 70 years and older, cardiovascular disease, cancer, chronic obstructive pulmonary disease, severe asthma, and diabetes. Prognostic factors were identified based on records for three years before 1st January 2016 from the Swedish National Inpatient and Outpatient Specialist Care Register, Prescribed Drug Register, and Cancer Register. Results: 22.1% of the study population had at least one prognostic factor for severe COVID-19 (2,131,319 individuals), and 1.6% had at least three factors (154,746 individuals). The prevalence of underlying medical conditions in the whole study population ranged from 0.8% with chronic obstructive pulmonary disease (78,516 individuals) to 7.4% with cardiovascular disease (708,090 individuals), and the county specific prevalence of at least one prognostic factor ranged from 19.2% in Stockholm (416,988 individuals) to 25.9% in Kalmar (60,005 individuals). Conclusions: The prevalence of prognostic factors for severe COVID-19 disease will aid authorities in optimally planning healthcare resources during the ongoing pandemic. Results can also be applied to underlying assumptions of disease burden in modelling efforts to support COVID-19 planning. This information is crucial when deciding appropriate strategies to mitigate the pandemic and reduce both the direct mortality burden from the disease itself, and the indirect mortality burden from potentially overwhelmed health systems.


title: Supportive Care for Patient with Respiratory Diseases: An Umbrella Review

text: Abstract Background: Supportive treatment is an important and effective part of the management for patients with life-threatening diseases. This study aims to identify and evaluate the forms of supportive care for patients with respiratory diseases. Methods: An umbrella review of supportive care for patient respiratory diseases was undertaken. We comprehensively searched the following databases: Medline, EMBASE, Web of Science, CNKI (China National Knowledge Infrastructure), Wanfang Data and CBM (SinoMed) from their inception to 31 March 2020, and other sources to identify systematic reviews and meta-analyses related to supportive treatments for patient with respiratory diseases including COVID-19, SARS, MERS and influenza. We assessed the methodological quality using the AMSTAR score and the quality of the evidence for the primary outcomes of each included systematic review and meta-analysis. Results: We included 18 systematic reviews and meta-analyses in this study. Most studies focused on the respiratory and circulatory support. Ten studies were of high methodological quality, five studies of medium quality, and three studies of low quality. According to four studies extracorporeal membrane oxygenation did not reduce mortality in adults (OR/RR ranging from 0.71 to 1.28), but two studies reported significantly lower mortality in patients receiving venovenous extracorporeal membrane oxygenation than in the control group (OR/RR ranging from 0.38 to 0.73). Besides, monitoring of vital signs and increasing the number of medical staff may also reduce the mortality in patients with respiratory diseases. Conclusions: Our overview suggests that supportive care may reduce the mortality of patients with respiratory diseases to some extent. However, the quality of evidence for the primary outcomes in the included studies was low to moderate. Further systematic reviews and meta-analyses are needed to address the evidence gap regarding the supportive care for SARS, MERS and COVID-19.


title: Global Health Training in U.S. Emergency Medicine Residency Programs

text: Objectives: Formal education in global health (GH) and short-term experiences in GH (STEGH) are offered by many emergency medicine (EM) residency programs in the United States. In an increasingly connected world, training in GH and STEGH can provide essential knowledge and practical skills to trainees, particularly at the graduate medical education level. The current core programmatic components and the essential competencies and curricula that support ethical and effective STEGH, however, still vary widely. The authors conducted a survey of the 228 EM residency programs in the United States to describe the current state of GH training and STEGH. Methods: An online survey was developed in REDCap by a team of GH faculty. In July 2018, programs were invited to participate via individual invitation of program directors from a directory. The programs received two reminders to participate until January 2019. Results: Of the 84 programs that responded, 75% offer STEGH and 39% have longitudinal GH curricula. Within these programs, only 55% have dedicated GH faculty and only 70% have dedicated sites. Both faculty and residents encounter funding and insurance barriers; most notably, only 20% of programs that offer STEGH provide evacuation insurance for their residents. Most residents (95%) engage in clinical work along with teaching and other activities, but 24% of programs do not allow these activities to fulfill any residency requirements. Finally, only 80 and 85% of programs offer preparatory and debriefing activities for residents, respectively. Conclusions: While the results of this survey show progress relative to prior surveys, there are still barriers to implementing GH curricula and supporting safe, ethical, and effective STEGH, particularly in the form of continued financial and logistic support for faculty and for residents, in U.S. EM training programs.


Working at the time of COVID-19/ Lavorare ai tempi del covid-19


title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection

text: Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection.


title: A modelling framework to assess the likely effectiveness of facemasks in combination with 'lock-down' in managing the COVID-19 pandemic

text: COVID-19 is characterized by an infectious presymptomatic period,when newly infected individuals can unwittingly infect others We are interested in what benefits facemasks could offer as a nonpharmaceutical intervention, especially in the settings where high-technology interventions, such as contact tracing using mobile apps or rapid case detection via molecular tests, are not sustainable Here, we report the results of two mathematical models and show that facemask use by the public could make a major contribution to reducing the impact of the COVID-19 pandemic Our intention is to provide a simple modelling framework to examine the dynamics of COVID-19 epidemics when facemasks are worn by the public, with or without imposed 'lock-down' periods Our results are illustrated for a number of plausible values for parameter ranges describing epidemiological processes and mechanistic properties of facemasks, in the absence of current measurements for these values We show that, when facemasks are used by the public all the time (not just from when symptoms first appear), the effective reproduction number, Re, can be decreased below 1, leading to the mitigation of epidemic spread Under certain conditions, when lock-down periods are implemented in combination with 100% facemask use, there is vastly less disease spread, secondary and tertiary waves are flattened and the epidemic is brought under control The effect occurs even when it is assumed that facemasks are only 50% effective at capturing exhaled virus inoculum with an equal or lower efficiency on inhalation Facemask use by the public has been suggested to be ineffective because wearers may touch their facesmore often, thus increasing the probability of contracting COVID-19 For completeness, our models show that facemask adoption provides population-level benefits, even in circumstances where wearers are placed at increased risk At the time of writing, facemask use by the public has not been recommended in many countries, but a recommendation for wearing face-coverings has just been announced for Scotland Even if facemask use began after the start of the first lock-down period, our results show that benefits could still accrue by reducing the risk of the occurrence of further COVID-19 waves We examine the effects of different rates of facemask adoption without lock-down periods and show that, even at lower levels of adoption, benefits accrue to the facemask wearers These analyses may explain why some countries, where adoption of facemask use by the public is around 100%, have experienced significantly lower rates of COVID-19 spread and associated deaths We conclude that facemask use by the public, when used in combination with physical distancing or periods of lock-down, may provide an acceptable way of managing the COVID- 19 pandemic and re-opening economic activity These results are relevant to the developed as well as the developing world, where large numbers of people are resource poor, but fabrication of home-made, effective facemasks is possible A key message from our analyses to aid the widespread adoption of facemasks would be: 'my mask protects you, your mask protects me' [ABSTRACT FROM AUTHOR] Copyright of Proceedings of the Royal Society A: Mathematical, Physical & Engineering Sciences is the property of Royal Society and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission However, users may print, download, or email articles for individual use This abstract may be abridged No warranty is given about the accuracy of the copy Users should refer to the original published version of the material for the full abstract (Copyright applies to all Abstracts )


title: Delirium Incidence, Duration and Severity in Critically Ill Patients with COVID-19

text: Background Delirium incidence, duration and severity in patients admitted to the intensive care unit (ICU) due to COVID-19 is not known. Methods We conducted an observational study at two large urban academic Level 1 trauma centers. Consecutive patients admitted to the ICU with a positive SARS-CoV-2 nasopharyngeal swab polymerase chain reaction test from March 1st, 2020 to April 27, 2020 were included. Individuals younger than 18 years of age, without any documented delirium assessments (CAM-ICU), or without a discharge disposition were excluded. The primary outcomes were delirium rates and delirium duration and the secondary outcome was delirium severity. Outcomes were assessed for up to the first 14 days of ICU stay. Results Of 243 consecutive patients with confirmed COVID-19 admitted to the ICU, 144 met eligibility criteria and were included in the analysis. Delirium occurred in 73.6% (106/144) and delirium or coma occurred in 76.4% (110/144). Sixty-three percent of patients were positive for delirium on the first CAM-ICU assessment. The median duration of delirium and coma was 7 days (IQR: 3-10), and the median delirium duration was 5 days (IQR: 2-7). The median CAM-ICU-7 score was 6 (IQR: 4-7) representing severe delirium. Mechanical ventilation was associated with greater odds of developing delirium (OR: 42.1, 95%CI: 13.0-137.1). Mortality was 26.4% in patients with delirium compared to 15.8% in patients without delirium. Conclusions 73.6% of patients admitted to the ICU with COVID-19 experience delirium that persists for approximately 1 week. Invasive mechanical ventilation is significantly associated with odds of delirium. Clinical attention to prevent and manage delirium and reduce delirium duration and severity is urgently needed for patients with COVID-19.


title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

text: Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract


title: Mass testing, school closings, lockdowns: Countries pick tactics in ‘war’ against coronavirus

text: The United States and Europe have stopped hitting the snooze button After 2 months of mostly waiting and seeing while the coronavirus disease 2019 (COVID-19) alarm sounded ever more loudly, many countries have suddenly implemented strict measures to slow the spread of the disease, which the World Health Organization (WHO) officially declared a pandemic on 13 March Thousands of events have been canceled;schools, restaurants, bars, and clubs have been closed;and transit systems are at a standstill


title: Forecasting COVID-19 new cases in Algeria using Autoregressive fractionally integrated moving average Models (ARFIMA)

text: In this research, an ARFIMA model is proposed to forecast new COVID-19 cases in Algeria two weeks ahead. In the present study, public health database from Algeria health ministry has been used to build an ARFIMA model and used to forecast COVID-19 new cases in Algeria until May 11, 2020.


Premature evaluation? Some cautionary thoughts on global pandemics and scholarly publishing


title: Substantial underestimation of SARS-CoV-2 infection in the United States due to incomplete testing and imperfect test accuracy

text: Accurate estimates of the burden of SARS-CoV-2 infection are critical to informing pandemic response. Current confirmed COVID-19 case counts in the U.S. do not capture the total burden of the pandemic because testing has been primarily restricted to individuals with moderate to severe symptoms due to limited test availability. Using a semi-Bayesian probabilistic bias analysis to account for incomplete testing and imperfect diagnostic accuracy, we estimated 6,275,072 cumulative infections compared to 721,245 confirmed cases (1.9% vs. 0.2% of the population) as of April 18, 2020. Accounting for uncertainty, the number of infections was 3 to 20 times higher than the number of confirmed cases. 86% (simulation interval: 64-99%) of this difference was due to incomplete testing, while 14% (0.3-36%) was due to imperfect test accuracy. Estimates of SARS-CoV-2 infections that transparently account for testing practices and diagnostic accuracy reveal that the pandemic is larger than confirmed case counts suggest.


title: Steroid-responsive severe encephalopathy in SARS-CoV-2 infection

text: SARS-CoV-2 infection has the potential for targeting central nervous system and several neurological symptoms have been described in patients with severe respiratory distress. Here we described the case of an otherwise healthy 60-year old subject with SARS-CoV-2 infection but only mild respiratory abnormalities who developed severe progressive encephalopathy associated with mild pleocytosis and hyperproteinorrachia. MRI was negative whereas EEG showed theta waves on the anterior brain regions. Serum and CSF analyses excluded other known infectious or autoimmune disorders. The patient dramatically improved after high-doses steroid treatment suggesting an inflammatory-mediated brain involvement related to SARS-CoV-2 infection


title: L\'evy walk dynamics in an external harmonic potential

text: L\'evy walks (LWs) are spatiotemporally coupled random-walk processes describing superdiffusive heat conduction in solids, propagation of light in disordered optical materials, motion of molecular motors in living cells, or motion of animals, humans, robots, and viruses. We here investigate a key feature of LWs, their response to an external harmonic potential. In this generic setting for confined motion we demonstrate that LWs equilibrate exponentially and may assume a bimodal stationary distribution. We also show that the stationary distribution has a horizontal slope next to a reflecting boundary placed at the origin, in contrast to correlated superdiffusive processes. Our results generalize LWs to confining forces and settle some long-standing puzzles around LWs.


title: Machine learning in predicting respiratory failure in patients with COVID-19 pneumonia - challenges, strengths, and opportunities in a global health emergency

text: Background Machine learning can assist clinicians in forecasting patients with COVID-19 who develop respiratory failure requiring mechanical ventilation. This analysis aimed to determine a 48 hours prediction of moderate to severe respiratory failure, as assessed with PaO2/FiO2 < 150 mmHg, in hospitalized patients with COVID-19 pneumonia. Methods This was an observational study that comprised all consecutive adult patients with COVID-19 pneumonia admitted to the Infectious Diseases Clinic of the University Hospital of Modena, Italy from 21 February to 6 April 2020. COVID-19 was confirmed with PCR positive nasopharyngeal swabs while the presence of pneumonia was radiologically confirmed. Patients received standard of care according to national guidelines for clinical management of SARS-CoV-2 infection. The patients' full medical history, demographic and epidemiological features, clinical data, complete blood count, coagulation, inflammatory and biochemical markers were routinely collected and aggregated in a clinically-oriented logical framework in order to build different datasets. The dataset was used to train a learning framework relying on Microsoft LightGBM and leveraging a hybrid approach, where clinical expertise is applied alongside a data-driven analysis. Shapley Additive exPlanations (SHAP) values were used to quantify the positive or negative impact of each variable included in the model on the predicted outcome. The study outcome was the onset of moderate to severe respiratory failure defined as PaO2/FiO2 ratio < 150 mmHg ([≥] 13.3 kPa) in at least one of two consecutive arterial blood gas analyses in the following 48 hours. Results A total of 198 patients contributed to generate 1068 valuable observations which allowed to build 3 prediction models based respectively on 31-variables signs and symptoms, 39-variables laboratory biomarkers and 91-variables as a composition of the two. A fourth boosted mixed model which included 20 variables was selected from the model 3, achieved the best predictive performance (AUC=0.84). Its clinical performance was applied in a narrative case report as an example. Conclusion This study developed a machine learning algorithm, with a 84% prediction accuracy, which is potentially able to assist clinicians in decision making process with therapeutic implications.


title: Heg.IA: An intelligent system to support diagnosis of Covid-19 based on blood tests

text: A new kind of coronavirus, the SARS-Cov2, started the biggest pandemic of the century. It has already killed more than 250,000 people. Because of this, it is necessary quick and precise diagnosis test. The current gold standard is the RT-PCR with DNA sequencing and identification, but its results takes too long to be available. Tests base on IgM/IgG antibodies have been used, but their sensitivity and specificity may be very low. Many studies have been demonstrating the Covid-19 impact in hematological parameters. This work proposes an intelligent system to support Covid-19 diagnosis based on blood testing. We tested several machine learning methods, and we achieved high classification performance: 95.159% +- 0.693 of overall accuracy, kappa index of 0.903 +- 0.014, sensitivity of 0.968 +- 0.007, precision of 0.938 +- 0.010 and specificity of 0.936 +- 0.011. These results were achieved using classical and low computational cost classifiers, with Bayes Network being the best of them. In addition, only 24 blood tests were needed. This points to the possibility of a new rapid test with low cost. The desktop version of the system is fully functional and available for free use.


title: Perceived preparedness to respond to the COVID-19 pandemic: A study with healthcare workers in Ghana

text: Introduction: Healthcare workers' (HCWs) preparedness to respond to pandemics is critical to containing disease spread. Low-resource countries, however, experience barriers to preparedness due to limited resources. In Ghana, a country with a constrained healthcare system and high COVID-19 cases, we examined HCWs' perceived preparedness to respond to COVID-19 and associated factors. Methods: 472 HCWs completed questions in a cross-sectional self-administered online survey. Perceived preparedness was assessed using a 15-question scale (Cronbach alpha=0.91) and summative scores were created (range=0-45). Higher scores meant greater perceived preparedness. We used linear regression with robust standard errors to examine associations between perceived preparedness and potential predictors. Results: The average preparedness score was 24 (SD=8.9); 27.8% of HCWs felt prepared. In multivariate analysis, factors associated with higher perceived preparedness were: training ({beta}=3.35, 95%CI: 2.01 to 4.69); having adequate PPE ({beta}=2.27, 95%CI: 0.26 to 4.29), an isolation ward ({beta}=2.74, 95%CI: 1.15 to 4.33), and protocols for screening ({beta}=2.76, 95%CI: 0.95 to 4.58); and good perceived communication from management ({beta}=5.37, 95%CI: 4.03 to 7.90). When added to the model, perceived knowledge decreased the effect of training by 28.0%, although training remained significant, suggesting a partial mediating role. Perceived knowledge was associated with a 6-point increase in perceived preparedness score ({beta}=6.04, 95%CI: 4.19 to 7.90). Conclusion: HCWs reported low perceived preparedness to respond to COVID-19. Training, clear protocols, PPE availability, isolation wards, and communication play an important role in increasing preparedness. Government stakeholders must institute necessary interventions to increase HCWs' preparedness to respond to the ongoing pandemic and prepare for future pandemics.


title: Machine Learning Models Identify Inhibitors of SARS-CoV-2

text: With the ongoing SARS-CoV-2 pandemic there is an urgent need for the discovery of a treatment for the coronavirus disease (COVID-19). Drug repurposing is one of the most rapid strategies for addressing this need and numerous compounds have been selected for in vitro testing by several groups already. These have led to a growing database of molecules with in vitro activity against the virus. Machine learning models can assist drug discovery through prediction of the best compounds based on previously published data. Herein we have implemented several machine learning methods to develop predictive models from recent SARS-CoV-2 in vitro inhibition data and used them to prioritize additional FDA approved compounds for in vitro testing selected from our in-house compound library. From the compounds predicted with a Bayesian machine learning model, CPI1062 and CPI1155 showed antiviral activity in HeLa-ACE2 cell-based assays and represent potential repurposing opportunities for COVID-19. This approach can be greatly expanded to exhaustively virtually screen available molecules with predicted activity against this virus as well as a prioritization tool for SARS-CoV-2 antiviral drug discovery programs. The very latest model for SARS-CoV-2 is available at www.assaycentral.org.


title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors

text: Background: The pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has tremendous consequences for our societies. Knowledge of the seroprevalence of SARS-CoV-2 is needed to accurately monitor the spread of the epidemic and also to calculate the infection fatality rate (IFR). These measures may help the authorities to make informed decisions and adjust the current societal interventions. Blood donors comprise approximately 4.7% of the similarly aged population of Denmark and blood is donated in all areas of the country. The objective of this study was to perform real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. Methods: All Danish blood donors aged 17-69 years giving blood April 6 to 17 were tested for SARS-CoV-2 immunoglobulin M and G antibodies using a commercial lateral flow test. Antibody status was compared between areas and an estimate of the IFR was calculated. The seroprevalence was adjusted for assay sensitivity and specificity taking the uncertainties of the test validation into account when reporting the 95% confidence intervals (CI). Results: The first 9,496 blood donors were tested and a combined adjusted seroprevalence of 1.7% (CI: 0.9-2.3) was calculated. The seroprevalence differed across areas. Using available data on fatalities and population numbers a combined IFR in patients younger than 70 is estimated at 82 per 100,000 (CI: 59-154) infections. Conclusions: The IFR was estimated to be slightly lower than previously reported from other countries not using seroprevalence data. The IFR, including only individuals with no comorbidity, is likely several fold lower than the current estimate. This may have implications for risk mitigation. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic.


Health Condition and Test Availability as Predictors of Adults' Mental Health during the COVID-19 Pandemic


title: Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure

text: The rapid development of SARS-CoV-2 mediated COVID-19 pandemic has been the cause of significant health concern, highlighting the immediate need for the effective antivirals. SARS-CoV-2 is an RNA virus that has an inherent high mutation rate. These mutations drive viral evolution and genome variability, thereby, facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared the available RdRp sequences of SARS-CoV-2 from Indian isolates and ‘Wuhan wet sea food market virus’ sequence to identify, if any, variation between them. We report seven mutations observed in Indian SARS-CoV-2 isolates and three unique mutations that showed changes in the secondary structure of the RdRp protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that these mutations alter the stability of RdRp protein. Therefore, we propose that RdRp mutations in Indian SARS-CoV-2 isolates might have functional consequences that can interfere with RdRp targeting pharmacological agents.


title: What cost decisiveness? A cost benefit analysis of the lockdown to contain COVID-19 in India

text: On 24th March, 2020 the Government of India announced a national level lockdown to contain the spread of COVID. The lockdown policy has generated considerable controversy, with critics arguing that it was done without adequate notice or planning, exposed vulnerable section of the population to a humanitarian crisis, and failed to contain the spread of COVID. In response, the Government has claimed that lockdown slowed the transmission process of COVID, thereby reducing the number of cases and deaths substantially. The consequent pressure on the health infrastructure was also much less. To judge between competing claims, this study has undertaken the first cost-benefit analysis of the worlds biggest lockdown. Although the data for a proper cost-benefit analysis is currently not available, we have made a ball point estimate of the net benefit of the lockdown under alternative scenarios. Our estimates reveal the net benefits of lockdown to be negative; moreover, the results are robust under all scenarios.


title: Estimation of the Final Size of the COVID-19 Epidemic inBalochistan, Pakistan.

text: COVID-19 is a new disease that is spreading very fast in Pakistan. Cases have been reported from all the provinces in Pakistan including Balochistan. The first two confirmed cases in Pakistan had travel history from Iran to Pakistan, The some of the initial cases were quarantine at Taftan boarder in Balochistan, hence SIR model is used to predict the magnitude of the disease in Balochistan from May 2020 on wards when lock down and other social distancing measures were loosen up by the government of Balochistan. Our Prediction model shows that about 30,00000 individuals in Balochistan will be infected by 5th of July 2020.Over all 25% of the total population of Balochistan will be affected by this disease with 98% (2940,000 ) recovery rate by the end of 15th July 2020.


title: Psychological Distress Among People Losing Work During the COVID-19 Pandemic in Australia

text: Introduction: This study estimated the extent of psychological distress among people losing work during the coronavirus disease of 2019 (COVID-19) pandemic in Australia, and examined associations between distress, nature of work loss and degree of social interaction. Methods: Data were from a baseline online survey of an inception cohort recruited in the weeks following the introduction of physical distancing and movement restrictions to contain the spread of COVID-19 in Australia. These restrictions resulted in widespread unemployment and working hour reduction. Psychological distress was measured using the Kessler-6 scale. Data on nature of work loss, social interactions, demographic, job and occupational characteristics were also collected. Regression modelling was conducted to determine the relationship between work loss, social interactions and psychological distress, accounting for confounders. Results: Among the 551 study participants 31% reported severe psychological distress, 35% in those with job loss and 28% in those still employed but working less. Those who had significantly greater odds of high psychological distress were younger, female, had lost their job and had lower social interactions. The relationship between job loss and distress became non-significant when financial stress, and occupation were included in the regression model, but the protective effect of higher social interactions remained significant. Discussion: There was a high prevalence of psychological distress in people losing work during the COVID-19 pandemic. Age, gender, job loss and social interactions were strongly associated with distress. Interventions that promote social interaction may help to reduce distress during among people losing work during the COVID-19 pandemic.


title: A focus on CORONA VIRUS (COVID-19)

text: The coronavirus episode is a worldwide concern. As time passes, the circumstance appears to change for the most noticeably terrible. An ever-increasing number of individuals are affirmed as contaminated, the death rate goes up somewhat with each deadly case and the infection is advancing outside the Chinese outskirts. The news outlets are everywhere throughout the point, giving day by day or even hourly updates to the inexorably critical circumstance. Be that as it may, most articles and reports appear to concentrate more on instigating alarm and making disarray as opposed to giving an account of log-ical realities or advancing avoidance measures Along these lines, for this arti-cle, how about we leave the frenzy aside and see where that brings us. The Wuhan infection is the main significant wellbeing danger of 2020, yet it’s a long way from being the first or the most noticeably awful wellbeing emergency that humankind confronted. Before we had the Ebola infection, Avian flu and SARS, with the keep goisecng on this rundown, really being a kind of coro-navirus. All were profoundly infectious and possibly savage, yet none caused such an instinctive response from the populace. Regardless of whether we dis-miss those, we have the basic influenza infection that causes a large number of passing right off the bat, and we don’t hear much about that in the news, isn’t that right?.


title: TAMING COVID-19 EPIDEMIC IN SAO PAULO WITH ALOGISTIC MODEL AND NON-PHARMACEUTICAL MEASURES

text: In this paper we use the simple logistic mathematical model to represent the development of COVID-19 epidemic in Saao Paulo city under quarantine regime and we estimate the total amount of time it is necessary to decrease the number of seriously ill in order to reduce the demand for ICU hospital beds to tolerable levels. Clearly the same reasoning used here can be used for any other city in similar conditions.


Role of dermatologists in the uprising of the novel corona virus (COVID'19): Perspectives and opportunities


title: Learning the language of viral evolution and escape

text: Viral mutation that escapes from human immunity remains a major obstacle to antiviral and vaccine development. While anticipating escape could aid rational therapeutic design, the complex rules governing viral escape are challenging to model. Here, we demonstrate an unprecedented ability to predict viral escape by using machine learning algorithms originally developed to model the complexity of human natural language. Our key conceptual advance is that predicting escape requires identifying mutations that preserve viral fitness, or “grammaticality,” and also induce high antigenic change, or “semantic change.” We develop viral language models for influenza hemagglutinin, HIV Env, and SARS-CoV-2 Spike that we use to construct antigenically meaningful semantic landscapes, perform completely unsupervised prediction of escape mutants, and learn structural escape patterns from sequence alone. More profoundly, we lay a promising conceptual bridge between natural language and viral evolution. One sentence summary Neural language models of semantic change and grammaticality enable unprecedented prediction of viral escape mutations.


Diabetic Kidney Disease and COVID-19: The Crash of Two Pandemics


title: Hidden in plain sight: The effects of BCG vaccination in COVID-19 pandemic

text: To investigate the relationship between BCG vaccination and SARS-CoV-2 by bioinformatic approach. Two datasets for Sars-CoV-2 infection group and BCG-vaccinated group were downloaded. Differentially Expressed Genes were identified. Gene ontology and pathways were functionally enriched, and networking was constructed in NetworkAnalyst. Lastly, correlation between post-BCG vaccination and COVID-19 transcriptome signatures were established. A total of 161 DEGs (113 upregulated DEGs and 48 downregulated genes) were identified in the Sars-CoV-2 group. In the pathway enrichment analysis, cross-reference of upregulated KEGG pathways in Sars-CoV-2 with downregulated counterparts in the BCG-vaccinated group, resulted in the intersection of 45 common pathways, accounting for 86.5% of SARS-CoV-2 upregulated pathways. Of these intersecting pathways, a vast majority were immune and inflammatory pathways with top significance in IL-17, TNF, NOD-like receptors, and NF-κB signaling pathways. Our data suggests BCG-vaccination may incur a protective role in COVID-19 patients until a targeted vaccine is developed. Supplementary Materials (https://drive.google.com/open?id=15Na738L282XNaQAJUh0cZf1WoG9jJfzJ)


title: Demographic and Socio-Economic Factors, and Healthcare Resource Indicators Associated with the Rapid Spread of COVID-19 in Northern Italy: An Ecological Study

text: Background: COVID-19 rapidly escalated into a pandemic, threatening 213 countries, areas, and territories the world over. We aimed to identify potential province-level socioeconomic determinants of the virus's dissemination, and explain between-province differences in the speed of its spread, based on data from 36 provinces of Northern Italy. Methods: This is an ecological study. We included all confirmed cases of SARS-CoV-2 reported between February 24th and March 30th, 2020. For each province, we calculated the trend of contagion as the relative increase in the number of individuals infected between two time endpoints, assuming an exponential growth. Pearson's test was used to correlate the trend of contagion with a set of healthcare-associated, economic, and demographic parameters by province. The virus's spread was input as a dependent variable in a stepwise OLS regression model to test the association between rate of spread and province-level indicators. Findings: Multivariate analysis showed that the spread of COVID-19 was correlated negatively with aging index (p-value=0.003), and positively with public transportation per capita (p-value=0.012), the % of private long-term care hospital beds and, to a lesser extent (p-value=0.070), the % of private acute care hospital beds (p-value=0.006). Interpretation: Demographic and socioeconomic factors, and healthcare organization variables were found associated with a significant difference in the rate of COVID-19 spread in 36 provinces of Northern Italy. An aging population seemed to naturally contain social contacts. The availability of healthcare resources and their coordination could play an important part in spreading infection.


title: Clinical analysis of 10 neonates born to mothers with 2019-nCoV pneumonia

text: Background: The newly identified 2019-nCoV, which appears to have originated in Wuhan, the capital city of Hubei province in central China, is spreading rapidly nationwide. A number of cases of neonates born to mothers with 2019-nCoV pneumonia have been recorded. However, the clinical features of these cases have not been reported, and there is no sufficient evidence for the proper prevention and control of 2019- nCoV infections in neonates. Methods: The clinical features and outcomes of 10 neonates (including 2 twins) born to 9 mothers with confirmed 2019-nCoV infection in 5 hospitals from January 20 to February 5, 2020 were retrospectively analyzed. Results: Among these 9 pregnant women with confirmed 2019-nCoV infection, onset of clinical symptoms occurred before delivery in 4 cases, on the day of delivery in 2 cases, and after delivery in 3 cases. In most cases, fever and a cough were the first symptoms experienced, and 1 patient also had diarrhea. Of the newborns born to these mothers, 8 were male and 2 were female; 4 were full-term infants and 6 were born premature; 2 were small-for-gestational-age (SGA) infants and 1 was a large-for-gestational-age (LGA) infant; there were 8 singletons and 2 twins. Of the neonates, 6 had a Pediatric Critical Illness Score (PCIS) score of less than 90. Clinically, the first symptom in the neonates was shortness of breath (n=6), but other initial symptoms such as fever (n=2), thrombocytopenia accompanied by abnormal liver function (n=2), rapid heart rate (n=1), vomiting (n=1), and pneumothorax (n=1) were observed. Up to now, 5 neonates have been cured and discharged, 1 has died, and 4 neonates remain in hospital in a stable condition. Pharyngeal swab specimens were collected from 9 of the 10 neonates 1 to 9 days after birth for nucleic acid amplification tests for 2019-nCoV, all of which showed negative results. Conclusions: Perinatal 2019-nCoV infection may have adverse effects on newborns, causing problems such as fetal distress, premature labor, respiratory distress, thrombocytopenia accompanied by abnormal liver function, and even death. However, vertical transmission of 2019-nCoV is yet to be confirmed.


title: COVID-19 managed with early non-invasive ventilation and a bundle pharmacotherapy: A case report

text: BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has become an immense public health burden, first in China and subsequently worldwide. Developing effective control measures for COVID-19, especially measures that can halt the worsening of severe cases to a critical status is of urgent importance. CASE SUMMARY A 52-year-old woman presented with a high fever (38.8 °C), chills, dizziness, and weakness. Epidemiologically, she had not been to Wuhan where COVID-19 emerged and did not have a family history of a disease cluster. A blood test yielded a white blood cell count of 4.41 x 109/L (60.6 ± 2.67% neutrophils and 30.4 ± 1.34% lymphocytes). Chest imaging revealed bilateral ground-glass lung changes. Based on a positive nasopharyngeal swab nucleic acid test result and clinical characteristics, the patient was diagnosed with COVID-19. Following treatment with early non-invasive ventilation and a bundle pharmacotherapy, she recovered with a good outcome. CONCLUSION Early non-invasive ventilation with a bundle pharmacotherapy may be an effective treatment regimen for the broader population of patients with COVID-19.


title: Heart injury signs are associated with higher and earlier mortality in coronavirus disease 2019 (COVID-19)

text: Importance: Heart injury can be easily induced by viral infection such as adenovirus and enterovirus. However, whether coronavirus disease 2019 (COVID-19) causes heart injury and hereby impacts mortality has not yet been fully evaluated. Objective: To explore whether heart injury occurs in COVID-19 on admission and hereby aggravates mortality later. Design, Setting, and Participants A single-center retrospective cohort study including 188 COVID-19 patients admitted from December 25, 2019 to January 27, 2020 in Wuhan Jinyintan Hospital, China; follow up was completed on February 11, 2020. Exposures: High levels of heart injury indicators on admission (hs-TNI; CK; CK-MB; LDH; α-HBDH). Main Outcomes and Measures: Mortality in hospital and days from admission to mortality (survival days). Results: Of 188 patients with COVID-19, the mean age was 51.9 years (standard deviation: 14.26; range: 21~83 years) and 119 (63.3%) were male. Increased hs-TnI levels on admission tended to occur in older patients and patients with comorbidity (especially hypertension). High hs-TnI on admission (≥ 6.126 pg/mL), even within the clinical normal range (0~28 pg/mL), already can be associated with higher mortality. High hs-TnI was associated with increased inflammatory levels (neutrophils, IL-6, CRP, and PCT) and decreased immune levels (lymphocytes, monocytes, and CD4+ and CD8+ T cells). CK was not associated with mortality. Increased CK-MB levels tended to occur in male patients and patients with current smoking. High CK-MB on admission was associated with higher mortality. High CK-MB was associated with increased inflammatory levels and decreased lymphocytes. Increased LDH and α-HBDH levels tended to occur in older patients and patients with hypertension. Both high LDH and α-HBDH on admission were associated with higher mortality. Both high LDH and α-HBDH were associated with increased inflammatory levels and decreased immune levels. hs-TNI level on admission was negatively correlated with survival days (r= -0.42, 95% CI= -0.64~-0.12, P=0.005). LDH level on admission was negatively correlated with survival days (r= -0.35, 95% CI= -0.59~-0.05, P=0.022). Conclusions and Relevance: Heart injury signs arise in COVID-19, especially in older patients, patients with hypertension and male patients with current smoking. COVID-19 virus might attack heart via inducing inflammatory storm. High levels of heart injury indicators on admission are associated with higher mortality and shorter survival days. COVID-19 patients with signs of heart injury on admission must be early identified and carefully managed by cardiologists, because COVID-19 is never just confined to respiratory injury.


title: Predicting Geographic Location from Genetic Variation with Deep Neural Networks

text: Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches. In simulations, Locator infers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverage Locator’s computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively.


title: Low-Dose Whole-Lung Radiation for COVID-19 Pneumonia

text: Background: Safety of whole-lung low-dose radiation therapy (LD-RT) for COVID-19 pneumonia has been established in two phase I trials. By focally dampening pulmonary cytokine hyperactivation, LD-RT may improve outcomes in hospitalized and oxygen-dependent COVID-19 patients. Methods: Patients with COVID-19 pneumonia were treated with 1.5 Gy whole-lung LD-RT, followed for 28 days or at least until hospital discharge, and compared to an age- and comorbidity-matched control cohort. COVID-19-positive patients eligible for this protocol were hospitalized, had radiographic consolidations, and required supplemental oxygen. Efficacy endpoints were time to clinical recovery, radiographic improvement, and serologic responses. Results: Ten patients received whole-lung LD-RT between April 24 and May 24, 2020 and were compared to ten matched control patients, of whom six received COVID-directed therapy. Median time to clinical recovery was 12 days for the control cohort vs 3 days for LD-RT (HR 2.9, p=0.05). Median time to hospital discharge (20 and 12 days, p=0.19), and intubation rates (40% and 10%, p=0.12) were shorter for the LD-RT cohort. The LD-RT cohort had faster radiographic improvement (p=0.03), even among patients with high COVID burden. Serologic recovery in specific hematologic, cardiac, hepatic, clotting, and inflammatory markers occurred more rapidly following LD-RT than among matched controls. Conclusions: Strong efficacy signals, including a 3-fold risk reduction in time to clinical improvement, were observed following LD-RT compared to matched patients receiving COVID-directed therapy for COVID-19 pneumonia. Given the global availability of radiation accelerators, ongoing international efforts to investigate the optimal role of LD-RT in COVID-19 pneumonia are justified. Clinical Trial Registration: NCT04366791.


title: Ethnically diverse mutations in PIEZO1 associate with SARS-CoV-2 positivity

text: COVID-19, caused by the SARS-CoV-2 virus, carries significant risk of mortality and has spread globally with devastating societal consequences. Endothelial infection has been identified as a feature of the disease and so there is motivation to determine the relevance of endothelial membrane mechanisms affecting viral entry and response. Here, through a study of patient data in UK Biobank released on 16 April 2020, we suggest relevance of PIEZO1, a non-selective cation channel protein that both mediates endothelial responses to mechanical force and unusually indents the cell membrane. PIEZO1 notably has roles that may also be relevant in red blood cell function, pulmonary inflammation, bacterial infection and fibrotic auto-inflammation. We provide evidence that single nucleotide polymorphisms (SNPs) in the gene encoding PIEZO1 are more common in individuals who test positive for SARS-CoV-2 regardless of pre-existing hypertension, myocardial infarction, stroke, diabetes mellitus or arthritis. Some of these SNPs are more common in African and Caribbean populations, which are groups that were recently shown to have greater susceptibility to infection. One of the SNPs is a missense mutation that results in an amino acid change in an evolutionarily conserved and previously unexplored N-terminal region PIEZO1. The data support the notion of genetic factors influencing SARS-CoV-2 infection and suggest a specific role for PIEZO1.


title: South Africa hopes its battle with HIV and TB helped prepare it for COVID-19

text: As the COVID-19 pandemic sweeps into South Africa, the decades the country has spent fighting the world’s worst combined epidemic of tuberculosis (TB) and HIV could give it an advantage But those infections could also worsen the pandemic’s impact By 6 April, South Africa had 1686 confirmed COVID-19 infections, the highest number on the continent—and that is almost certainly an undercount At the same time, one in every five people aged 15 to 49 is HIV positive and two to three people die every hour from TB South African scientists hope the resources and health networks built to fight those diseases will help them battle the new pandemic “The COVID-19 response draws on the same skills as TB and HIV,” says Gavin Churchyard, director of the Aurum Institute, a Johannesburg-based research and health care nonprofit


title: Does Gender or Religion Contribute to the Risk of COVID-19 in Hospital Doctors?

text: The novel coronavirus pandemic is posing significant challenges to healthcare workers (HCWs) in adjusting to redeployed clinical settings and enhanced risk to their own health. Studies suggest a variable impact of COVID-19 based on factors such as age, gender, comorbidities and ethnicity. Workplace measures such as personal protective equipment (PPE), social distancing (SD) and avoidance of exposure for the vulnerable, mitigate this risk. This online questionnaire-based study explored the impact of gender and religion in addition to workplace measures associated with risk of COVID-19 in hospital doctors in acute and mental health institutions in the UK. The survey had 1206 responses, majority (94%) from BAME backgrounds. A quarter of the respondents had either confirmed or suspected COVID-19, a similar proportion reported inadequate PPE and 2/3 could not comply with SD. One third reported being reprimanded in relation to PPE or avoidance of risk. In univariate analysis, age over 50 years, being female, Muslim and inability to avoid exposure in the workplace was associated with risk of COVID-19. On multivariate analysis, inadequate PPE remained an independent predictor with a twofold (OR 2.29, (CI - 1.22-4.33), p=0.01) risk of COVID-19. This study demonstrates that PPE, SD and workplace measures to mitigate risk remain important for reducing risk of COVID-19 in hospital doctors. Gender and religion did not appear to be independent determinants. It is imperative that employers consolidate risk reduction measures and foster a culture of safety to encourage employees to voice any safety concerns.


title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection

text: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that have been found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs that would target their own genes or alter the host gene expression, there are examples of miRNAs functioning as an antiviral defense mechanism. In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Our PANTHER gene function analysis results indicate that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription. For instance, a transcriptional regulator, STAT1 and transcription machinery might be targeted by virus-derived miRNAs. In addition, many known human miRNAs appear to be able to target viral genes. Considering the fact that miRNA-based therapies have been successful before, comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics.


title: Cholesterol Metabolism--Impact for SARS-CoV-2 Infection Prognosis, Entry, and Antiviral Therapies

text: Abstract The recently emerged pathogenic SARS-coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global pandemic. In this study, we show that SARS-CoV-2 infection was associated with clinically significant lower level of HDL cholesterol (HDL-C), which can be used as indicators of disease severity and poor prognosis. Importantly, we found the spike protein of SARS-CoV-2 (SARS-2-S) bound to HDL. Antagonists of HDL receptor-Scavenger receptor class B type I (SR-B1), strongly inhibited SARS-CoV-2 infection. Notably, the lipids transfer function of SR-B1 was indispensable for this inhibition, offering explanations for the reduced serum HDL level observed in COVID-19 patients. Basing on findings here, we speculate that SR-B1-mediated pulmonary HDL-vitamin E uptake could participate in mediating SARS-CoV-2 infection of lung cells, and the unique expression profile of SR-B1 may also affect SARS-CoV-2 cell and tissue tropism. These findings might help to provide further insights into viral transmission, pathological characteristics and reveal therapeutic targets.


title: High levels of SARS-CoV-2 specific T-cells with restricted functionality in patients with severe course of COVID-19

text: Patients infected with SARS-CoV-2 differ in the severity of disease. In this study, SARS-CoV-2 specific T-cells and antibodies were characterized in patients with different COVID-19 related disease severity. Despite severe lymphopenia affecting all major lymphocyte subpopulations, patients with severe disease mounted significantly higher levels of SARS-CoV-2 specific T-cells as compared to convalescent individuals. SARS-CoV-2 specific CD4 T-cells dominated over CD8 T-cells and closely correlated with the number of plasmablasts and SARS-CoV-2 specific IgA- and IgG-levels. Unlike in convalescents, SARS-CoV-2 specific T-cells in patients with severe disease showed marked alterations in phenotypical and functional properties, which also extended to CD4 and CD8 T-cells in general. Given the strong induction of specific immunity to control viral replication in patients with severe disease, the functionally altered phenotype may result from the need for contraction of specific and general immunity to counteract excessive immunopathology in the lung.


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.