title: The spectrum of COVID-19-associated dermatologic manifestations: an international registry of 716 patients from 31 countries

text: Question: What are the cutaneous manifestations associated with COVID-19 and do they provide insight into the pathophysiology or prognosis? Findings: In this international registry-based case series of 716 patients representing 31 countries, the most common dermatologic morphologies encountered in the 171 COVID-19 confirmed case included morbilliform, pernio-like, urticarial, macular erythema, vesicular, papulosquamous, and retiform purpura. Retiform purpura was seen exclusively in critically ill, hospitalized patients. Meaning: COVID-19 is associated with a spectrum of skin findings in affected patients. These cutaneous manifestations may vary depending on the severity of COVID-19.


title: Human organs-on-chips as tools for repurposing approved drugs as potential influenza and COVID19 therapeutics in viral pandemics

text: Rapidly spreading viral pandemics, such as those caused by influenza and SAR-CoV-2 (COVID19), require rapid action and the fastest way to combat this challenge is by repurposing existing drugs as anti-viral therapeutics. Here we first show that human organ-on-a-chip (Organ Chip) microfluidic culture devices lined by a highly differentiated, primary, human lung airway epithelium cultured under an air-liquid interface and fed by continuous medium flow can be used to model virus entry, replication, strain-dependent virulence, host cytokine production, and recruitment of circulating immune cells in response to infection by influenza, as well as effects of existing and novel therapeutics. These Airway Chips, which contain human lung epithelial cells that express high levels of ACE2 and TMPRSS2, were then used to assess the inhibitory activities of 7 clinically approved drugs (chloroquine, arbidol, toremifene, clomiphene, amodiaquine, verapamil, and amiodarone) that we found inhibit infection by viral pseudoparticles expressing SARS-CoV-2 spike protein in human Huh-7 cells, and others recently showed suppress infection by native SARS-CoV-2 in Vero cells. However, when these drugs were administered under flow at the maximal concentration in blood reported in clinical studies in human Airway Chips, only two of these drugs — amodiaquine and toremifene — significantly inhibited entry of the pseudotyped SARS-CoV-2 virus. This work suggests that human Organ Chip technology may be used in conjunction with existing rapid cell-based screening assays to study human disease pathogenesis and expedite drug repurposing in biothreat crises caused by pandemic viruses.


title: Coronavirus Disease (COVID-19) and Traumatic Stress: Probable Risk Factors and Correlates of Posttraumatic Stress Disorder

text: The Coronavirus Disease (COVID-19) outbreak, which first began in December 2019 in China, has since become a global health crisis with vast and devastating consequences for individuals and societies. Both earlier research and recent findings suggest that infectious disease epidemics and pandemics can be highly traumatic experiences for some individuals and lead to posttraumatic stress disorder (PTSD) and chronic psychological distress. Mental health risks associated with COVID-19 have yet to be systematically studied; however, the emerging literature on COVID-19, as well as previous studies on infectious disease outbreaks provide insights into probable risk factors and correlates of PTSD. In this paper, we provide a brief review of these studies and discuss probable risk factors for PTSD and chronic psychological distress related to COVID-19.


title: AN INTERACTIVE COVID-19 MOBILITY IMPACT AND SOCIAL DISTANCING ANALYSIS PLATFORM

text: The research team has utilized privacy-protected mobile device location data, integrated with COVID-19 case data and census population data, to produce a COVID-19 impact analysis platform that can inform users about the effects of COVID-19 spread and government orders on mobility and social distancing. The platform is being updated daily, to continuously inform decision-makers about the impacts of COVID-19 on their communities using an interactive analytical tool. The research team has processed anonymized mobile device location data to identify trips and produced a set of variables including social distancing index, percentage of people staying at home, visits to work and non-work locations, out-of-town trips, and trip distance. The results are aggregated to county and state levels to protect privacy and scaled to the entire population of each county and state. The research team are making their data and findings, which are updated daily and go back to January 1, 2020, for benchmarking, available to the public in order to help public officials make informed decisions. This paper presents a summary of the platform and describes the methodology used to process data and produce the platform metrics.


What is the current state of knowledge about the novel coronavirus infection during pregnancy?


title: A Novel Method of Immunomodulation of Endothelial cells Using Streptococcus Pyogenes and its Lysate

text: Background Coronary artery diseases and autoimmune disorders are common in clinical practice. In this study, a novel method of immune-modulation to modify the endothelial function was studied to modulate the features of the endothelial cells, and thereby to reduce coronary artery disease and other disorders modulated by endothelium. Methods HUVEC cells were seeded in the cell culture, and streptococcus pyogenes were added to the cell culture, and the supernatant was studied for the secreted proteins. In the second phase, the bacterial lysate was synthesized, and the lysate was added to cell culture; and the proteins in the supernatant were studied at various time intervals. Results When streptococcus pyogenes alone was added to culture, E Cadherin, Angiostatin, EpCAM and PDGF-AB were some of the biomarkers elevated significantly. HCC1, IGFBP2 and TIMP were some of the biomarkers which showed a reduction. When the lysate was added, the cell-culture was maintained for a longer time, and it showed the synthesis of immune regulatory cytokines. Heatmap analysis showed a significant number of proteins/cytokines concerning the immune/pathways, and toll-like receptors superfamily were modified. BLC, IL 17, BMP 7, PARC, Contactin2, IL 10 Rb, NAP 2 (CXCL 7), Eotaxin 2 were maximally increased. By principal component analysis, the results observed were significant. Conclusion There is potential for a novel method of immunomodulation of the endothelial cells, which have pleiotropic functions, using streptococcus pyogenes and its lysates.


title: Clinical characteristics and fecal-oral transmission potential of patients with COVID-19

text: Background: A significant proportion of patients with COVID-19 generate negative pharyngeal swab viral nucleic acid test results but test positive using fecal samples. However, fecal-oral transmission of COVID-19 has not been established to date. The purpose of this study was to evaluate the duration of fecal swab positivity in COVID-19 patients after pharyngeal swab nucleic acid test turned negative and to explore its potential for fecal-oral transmission. Methods: A retrospective analysis of clinical records, laboratory results, and chest computed tomography (CT) findings of 17 COVID-19 patients confirmed by laboratory tests from January 22 to February 7, 2020 at a tertiary hospital was performed. The potential of fecal-oral transmission was assessed by detecting the presence of SARS-CoV-2 nucleic acid in fecal swab samples. Results: A total of 16 patients (94.1%) had fever; other symptoms included dry cough, dyspnea, nausea, diarrhea, sore throat, fatigue, and muscle pain. Three patients had decreased white blood cell counts, 7 had decreased lymphocyte numbers, and 7 had increased C-reactive protein levels. Fecal samples of 11 patients tested positive for SARS-CoV-2 nucleic acid, of whom the time for the fecal samples to become SARS-CoV-2 nucleic acid-negative was longer in 10 patients than that for pharyngeal swab samples, and only one case exhibited a shorter time for his fecal sample to become SARS-CoV-2 nucleic acid-negative compared to his pharyngeal swab sample. The remaining 6 patients were negative for SARS-CoV-2 nucleic acid in fecal samples. Conclusion: In COVID-19 patients who tested positive for SARS-CoV-2 nucleic acid in both pharyngeal swab and fecal samples, the time for the fecal samples to become SARS-CoV-2 nucleic acid-negative was generally longer than that in pharyngeal swab samples. However, there is currently no evidence demonstrating that the virus can be transmitted through the fecal-oral route.


title: Global Status of COVID-19 Diagnosis: An Overview

text: Since the beginning of the New Year 2020, countries around the world are stumbling due to the coronavirus disease (COVID-19) pandemic Better approaches of diagnostics and medical facilities have helped some countries recover early Previous exposures to epidemics have imparted lessons to handle such a pandemic with a high level of preparedness The World Health Organization (WHO) and national health authorities are taking great efforts via efficient and impactful interventions to contain the virus Diagnostic tests such as reverse transcription-polymerase chain reaction are increasingly being used to confirm the diagnosis because testing biological samples for the presence of the virus is the definitive method to identify the disease, analyze the risk for transmission, and determine whether someone has been cured or not It is also important to screen asymptomatic individuals to get the exact overview of the virus spread Antibody detection plays a pivotal role in diagnosis;however, using it at the wrong time yields negative results and conveys dissenting opinion about the tests Although the scaling up of testing has been significant, overall testing has been limited by the availability of diagnostics Rapid diagnoses and discontinuation of transmission are keys to ending this pandemic Diagnostics manufacturers are developing test kits and distributing them to different countries Therefore, more than 500 commercial test kits for molecular- and immunoassays, most with Emergency Use Authorization, are now becoming available in the market In this review, we discuss the importance of diagnostics, approaches of different countries toward the epidemic, global testing situation, and lessons to countries at the start of the epidemic for better preparedness


Prise en charge de l’épidémie de COVID-19 en santé au travail des soignants : situation à Taiwan et en Italie au 20 mars 2020


title: How many lives can be saved? A global view on the impact of testing, herd immunity and demographics on COVID-19 fatality rates

text: In this work, we assess the global impact of COVID-19 showing how demographic factors, testing policies and herd immunity are key for saving lives. We extend a standard epidemiological SEIR model in order to: (a) identify the role of demographics (population size and population age distribution) on COVID-19 fatality rates; (b) quantify the maximum number of lives that can be saved according to different testing strategies, different levels of herd immunity, and specific population characteristics; and (d) infer from the observed case fatality rates (CFR) what the true fatality rate might be. Different from previous SEIR model extensions, we implement a Bayesian Melding method in our calibration strategy which enables us to account for data limitation on the total number of deaths. We derive a distribution of the set of parameters that best replicate the observed evolution of deaths by using information from both the model and the data.


title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy

text: The infection of the novel coronavirus SARS-CoV-2 have caused more than 150,000 deaths, but no vaccine or specific therapeutic antibody is currently available. SARS-CoV-2 relies on its spike protein, in particular the receptor binding domain (RBD), to bind human cell receptor angiotensin-converting enzyme 2 (ACE2) for viral entry, and thus targeting RBD holds the promise for preventing SARS-CoV-2 infection. In this work, a competitive biopanning strategy of a phage display antibody library was applied to screen blocking antibodies against RBD. High-affinity antibodies were enriched after the first round using a standard panning process in which RBD-His recombinant protein was immobilized as a bait. At the next two rounds, immobilized ACE2-Fc and free RBD-His proteins were mixed with the enriched phage antibodies. Antibodies binding to RBD at epitopes different from ACE2-binding site were captured by the immobilized ACE2-Fc, forming a “sandwich” complex. Only antibodies competed with ACE2 for recognizing RBD at the same or similar epitopes can bind to the free RBD-His in the supernatant and be subsequently separated by the Ni-NTA magnetic beads. Top 1 lead from the competitive biopanning of a synthetic antibody library, Lib AB1, was produced as the full-length IgG1 format. It was proved to competitively block the binding of RBD to ACE2 protein, and potently inhibit SARS-CoV-2 pseudovirus infection of ACE2-overexpressing Hela cells with IC50 values of 12nM. Nevertheless, top 1 lead from the standard biopanning of Lib AB1, can only bind to RBD in vitro but not have the blocking or neutralization activity. Our strategy can efficiently isolate the blocking antibodies of RBD, and it would speed up the discovery of neutralizing antibodies against SARS-CoV-2.


title: COVID-19: Projecting the impact in Rohingya refugee camps and beyond

text: Background: COVID-19 could have even more dire consequences among refugees living in camps than in general populations. Bangladesh has confirmed COVID-19 cases and hosts almost 1 million Rohingya refugees from Myanmar with 600,000 concentrated in Kutupalong-Balukhali Expansion Site. Projections of the potential COVID-19 infection burden, epidemic speed, and healthcare needs in such settings are critical to inform preparedness planning. Methods: To explore the potential impact of the introduction of SARS-CoV-2 in Kutupalong-Balukhali Expansion Site, we used a stochastic disease transmission model with parameters derived from emerging literature. We considered three scenarios with different assumptions about the transmission potential of SARS-CoV-2. We estimated the number and daily rate of infections, hospitalizations, deaths, and healthcare needs expected under each scenario. Findings: A large-scale outbreak is highly likely after a single introduction of the virus into the camp across scenarios with 65-95% of simulations leading to at least 1,000 infections. Estimated infections range from 119-504 between low and high transmission scenarios in the first 30 days; and between 424,798 and 543,647 in 12 months. Hospitalization needs exceeded the existing hospitalization capacity of 340 beds after 58-139 days between the low and high transmission scenarios. Estimated deaths range from 1,647-2,109 between low and high transmission scenarios. Interpretation: A COVID-19 epidemic in a refugee settlement may have profound consequences, requiring unrealistically large increases in healthcare capacity and infrastructure. Detailed and realistic planning for the worst in Kutupalong-Balukhali and all refugee camps worldwide must begin now. Plans should consider novel and radical strategies to reduce infectious contacts and fill health worker gaps while recognizing that refugees may not have access to national health systems. As global resources to fight this pandemic become scarce, displaced persons must not be forgotten.


title: Laboratory Findings of COVID-19 Infection are Conflicting in Different Age Groups and Pregnant Women: A Literature Review

text: Coronavirus disease 2019 (COVID-19), a new type and rapidly spread viral pneumonia, is now producing an outbreak of pandemic proportions. The clinical features and laboratory results of different age groups are different due to the general susceptibility of the disease. The laboratory findings of COVID-19 in pregnant women are also conflicting. Para-clinical investigations including laboratory tests and radiologic findings play an important role in early diagnosis and treatment monitoring of severe acute respiratory syndrome and coronavirus-2 (SARS-CoV-2). The majority of previous reports on the SARS-CoV-2 laboratory results were based on data from the general population and limited information is available based on age difference and pregnancy status. This review aimed to describe the COVID-19 laboratory findings in neonates, children, adults, elderly and pregnant women altogether for the first time. The most attracting and reliable markers of COVID-19 in patients were: normal C-reactive protein (CRP) and very different and conflicting laboratory results regardless of clinical symptoms in neonates, normal or temporary elevated CRP, conflicting WBC count results and procalcitonin elevation in children, lymphopenia and elevated lactate dehydrogenase (LDH) in adult patients, lymphopenia and elevated CRP and LDH in the elderly people and high CRP, leukocytosis and elevated neutrophil ratio in pregnant women.


La télémédecine est-elle devenue l’avenir de la médecine de la personne? Réflexions d’un confiné au temps du COVID


docid: noaofcyb

title: Myocardial injury is associated with higher mortality in patients with coronavirus disease 2019: a meta-analysis


title: A modification to the Maquet Flow-i anaesthesia machinefor ICU ventilation

text: The authors present an easily manufactured modification of the Getinge Group Maquet Flow-i anaesthesia machine that gives it potential to be used long-term as an Intensive Care ventilator for emergency circumstances. There are some 7000 such machines in use worldwide, which could assist in increasing ICU ventilated bed capacity in a number of nations. The authors believe this modification has potential as a solution to increasing ventilator numbers for the COVID-19 pandemic, in hospitals where the Flow-i is underutilised for its designed purpose during this emergency. The technical drawing files are downloadable on the GrabCAD website and are Creative Commons (CC-BY 4.0) licensed to allow local manufacture of the modification.


title: Acute gastrointestinal injury in critically ill patients with coronavirus disease 2019 in Wuhan, China

text: Background: To investigate the prevalence and outcomes of acute gastrointestinal injury (AGI) in critically ill patients with coronavirus disease 2019 (COVID-19). Methods: In this clinical retrospective study, demographic data, laboratory parameters, AGI grades, clinical severity and outcomes were collected. The primary endpoints were AGI incidence and 28-day mortality, the secondary endpoints were organ dysfunction and septic shock incidence. Results: From February 10 to March 10 2020, 83 critically ill patients of 1314 patients with COVID-19 were enrolled. Seventy-two (86.7%) patients had AGI during hospital stay, of them, 30 had AGI grade I, 35 had AGI grade II, 5 had AGI grade III, and 2 had AGI grade IV. The incidence of AGI grade II and above was 50.6%. As of March 16, 40 (48.2%) patients died within 28 days of admission, the median hospital stay was 12.0 days, ranging from 3 days to 27 days. Multiple organ dysfunction syndrome developed in 58 (69.9%) patients, septic shock in 16 (19.3%) patients. Patients with worse AGI grades had worse clinical variables, higher septic shock incidence and 28-day mortality. Sequential organ failure assessment scores (SOFA) (95% CI, 1.374-2.860; P <0.001), white blood cell (WBC) counts (95% CI, 1.037-1.379; P =0.014), duration of mechanical ventilation (MV) (95% CI, 1.020-1.340; P =0.025) were risk factors for the development of AGI grade II and above. Non-survivors were accompanied by higher incidence of AGI grade III to IV than survivors (17.5% vs. 0.0%, P =0.004). Conclusions: The AGI incidence was 86.7%, and hospital mortality was 48.2% in critically ill patients with COVID-19. SOFA scores, WBC counts, and duration of MV were risk factors for the development of AGI grade II and above. Patients with worse AGI grades had worse clinical severity variables, higher septic shock incidence and 28-day mortality.


title: Complexity signatures in the COVID-19 epidemic: power law behaviour in the saturation regime of fatality curves

text: We apply a versatile growth model, whose rate of change is given by a generalised beta distribution, to describe the complex behaviour of the fatality curves of the COVID-19 disease for several countries in Europe and Asia. We show that the COVID-19 epidemic curves not only may present a subexponential early growth but can also exhibit a similar subexponential (power-law) behaviour in the saturation regime. We argue that the power-law exponent of the latter regime, which measures how quickly the curve approaches the plateau, is directly related to control measures, in the sense that the less strict the control, the smaller the exponent and hence the slower the diseases progresses to its end. The power-law saturation uncovered here is an important result, because it signals to health authorities that it is important to keep control measures for as long as possible, so as to avoid a slow, power-law ending of the disease. The slower the approach to the plateau, the longer the virus lingers on in the population, and the greater not only the death toll but also the risk of resurgence.


title: Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens

text: Aims: This retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs). Methods and Results: All adults with SARS-CoV-2 infection in two Italian provinces were followed for a median of 24 days. ARBs and/or ACEi treatments, and hypertension, diabetes, cancer, COPD, renal and major cardiovascular diseases (CVD) were extracted from clinical charts and electronic health records, up to two years before infection. The sample consisted of 1603 subjects (mean age 58.0y; 47.3% males): 454 (28.3%) had severe symptoms, 192 (12.0%) very severe or lethal disease (154 deaths; mean age 79.3 years; 70.8% hypertensive, 42.2% with CVD). The youngest deceased person aged 44 years. Among hypertensive subjects (n=543), the proportion of those treated with ARBs or ACEi were 88.4%, 78.7% and 80.6% among patients with mild, severe and very severe/lethal disease, respectively. At multivariate analysis, no association was observed between therapy and disease severity (Adjusted OR for very severe/lethal COVID-19: 0.87; 95% CI: 0.50-1.49). Significant predictors of severe disease were older age (with AORs largely increasing after 70 years of age), male gender (AOR: 1.76; 1.40-2.23), diabetes (AOR: 1.52; 1.05-2.18), CVD (AOR: 1.88; 1.32-2.70) and COPD (1.88; 1.11-3.20). Only gender, age and diabetes also predicted very severe/lethal disease. Conclusion: No association was found between COVID-19 severity and treatment with ARBs and/or ACEi, supporting the recommendation to continue medication for all patients unless otherwise advised by their physicians.


title: Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2

text: Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV, also known as SARS-CoV-2), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV/SARS-CoV-2. Drug repurposing, representing as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV–host interactome and drug targets in the human protein–protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity with SARS-CoV (79.7%). Specifically, the envelope and nucleocapsid proteins of 2019-nCoV/SARS-CoV-2 are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. We further identify three potential drug combinations (e.g., sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) captured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations targeting 2019-nCoV/SARS-CoV-2.


title: Test, track, and trace: How is the NHSX Covid app performing in a hospital setting?

text: Objective To assess the uptake and use of the trial contact tracing app developed by NHSX by healthcare workers. Design Cross-sectional study using survey questionnaire. Setting Healthcare industry: St Mary's Hospital, a small NHS district hospital on the Isle of Wight, United Kingdom. Participants NHS staff members employed by the Isle of Wight NHS Trust. Results Of 3100 eligible staff members, 462 (~15%) responded to the survey. Of the respondents, 90% were aged between 31 and 65, and half had direct patient contact through their job role. Almost three quarters (73%) used social media apps on their smartphones. 421 out of 460 respondents had no trouble downloading and installing the NHSX Covid app on their smartphones. 20% of respondents were left confused by instructions to turn off Bluetooth when wearing PPE. Only 35 people either had to report symptoms or received an alert of contact with a suspected covid case. Of these over 20% were not clear what to do in such a situation. Conclusions The trial app has been embraced and adopted well. Many have experienced no problems with it. However, some healthcare workers have been unable to download or install the app due to compatibility issues and some have been left confused by having to turn off Bluetooth whilst wearing PPE. This raises questions as to the effectiveness of the app for its intended purpose in contact tracing efforts. Recommendations We recommend that the wording of alerts and guidance provided by the app be made clearer and more accessible. We also recommend developments to the app to facilitate use by healthcare workers in a clinical setting. We also propose that "app instructors" be made available in hospitals to ensure that patients and staff can access help and advice on use of the app.


title: Our fight against the rapidly evolving COVID-19 pandemic: A review of India's actions and proposed way forward

text: A new strain of coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has overwhelmed the world with its rapid spread and high number of cases. SARS-CoV-2 causes COVID-19 disease which may present with mild, moderate, or severe illness. In severe cases, pneumonia, acute respiratory distress syndrome, sepsis, and septic shock can occur. Individuals above 60 years and people with preexisting comorbidities are at higher risk for developing serious complications. The incubation period of this new pathogen ranges from 1 to 14 days and there is no preexisting immunity to the disease. Countries across the globe have adopted various prevention and control measures to minimize negative health impacts. India has adopted various public health measures which include social distancing measures, nationwide lockdown to reduce risk of exposure, widespread IEC messaging regarding hand-washing, usage of masks, and recommending avoidance of unnecessary travel to combat the spread of disease. This manuscript reviews the global situation, contextualizes India's disease control efforts, and outlines the possible way forward by identifying specific actions under the following headings: enhancing district preparedness, enabling care for patients, and broadening community and stakeholder engagement for India.


title: Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data

text: The geographic spread of 2019 novel coronavirus (COVID-19) infections from the epicenter of Wuhan, China, has provided an opportunity to study the natural history of the recently emerged virus. Using publicly available event-date data from the ongoing epidemic, the present study investigated the incubation period and other time intervals that govern the epidemiological dynamics of COVID-19 infections. Our results show that the incubation period falls within the range of 2-14 days with 95% confidence and has a mean of around 5 days when approximated using the best-fit lognormal distribution. The mean time from illness onset to hospital admission (for treatment and/or isolation) was estimated at 3-4 days without truncation and at 5-9 days when right truncated. Based on the 95th percentile estimate of the incubation period, we recommend that the length of quarantine should be at least 14 days. The median time delay of 13 days from illness onset to death (17 days with right truncation) should be considered when estimating the COVID-19 case fatality risk.


title: The SARS-CoV-2 pandemic course in Saudi Arabia: A dynamic epidemiological model

text: Objective: Saudi Arabia ranks second in the number of coronavirus disease 2019 (COVID-19) cases in the Eastern Mediterranean region. It houses the two most sacred religious places for Muslims: Mecca and Medina. It is important to know what the trend in case numbers will be in the next 4-6 months, especially during the Hajj pilgrimage season. Methods: Epidemiological data on COVID-19 were obtained from the Saudi Arabian Ministry of Health, the World Health Organization, and the Humanitarian Data Exchange. A susceptible-exposed-infectious-recovered (SEIR) prediction model was constructed to predict the trend in COVID-19 in Saudi Arabia in the next 6 months. Findings: The model predicts that the number of active cases will peak by 20 May 2020. The cumulative infected cases are predicted to reach 59,663 at that time. The total number of infected individuals is estimated reach to 102,647 by the end of the pandemic. Conclusion: Our estimates show that by the time the Hajj season commences in Saudi Arabia, the pandemic will be in the midst of its deceleration phase (phase 3). This information will likely be useful to policymakers in their management of the outbreak.


title: Atypical Presentations of COVID-19 in Care Home Residents presenting to Secondary Care: A UK Single Centre Study

text: Background: The United Kingdom (UK) care home population has experienced high mortality during the COVID-19 pandemic. Atypical presentations of COVID-19 are being reported in older adults and may pose difficulties for early isolation and treatment, particularly in institutional care settings. We aimed to characterise the presenting symptoms and associated mortality of COVID-19 in older adults, with a focus on care home residents and older adults living in the community. Methods: This was a retrospective cohort study of consecutive inpatients over 80 years old hospitalised with PCR confirmed COVID-19 between 10th March 2020 and 8th April 2020. Symptoms at presentation, including those associated with frailty, were analysed. Differences between community dwelling and care home residents, and associations with mortality, were assessed using between-group comparisons and logistic regression. Results: Care home residents were less likely to experience cough (46.9% vs 72.9%, p=0.002) but more likely to present with delirium (51.6% vs 31.4%, p=0.018), particularly hypoactive delirium (40.6% vs 24.3%, p=0.043). Mortality was more likely in the very frail (OR 1.25, 95% CI 1.00, 1.58, p=0.049) and those presenting with anorexia (OR 3.20, 95% CI 1.21, 10.09, p=0.028). There were no differences in either mortality or length of stay between those admitted from care homes and community dwelling older adults. Conclusion: COVID-19 in those over 80 does not always present with typical symptoms, particularly in those admitted from institutional care. These individuals have a reduced incidence of cough and increased hypoactive delirium. Individuals presenting atypically, especially with anorexia, have higher mortality.


title: First peak of COVID-19 outbreak in Japan might pass as of April 26, 2020

text: Background: The COVID-19 outbreak has two inconsistent phenomena: its reproduction number is almost two; and it shows earlier and lower peaks for new cases and the total number of patients. Object: To resolve this difficulty, we constructed a mathematical model that can explain these phenomena. Method: We applied a susceptible-infected-model with the proportion of asymptomatic patients among the infected (q) as a key parameter for estimation as well as the basic reproduction number (R0). Results: We observed the first outbreak peak in Japan on April 3 for those infected on March 29 .Their R0 and q were estimated respectively as 2.048 and 99.987%. Discussion and Conclusion: By introducing a very high proportion of asymptomatic cases, two inconsistent phenomena might be resolved. This hypothesis should be verified through additional study.


title: A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications

text: The SARS-CoV-2 pandemic has been growing exponentially, affecting nearly 900 thousand people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published, in scientific journals as well as through non-peer reviewed channels, to investigate SARS-CoV-2 genetic heterogeneity and spatiotemporal dissemination. We examined full genome sequences currently available to assess the presence of sufficient information for reliable phylogenetic and phylogeographic studies in countries with the highest toll of confirmed cases. Although number of-available full-genomes is growing daily, and the full dataset contains sufficient phylogenetic information that would allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 datasets still present severe limitations. Studies assessing within country spread or transmission clusters should be considered preliminary at best, or hypothesis generating. Hence the need for continuing concerted efforts to increase number and quality of the sequences required for robust tracing of the epidemic. Significance Statement Although genome sequences of SARS-CoV-2 are growing daily and contain sufficient phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution.


title: Work-related Covid-19 transmission

text: Importance: Our study helps fill the knowledge gap related to work-related transmission in the emerging coronaviral pandemic. Objective: To demonstrate high-risk occupations for early coronavirus disease 2019 (Covid-19) local transmission. Methods: In this observational study, we extracted confirmed Covid-19 cases from governmental investigation reports in Hong Kong, Japan, Singapore, Taiwan, Thailand, and Vietnam. We followed each country/area for 40 days after its first locally transmitted case, and excluded all imported cases. We defined a possible work-related case as a worker with evidence of close contact with another confirmed case due to work, or an unknown contact history but likely to be infected in the working environment (e.g. an airport taxi driver). We calculated the case number for each occupation, and illustrated the temporal distribution of all possible work-related cases and healthcare worker (HCW) cases. The temporal distribution was further defined as early outbreak (the earliest 10 days of the following period) and late outbreak (11th to 40th days of the following period). Results: We identified 103 possible work-related cases (14.9%) among a total of 690 local transmissions. The five occupation groups with the most cases were healthcare workers (HCWs) (22%), drivers and transport workers (18%), services and sales workers (18%), cleaning and domestic workers (9%) and public safety workers (7%). Possible work-related transmission played a substantial role in early outbreak (47.7% of early cases). Occupations at risk varied from early outbreak (predominantly services and sales workers, drivers, construction laborers, and religious professionals) to late outbreak (predominantly HCWs, drivers, cleaning and domestic workers, police officers, and religious professionals). Conclusions: Work-related transmission is considerable in early Covid-19 outbreaks, and the elevated risk of infection was not limited to HCW. Implementing preventive/surveillance strategies for high-risk working populations is warranted.


title: C&EN talks with Holden Thorp

text: When Holden Thorp became editor in chief of Science in October 2019, he wasn’t planning to write editorials challenging the US president during an international crisis But as the current pandemic began to unfold, Thorp was triggered by President Donald J Trump’s inaccurate comparisons of COVID-19—the disease caused by the novel coronavirus, SARS-CoV-2—to the flu and the unrealistic expectations he put on vaccine developers and pharmaceutical companies Thorp and his editorial team felt that Trump’s denial of what scientists had been saying “was just so dangerous that we wouldn’t be doing our job if we didn’t speak out,” he says And so he has, by writing a series of editorials about the role of science in addressing the pandemic One of the editorials was widely circulated and cited in the Washington Post and the New York Times—not common for an editorial in a research journal Thorp hopes that the editorials


title: Estimation of the true infection rate and infection fatality rate of COVID-19 in the whole population of each country

text: The true infection rate of COVID-19 and the infection fatality rate in the whole population have been estimated for each country. The estimate well coincided with local surveys. The fact that several tens of times, or more, of identified cases are already infected might require reconsideration of the strategy.


Joint Declaration on COVID-19 by the Japan Stroke and Japanese Circulation Societies


title: Improving COVID-19 Testing Efficiency using Guided Agglomerative Sampling

text: One of the challenges in the current COVID-19 crisis is the time and cost of performing tests especially for large-scale population surveillance. Since, the probability of testing positive in large population studies is expected to be small (<15%), therefore, most of the test outcomes will be negative. Here, we propose the use of agglomerative sampling which can prune out multiple negative cases in a single test by intelligently combining samples from different individuals. The proposed scheme builds on the assumption that samples from the population may not be independent of each other. Our simulation results show that the proposed sampling strategy can significantly increase testing capacity under resource constraints: on average, a saving of ~40% tests can be expected assuming a positive test probability of 10% across the given samples. The proposed scheme can also be used in conjunction with heuristic or Machine Learning guided clustering for improving the efficiency of large-scale testing further. The code for generating the simulation results for this work is available here: https://github.com/foxtrotmike/AS.


title: Infection Dynamics of Coronavirus Disease 2019 (Covid-19) Modeled with the Integration of the Eyring Rate Process Theory and Free Volume Concept

text: The Eyrings rate process theory and free volume concept, two very popular theories in chemistry and physics fields, are employed to treat infectious disease transmissions. The susceptible individ- uals are assumed to move stochastically from one place to another. The virus particle transmission rate is assumed to obey the Eyring rate process theory and also controlled by how much free volume available in a system. The transmission process is considered to be a sequential chemical reaction, and the concentrations or fractions of four epidemiological compartments, the susceptible, the exposed, the infected, and the removed, can be derived and calculated. The obtained equations show that the basic reproduction number, R0, is not a constant, dependent on the volume frac- tion of virus particles, virus particle size, and virus particle packing structure, the energy barrier associated with susceptible individuals, and environment temperature. The developed models are applied to treat coronavirus disease 2019 (Covid-19) transmission and make predictions on peak time, peak infected, and R0. Our work provides a simple and straightforward approach to estimate how infection diseases evolve and how many people may be infected.


title: Capillary Electrophoresis of PCR fragments with 5’-labelled primers for testing the SARS-Cov-2

text: Background Due to the huge demand for SARS-Cov-2 determination, alternatives to the standard qtPCR tests are potentially useful for increasing the number of samples screened. Our aim was to develop a direct fluorescent PCR capillary-electrophoresis detection of the viral genome. We validated this approach on several SARS-Cov-2 positive and negative samples. Study design We isolated the naso-pharingeal RNA from 20 positive and 10 negative samples. The cDNA was synthesised and two fragments of the SARS-Cov-2 were amplified. One of the primers for each pair was 5’-end fluorochrome labelled. The amplifications were subjected to capillary electrophoresis in ABI3130 sequencers to visualize the fluorescent peaks. Results The two SARS-Cov-2 fragments were successfully amplified in the positive samples, while the negative samples did not render fluorescent peaks. Conclusion We describe and alternative method to identify the SARS-Cov-2 genome that could be scaled to the analysis of approximately 100 samples in less than 5 hours. By combining a standard PCR with capillary electrophoresis our approach would overcome the limits imposed to many labs by the qtPCR (lack of reactive and real-time PCR equipment) and increase the testing capacity.


title: Serologic responses to SARS-CoV-2 infection among hospital staff with mild disease in eastern France

text: Background: The serologic response of individuals with mild forms of SARS-CoV-2 infection is poorly characterized. Methods: Hospital staff who had recovered from mild forms of PCR-confirmed SARS-CoV-2 infection were tested for anti-SARS-CoV-2 antibodies using three assays: a LuLISA targeting the N protein (99% specificity), a rapid immunodiagnostic test (99.4% specificity), and a S- Flow assay (>99.5% specificity). The neutralizing activity of the sera was tested with a pseudovirus-based assay. Results: Of 162 hospital staff who participated in the investigation, 160 reported SARS-CoV- 2 infection that had not required hospital admission and were included in these analyses. The median time from symptom onset to blood sample collection was 24 days (IQR: 21-28, range 13-39). The LuLISA N assay detected antibodies in 129 (80.6%) of the samples, with better performance for samples collected after 28 days (45/48 = 93.8%); the rapid immunodiagnostic test in 153 (95.6%); and the S-Flow assay in 159 (99.4%), failing to detect antibodies in one sample collected 18 days after symptom onset (none of the other tests detected antibodies in that patient). Neutralizing antibodies (NAbs) were detected in 79%, 92% and 98% of samples collected 13-20, 21-27 and 28-41 days after symptom onset, respectively (P=0.02). Conclusion: Antibodies against SARS-CoV-2 were detected in virtually all hospital staff after 13 days from the COVID-19 symptom onset. This finding supports the use of serologic testing for the diagnosis of individuals who have recovered from SARS-CoV-2 infection. The neutralizing activity of the antibodies increased overtime. Future studies will help assess the persistence of the humoral response and its associated neutralization capacity in recovered patients.


title: How digital natives learn and thrive in the digital age: Evidence from an emerging economy

text: As a generation of 'digital natives,' secondary students who were born from 2002 to 2010 have various approaches to acquiring digital knowledge. Digital literacy and resilience are crucial for them to navigate the digital world as much as the real world; however, these remain under-researched subjects, especially in developing countries. In Vietnam, the education system has put considerable effort into teaching students these skills to promote quality education as part of the United Nations-defined Sustainable Development Goal 4 (SDG4). This issue has proven especially salient amid the COVID??19 pandemic lockdowns, which had obliged most schools to switch to online forms of teaching. This study, which utilizes a dataset of 1061 Vietnamese students taken from the United Nations Educational, Scientific, and Cultural Organization (UNESCO)'s "Digital Kids Asia Pacific (DKAP)" project, employs Bayesian statistics to explore the relationship between the students' background and their digital abilities. Results show that economic status and parents' level of education are positively correlated with digital literacy. Students from urban schools have only a slightly higher level of digital literacy than their rural counterparts, suggesting that school location may not be a defining explanatory element in the variation of digital literacy and resilience among Vietnamese students. Students' digital literacy and, especially resilience, also have associations with their gender. Moreover, as students are digitally literate, they are more likely to be digitally resilient. Following SDG4, i.e., Quality Education, it is advisable for schools, and especially parents, to seriously invest in creating a safe, educational environment to enhance digital literacy among students.


docid: jqeyisoc

title: The SARS-CoV-2-like virus found in captive pangolins from Guangdong should be better sequenced

text: Viruses closely related to SARS-CoV-2, which is the virus responsible of the Covid-19 pandemic, were sequenced in several Sunda pangolins (Manis javanica) seized in the Guangdong and Guangxi provinces of China between 2017 and 20191-3. These viruses belong to two lineages: one from Guangdong (GD/P) and the other from Guangxi (GX/P). The GD/P viruses are particularly intriguing as the amino-acid sequence of the receptor binding domain of the spike protein is very similar to that of the human SARS-CoV-2 virus (97.4%)2. This characteristic suggests that GD/P viruses are capable of binding human ACE2 receptor and may therefore be able to mediate infection of human cells. Whereas all six GX/P genomes were deposited as annotated sequences in GenBank, none of the two GD/P genomes assembled in previous studies2,3 are currently available. To overcome this absence, I assembled these genomes from the Sequence Read Archive (SRA) data available for SARS-CoV-2-like viruses detected in five captive pangolins from Guangdong. I found the genome assemblies of GD/P virus of poor quality, having high levels of missing data. Additionally, unexpected reads in the Illumina sequencing data were identified. The GD/P2S dataset2 contains reads that are identical to SARS-CoV-2, suggesting either the coexistence of two SARS-CoV-2-like viruses in the same pangolin or contamination by the human virus. In the four other GD/P datasets1 many mitochondrial reads from pangolin were identified, as well as from three other species, namely, human, mouse and tiger. Importantly, I only identified three polymorphic nucleotide sites between the five GD/P sequences. Such low levels of polymorphism may reasonably be accounted for by sequencing errors alone, thus raising the possibility that the five pangolins seized in Guangdong in March 2019 were infected by the same virus strain, most probably during their captivity.


docid: wiyvrpij

title: Validation of a single-step, single-tube reverse transcription-loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA

text: Introduction The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues. Aim To establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs. Methodology We used a commercial RT-LAMP mastermix from OptiGene Ltd in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby as little as 1 μL of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65°C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals. Results Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87% and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 minutes (SD ±7 minutes). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 mL−1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay. Conclusion With a simplified workflow, N1-STOP-LAMP is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19. 3. Data summary The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.


title: SARS-COV-2 comorbidity network and outcome in hospitalized patients in Crema, Italy

text: Objective To provide Covid-19 fatality rate, correlations with comorbidities and sensitivity of nasopharingeal swab. Design Prospective cohort study performed between February 21th and March 19rd, 2020 Setting Hospital-based study Participants Of 2,217 admitted, 766 consecutive individuals either reporting or presenting with fever, cough or dyspnea, and suspected to carry Covid-19 infection were examined. Intervention All individuals underwent body temperature and pulse oximetry recording, hematological screening, chest X-ray and/or computed tomography (CT) and SARS-COV-2 assay on nasopharyngeal swab. Onset symptoms, course, comorbidities, number of drugs, use of angiotensin converting enzyme inhibitors and angiotensin-II-receptor antagonists, and follow-up swab, clinical, hematological, and radiological exams, treatments, non-invasive respiratory support, ICU admission, and deaths were recorded. Main outcome measures Primary outcomes were non-invasive respiratory support, intensive care unit (ICU) admission, and death. Results Median age of 411 Covid-19 patients was 70.5 years (range 1-99; 66.6% males). CT was positive in 74% and negative in 3.2%. Six patients died within 72 hours; another 66 during hospitalization. Fatality rate was 17.5% (74% males). No death occurred below 60 years. Mortality was 6.6% in 60-69 decade, 21.1% in 70-79, 38.8% in 80-89, and 83.3% above 90 years. Non-invasive respiratory support rate was 27.2%; ICU admission 6.8%. Older age, cough and dyspnea at onset, hypertension, cardiovascular diseases, diabetes, renal insufficiency, >7 drugs intake and positive X-ray at admission were significantly associated with death. Low lymphocyte count, high C-reactive protein, aspartate aminotransferase and lactate dehydrogenase, and low PO2 partial pressure with high lactate at arterial blood gas analysis at admission were also significantly associated with death. Of 32 swab negative patients, 40.6% turned positive at follow-up. Using CT as reference, nasopharyngeal swab had 80% sensitivity. Comorbidity network analysis revealed homogenous distribution of deceased and 60-80 aged patients across diseases. Conclusions Covid-19 caused high mortality among patients older than 70 years and correlated by pre-existing multiorgan impairment irrespective of the age.


title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study

text: Background The ongoing epidemics of coronavirus disease 2019 (COVID-19) have caused serious concerns about its potential adverse effects on pregnancy. There are limited data on maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia. Methods We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. Results During January 24 to February 29, 2020, there were sixteen pregnant women with confirmed COVID-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. Two had vaginal delivery and the rest took cesarean section. Few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest CT images of COVID-19 pneumonia. Compared to the controls, COVID-19 pneumonia patients had lower counts of white blood cells (WBC), neutrophils, C-reactive protein (CRP), and alanine aminotransferase (ALT) on admission. Increased levels of WBC, neutrophils, eosinophils, and CRP were found in postpartum blood tests of pneumonia patients. There were three (18.8%) and two (10.5%) of the mothers with confirmed or suspected COVID-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. None experienced respiratory failure during hospital stay. COVID-19 infection was not found in the newborns and none developed severe neonatal complications. Conclusion Severe maternal and neonatal complications were not observed in pregnant women with COVID-19 pneumonia who had vaginal delivery or caesarean section. Mild respiratory symptoms of pregnant women with COVID-19 pneumonia highlight the need of effective screening on admission.


title: Performance characteristics of the ID NOW COVID-19 assay: A regional health care system experience

text: Objectives: We compared the Abbott ID NOW COVID-19 point-of-care test (POCT) with polymerase chain reaction (PCR)-based methods to assess the claimed sensitivity and specificity of POCT and to optimize test utilization in our regional health care system. Methods: Assuming PCR to be the gold standard, we used a convenience sampling of mostly symptomatic COVID-19 suspect hospital patients who had already been tested for internal validation and guideline development purposes by both PCR and POCT to calculate the sensitivity and specificity of POCT with Clopper-Pearson 95% confidence intervals (CI). Results: During the study period, 113 paired patient samples met eligibility criteria. The sensitivity of POCT in this population was calculated to be 94.1% [CI 71.31-99.85%] and the specificity was 99.0% [CI 94.33-99.97%]. Conclusions: Based on the lower sensitivity of POCT and the estimated prevalence of COVID-19 in our symptomatic and asymptomatic hospital patients, we recommend a two-pronged testing approach in which COVID-19 suspect patients are tested by the more sensitive PCR, while asymptomatic patients with a low pre-test probability of infection are tested with POCT supplemented by PCR confirmation of positive results. Furthermore, isolation decisions should not be based on POCT results alone.


title: From predictions to prescriptions: A data-drivenresponse to COVID-19

text: The COVID-19 pandemic has created unprecedented challenges worldwide. Strained healthcare providers make difficult decisions on patient triage, treatment and care management on a daily basis. Policy makers have imposed social distancing measures to slow the disease, at a steep economic price. We design analytical tools to support these decisions and combat the pandemic. Specifically, we propose a comprehensive data-driven approach to understand the clinical characteristics of COVID-19, predict its mortality, forecast its evolution, and ultimately alleviate its impact. By leveraging cohort-level clinical data, patient-level hospital data, and census-level epidemiological data, we develop an integrated four-step approach, combining descriptive, predictive and prescriptive analytics. First, we aggregate hundreds of clinical studies into the most comprehensive database on COVID-19 to paint a new macroscopic picture of the disease. Second, we build personalized calculators to predict the risk of infection and mortality as a function of demographics, symptoms, comorbidities, and lab values. Third, we develop a novel epidemiological model to project the pandemic's spread and inform social distancing policies. Fourth, we propose an optimization model to reallocate ventilators and alleviate shortages. Our results have been used at the clinical level by several hospitals to triage patients, guide care management, plan ICU capacity, and re-distribute ventilators. At the policy level, they are currently supporting safe back-to-work policies at a major institution and equitable vaccine distribution planning at a major pharmaceutical company, and have been integrated into the US Center for Disease Control's pandemic forecast.


title: The scientific basis for currently proposed management options for Hector’s and Maui dolphins: a critique

text: New Zealand’s Ministry for Primary Industries (MPI) developed a risk analysis for Hector’s and Maui dolphins, in order to inform protection options being considered by the Ministers of Fisheries and Conservation. Unfortunately, MPI’s risk analysis combines several estimates that are biased, and the biases consistently act together to underestimate the level of bycatch and overestimate the species’ ability to sustain impacts. In essence, the approach uses abundance estimates that are likely biased high, multiplies them by a reproductive rate that has been arbitrarily raised, multiplied by an assumed figure for calf survival, to reach a number of dolphins that would be added each year if the population were to remain stable. From this number, they subtract their estimates of bycatch, which are almost certainly biased low. The remaining number of dolphins is apportioned a cause of death according to autopsy data from 55 Hector’s and Maui dolphins found dead on beaches. This is then compared to estimates of what level of takes would be sustainable, calculated using a formula that is not well understood and less conservative than the international standard (PBR, developed by the US National Marine Fisheries Service). This is a poor basis for rational management of an endangered, endemic marine mammal. A key problem with the MPI approach is that its definition of “risk” does not relate to the risk of population decline or extinction, and is inconsistent with the modern understanding of the behaviour of meta-populations. The approach defines risk as the likelihood of capture, which is apportioned to different areas according to fishing effort and the habitat model’s outputs for dolphin distribution. The protection options are therefore targeted where high densities of dolphins and high fishing effort coincide. Large populations are allocated the highest level of protection, while small populations remain poorly protected. This approach is likely to increase the risk of local extinctions, contractions of dolphin distribution, population fragmentation, loss of genetic variability and result in increased risk to the species as a whole. Many of these points were made by an International Expert Panel in 2018. MPI have failed to provide a list of recommendations from the Expert Panel Report with their responses (if any) to those recommendations. This standard step in scientific practice, following peer review (e.g. response to reviewers’ comments) has not been followed.


title: scRNA-seq reveals ACE2 and TMPRSS2 expression in TROP2+ Liver Progenitor Cells: Implications in COVID-19 associated Liver Dysfunction

text: The recent pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first reported in China (December 2019) and now prevalent in ∼170 countries across the globe. Entry of SARS-CoV-2 into mammalian cells require the binding of viral Spike (S) proteins to the ACE2 (angiotensin converting enzyme 2) receptor. Once entered the S protein is primed by a specialised serine protease, TMPRSS2 (Transmembrane Serine Protease 2) in the host cell. Importantly, beside respiratory symptoms, consistent with other common respiratory virus infection when patients become viraemic, a significant number of COVID-19 patients also develop liver comorbidities. We explored if specific target cell-type in the mammalian liver, could be implicated in disease pathophysiology other than the general deleterious response to cytokine storms. Here we employed single-cell RNA-seq (scRNA-seq) to survey the human liver and identified potentially implicated liver cell-type for viral ingress. We report the co-expression of ACE2 and TMPRSS2 in a TROP2+ liver progenitor population. Importantly, we fail to detect the expression of ACE2 in hepatocyte or any other liver (immune and stromal) cell types. These results indicated that in COVID-19 associated liver dysfunction and cell death, viral infection of TROP2+ progenitors in liver may significantly impaired liver regeneration and could lead to pathology. Highlights - EPCAM+ Liver progenitors co-express ACE2 and TMPRSS2 - ACE2 and TMPRSS2 expression is highest in TROP2high progenitors - ACE2 and TMPRSS2 cells express cholangiocyte biased fate markers - ACE2 and TMPRSS2 positive cells are absent in human fetal liver


title: The Role of Psychological First Aid to Support Public Mental Health in the COVID-19 Pandemic

text: Psychological first aid (PFA) is one of the vital tools in delivering psychological interventions to those who have undergone or experienced traumatic events Traumatic experiences during calamities, outbreaks of infections, and war can induce a significant amount of stress in the absence of early and effective intervention provided by trained caregivers The coronavirus pandemic has caused significant levels of fear as governments impose quarantine and lockdown to contain the infection Countries around the globe have halted several social and economic operations to curb the spread of coronavirus disease-19 (COVID-19) However, panic, helplessness, and horror aided by the infection due to the lack of a definitive cure has exposed the population to significant mental distress, thus warranting psychological intervention


title: A transcription regulatory network within the ACE2 locus may promote a pro-viral environment for SARS-CoV-2 by modulating expression of host factors

text: Introduction A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was recently identified as the pathogen responsible for the COVID-19 outbreak. SARS-CoV-2 triggers severe pneumonia, which leads to acute respiratory distress syndrome and death in severe cases. As reported, SARS-CoV-2 is 80% genetically identical to the 2003 SARS-CoV virus. Angiotensin-converting enzyme 2 (ACE2) has been identified as the main receptor for entry of both SARS-CoV and SARS-CoV-2 into human cells. ACE2 is normally expressed in cardiovascular and lung type II alveolar epithelial cells, where it positively modulates the RAS system that regulates blood flow, pressure, and fluid homeostasis. Thus, virus-induced reduction of ACE2 gene expression is considered to make a significant contribution to severe acute respiratory failure. Chromatin remodeling plays a significant role in the regulation of ACE2 gene expression and the activity of regulatory elements within the genome. Methods Here, we integrated data on physical chromatin interactions within the genome organization (captured by Hi-C) with tissue-specific gene expression data to identify spatial expression quantitative trait loci (eQTLs) and thus regulatory elements located within the ACE2 gene. Results We identified regulatory elements within ACE2 that control the expression of PIR, CA5B, and VPS13C in the lung. The gene products of these genes are involved in inflammatory responses, de novo pyrimidine and polyamine synthesis, and the endoplasmic reticulum, respectively. Conclusion Our study, although limited by the fact that the identification of the regulatory interactions is putative until proven by targeted experiments, supports the hypothesis that viral silencing of ACE2 alters the activity of gene regulatory regions and promotes an intra-cellular environment suitable for viral replication.


title: Optimal sample pooling: an efficient tool against SARS-CoV-2

text: The SARS-CoV-2 pandemic situation has presented multiple imminent challenges to the nations around the globe. While health agencies around the world are exploring various options to contain the spread of this fatal viral infection, multiple strategies and guidelines are being issued to boost the fight against the disease. Identifying and isolating infected individuals at an early phase of the disease has been a very successful approach to stop the chain of transmission. But this approach faces a practical challenge of limited resources. Sample pooling solves this enigma by significantly improving the testing capacity and result turn around time while using no extra resources. However, the general sample pooling method also has the scope of significant improvements. This article describes a process to further optimize the resources with optimal sample pooling. This is a user-friendly technique, scalable on a national or international scale. A mathematical model has been built and validated for its performance using clinical data.


title: Planning phase-2 for the endoscopic units in Northern Italy after COVID-19 lockdown: an exit strategy with a lot of critical issues and a few opportunities.

text: Background and aims: Restarting activity in Endoscopic Departments (ED) after COVID-19 lockdown raises critical issues. This survey investigates strategies and uncertainties on resumption of elective activity. Methods: Directors of 55 EDs in Northern Italy received a questionnaire focusing on the impact of pandemic on activity and organization and on the resources available at re-opening. A section was devoted to gather forecasts and proposals on the return path to normality. Results: All centres had reduced their activities of at least 50% of the pre-COVID-19 period. A rate of endoscopists (13.6%), nurses (25.2%), and health assistants (14%) were not available since infected, or relocated to other departments. One third of endoscopic rooms were converted to COVID-19 care. Two third had the waiting or the recovery areas too small for distancing. A dedicated pathway for infected patients could not be guaranteed in 20% of EDs. Only one third of EDs judged realistic to completely restore a pre-crisis workload by the next months. Optimizing appropriateness of procedures, closer interaction with GPs and triaging patients with telemedicine were the proposals to re-open EDs. Conclusions: The critical issues while re-opening EDs calls for reducing the workload in the endoscopy units through appropriate rescheduling of procedures.


title: Development of a Clinical Decision Support System for Severity Risk Prediction and Triage of COVID-19 Patients at Hospital Admission: an International Multicenter Study

text: IMPORTANCE The outbreak of the coronavirus disease 2019 (COVID-19) has globally strained medical resources and caused significant mortality for severely and critically ill patients. However, the availability of validated nomograms and the machine-learning model to predict severity risk and triage of affected patients is limited. OBJECTIVE To develop and validate nomograms and machine-learning models for severity risk assessment and triage for COVID-19 patients at hospital admission. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort of 299 consecutively hospitalized COVID-19 patients at The Central Hospital of Wuhan, China, from December 23, 2019, to February 13, 2020, was used to train and validate the models. Six cohorts with 426 patients from eight centers in China, Italy, and Belgium, from February 20, 2020, to March 21, 2020, were used to prospectively validate the models. MAIN OUTCOME AND MEASURES The main outcome was the onset of severe or critical illness during hospitalization. Model performances were quantified using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. RESULTS Of the 299 hospitalized COVID-19 patients in the retrospective cohort, the median age was 50 years ((interquartile range, 35.5-63.0; range, 20-94 years) and 137 (45.8%) were men. Of the 426 hospitalized COVID-19 patients in the prospective cohorts, the median age was 62.0 years ((interquartile range, 50.0-72.0; range, 19-94 years) and 236 (55.4%) were men. The model was prospectively validated on six cohorts yielding AUCs ranging from 0.816 to 0.976, with accuracies ranging from 70.8% to 93.8%, sensitivities ranging from 83.7% to 100%, and specificities ranging from 41.0% to 95.7%. The cut-off values of the low, medium, and high-risk probabilities were 0.072 and 0.244. The developed online calculators can be found at www.predict19risk.ai. CONCLUSION AND RELEVANCE The machine learning models, nomograms, and online calculators might be useful for the prediction of onset of severe and critical illness among COVID-19 patients and triage at hospital admission. Further prospective research and clinical feedback are necessary to evaluate the clinical usefulness of this model and to determine whether these models can help optimize medical resources and reduce mortality rates compared with current clinical practices.


Sharing information is probably more helpful than providing generic training recommendations on return to play after COVID-19 home confinement


title: Dose-dependent response to infection with SARS-CoV-2 in the ferret model: evidence of protection to re-challenge

text: In December 2019 an outbreak of coronavirus disease (COVID-19) emerged in Wuhan, China. The causative agent was subsequently identified and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which rapidly spread worldwide causing a pandemic. Currently there are no licensed vaccines or therapeutics available against SARS-CoV-2 but numerous candidate vaccines are in development and repurposed drugs are being tested in the clinic. There is a vital need for authentic COVID-19 animal models to further our understanding of pathogenesis and viral spread in addition to pre-clinical evaluation of candidate interventions. Here we report a dose titration study of SARS-CoV-2 to determine the most suitable infectious dose to use in the ferret model. We show that a high (5×106 pfu) and medium (5×104 pfu) dose of SARS-CoV-2 induces consistent upper respiratory tract (URT) viral RNA shedding in both groups of six challenged animals, whilst a low dose (5×102 pfu) resulted in only one of six displaying signs of URT viral RNA replication. The URT shedding lasted up to 21 days in the high dose animals with intermittent positive signal from day 14. Sequential culls revealed distinct pathological signs of mild multifocal bronchopneumonia in approximately 5-15% of the lung, observed on day 3 in high and medium dosed animals, with presence of mild broncho-interstitial pneumonia on day 7 onwards. No obvious elevated temperature or signs of coughing or dyspnoea were observed although animals did present with a consistent post-viral fatigue lasting from day 9-14 in the medium and high dose groups. After virus shedding ceased, re-challenged ferrets were shown to be fully protected from acute lung pathology. The endpoints of URT viral RNA replication in addition to distinct lung pathology and post viral fatigue were observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease (as displayed by 80% of patients infected with SARS-CoV-2). In addition, intermittent viral shedding on days 14-21 parallel observations reported in a minority of clinical cases.


docid: pruqumjs

title: Global Assessment of the Relationship between Government Response Measures and COVID-19 Deaths

text: Objective: To provide an early global assessment of the impact of government stringency measures on the rate of growth in deaths from COVID-19. We hypothesized that the overall stringency of a government's interventions and the speed of implementation would affect the growth and level of deaths related to COVID-19 in that country. Design: Observational study based on an original database of global governmental responses to the COVID-19 pandemic. Daily data was collected on a range of containment and closure policies for 170 countries from January 1, 2020 until May 27, 2020 by a team of researchers at Oxford University, UK. These data were combined into an aggregate stringency index (SI) score for each country on each day (range: 0-100). Regression was used to show correlations between the speed and strength of government stringency and deaths related to COVID-19 with a number of controls for time and country-specific demographic, health system, and economic characteristics. Interventions: Nine non-pharmaceutical interventions such as school and work closures, restrictions on international and domestic travel, public gathering bans, public information campaigns, as well as testing and contact tracing policies. Main outcomes measures: The primary outcome was deaths related to COVID-19, measured both in terms of maximum daily deaths and growth rate of daily deaths. Results: For each day of delay to reach an SI 40, the average daily growth rate in deaths was 0.087 percentage points higher (0.056 to 0.118, P<0.001). In turn, each additional point on the SI was associated with a 0.080 percentage point lower average daily growth rate (-0.121 to -0.039, P<.001). These daily differences in growth rates lead to large cumulative differences in total deaths. For example, a week delay in enacting policy measures to SI 40 would lead to 1.7 times as many deaths overall. Conclusions: A lower degree of government stringency and slower response times were associated with more deaths from COVID-19. These findings highlight the importance of non-pharmaceutical responses to COVID-19 as more robust testing, treatment, and vaccination measures are developed.


title: Correlation Between Temperature and COVID-19 (Suspected, Confirmed and Death) Cases based on Machine Learning Analysis

text: Currently, the whole world is struggling with the biggest health problem COVID-19 name coined by the World Health Organization (WHO) This was raised from China in December 2019 This pandemic is going to change the world Due to its communicable nature, it is contagious to both medically and economically Though different contributing factors are not known yet Herein, an effort has been made to find the correlation between temperature and different cases situation (suspected, confirmed, and death cases) For a said purpose, k-means clustering-based machine learning method has been employed on the data set from different regions of China, which has been obtained from the WHO The novelty of this work is that we have included the temperature field in the original WHO data set and further explore the trends The trends show the effect of temperature on each region in three different perspectives of COVID-19 - suspected, confirmed and death


title: Routine measurement of serum procalcitonin allows antibiotics to be safely withheld in patients admitted to hospital with SARS-CoV-2 infection.

text: Background. It can be a diagnostic challenge to identify COVID-19 patients without bacterial co-infection in whom antibiotics can be safely stopped. We sought to evaluate the validity of a guideline that recommends withholding antibiotics in patients with a low serum procalcitonin (PCT). Methods. We retrospectively collected 28-day outcome data on patients admitted to Sheffield Teaching Hospitals NHS Foundation Trust, UK, between 5 March and 15 April 2020, with a positive SARS-CoV-2 polymerase chain reaction (PCR) and PCT within 48 hours of diagnosis. PCT was considered negative if [≤]0.25ng/ml and positive if >0.25ng/ml. Primary outcomes included antibiotic consumption, mortality, intensive care admission and length of hospital stay. Results. 368 patients met the inclusion criteria; 218 (59%) had a negative PCT and 150 (41%) positive. At 48 hours post-diagnosis, 73 (33%) of those with a negative PCT were receiving antimicrobials compared to 126 (84%) with a positive PCT (p<0.001), with a corresponding reduction in antimicrobial usage over 28 days (median DDD of 3.0 vs 6.8 (p<0.001); median DOT 2 vs 5 days (p<0.001) between the negative and positive PCT groups.) In the negative PCT group, there were fewer deaths (62 (28%) vs. 54 (36%), (p=0.021)) and critical care admissions (19 (9%) vs. 28 (19%), (p=0.007)) than in the positive PCT group. Median length of hospital stay was 8.7 and 9 days in the negative and positive PCT groups respectively. Conclusions. Procalcitonin is a valuable tool in the assessment of patients with SARS-CoV-2 infection, safely reducing the potential burden of unnecessary antibiotic usage.


title: The effects of border control and quarantine measures on global spread of COVID-19

text: The rapid expansion of coronavirus (COVID-19) has been observed in many parts of the world. Many newly reported cases of this new coronavirus during early outbreak phases have been associated with travel history from an epidemic region (identified as imported cases). For those cases without travel history, the risk of wider spreads through community contact is even higher. However, most population models assume a homogeneous infected population without considering that the imported and secondary cases contracted by the imported cases can pose a different risk to community spread. We have developed an “easy-to-use” mathematical framework extending from a meta-population model embedding city-to-city connections to stratify the dynamics of transmission waves caused by imported, secondary, and others from an outbreak source region when control measures are considered. Using the dynamics of the secondary cases, we are able to determine the probability of community spread. Using the top 10 visiting cities from Wuhan in China as an example, we first demonstrated that the arrival time and the dynamics of the outbreaks at these cities can be successfully predicted under the reproductive number R0 = 2.92 and latent period τ = 5.2 days. Next, we showed that although control measures can gain extra 32.5 and 44.0 days in arrival time through a high intensive border control measure and a shorter time to quarantine under a low R0 (1.4), if the R0 is higher (2.92), only 10 extra days can be gained for each of the same measures. This suggests the importance of lowering the incidence at source regions together with infectious disease control measures in susceptible regions. The study allows us to assess the effects of border control and quarantine measures on the emergence and the global spread in a fully connected world using the dynamics of the secondary cases.


title: Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences

text: The recently emerged SARS-CoV-2 (Coronaviridae; Betacoronavirus) is the underlying cause of COVID-19 disease. Here we assessed SARS-CoV2 from the Kingdom of Saudi Arabia alongside sequences of SARS-CoV, bat SARS-like CoVs and MERS-CoV, the latter currently detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to MERS-CoV. Moreover, genome recombination analysis revealed two recombination events between SARS-CoV-2 and bat SARS-like CoVs. This was further assessed by S gene recombination analysis. These recombination events may be relevant to the emergence of this novel virus. Moreover, positive selection pressure was detected between SARS-CoV-2, bat SL-CoV isolates and human SARS-CoV isolates. However, the highest positive selection occurred between SARS-CoV-2 isolates and 2 bat-SL-CoV isolates (Bat-SL-RsSHC014 and Bat-SL-CoVZC45). This further indicates that SARS-CoV-2 isolates were adaptively evolved from bat SARS-like isolates, and that a virus with originating from bats triggered this pandemic. This study thuds sheds further light on the origin of this virus. AUTHOR SUMMARY The emergence and subsequent pandemic of SARS-CoV-2 is a unique challenge to countries all over the world, including Saudi Arabia where cases of the related MERS are still being reported. Saudi SARS-CoV-2 sequences were found to be likely of the same or similar origin. In our analysis, SARS-CoV-2 were more closely related to bat SARS-like CoVs rather than to MERS-CoV (which originated in Saudi Arabia) or SARS-CoV, confirming other phylogenetic efforts on this pathogen. Recombination and positive selection analysis further suggest that bat coronaviruses may be at the origin of SARS-CoV-2 sequences. The data shown here give hints on the origin of this virus and may inform efforts on transmissibility, host adaptation and other biological aspects of this virus.


title: Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China

text: Background: As of March 2, 2020, SARS-CoV-2 has infected more than 80174 people and caused 2915 deaths in China. This virus rapidly spreads to 56 countries worldwide. Thus, in order to effectively block its transmission, it is urgent to uncover all the possible transmission routes of SARS-CoV-2. Methods: From January 28 to February 18, 2020, 35 female patients diagnosed with COVID-19 in Tongji Hospital were included in this descriptive study. The gynecologic history, clinical characteristics, laboratory findings and chest computed tomography (CT) of all patients were recorded in detail. To examine whether there is sexual transmission through vaginal from female to her partner, we employed real-time polymerase chain reaction testing (RT-PCR) to detect SARS-CoV-2 in vaginal environment (including vaginal discharge, cervical or vaginal residual exfoliated cells) and anal swab samples, and inquired recent sexual behaviors from the patients. Findings: The age range of the 35 patients with COVID-19 was 37-88 years. Over 50% patients infected with SARS-CoV-2 had chronic diseases. We tested the vaginal environment and anal swabs from the 35 female patients with COVID-19 and found that only an anal swab sample from one patient was positive for SARS-CoV-2. All the samples from vaginal environment were negative for SARS-CoV-2. The infection rate of the patients' sexual partner was 42.9%. Additionally, two female patients admitted having sex with their partners during a possible infection incubation period, while one patient's partner was uninfected and the other patient's partner was diagnosed with COVID-19 (after the diagnosis of the female patient). Conclusion: No positive RT-PCR result was found in the vaginal environment perhaps due to the lack of ACE2 expression, which is the receptor of SARS-CoV-2, in the vagina and cervix tissues (human protein atlas). The results from this study show no evidence of transmission of SARS-CoV-2 through vaginal sex from female to her partner. However, the risk of infection of non vaginal sex and other intimate contacts during vaginal sex should not be ignored.


title: ENVIRONMENTAL SAFETY EVALUATION OF THE PROTECTION AND ISOLATION SYSTEM FOR PATIENTS WITH COVID-19.

text: Background SARS-CoV-2 has high transmissibility through respiratory droplets and aerosol, making COVID-19 a worldwide pandemic. In its severe form, patients progress to respiratory failure. Non-invasive mechanical ventilation restrictions and early orotracheal intubation have collapsed health systems due to insufficient intensive care unit beds and mechanical ventilators. COVID-19 dedicated healthcare professionals have high infection rates. This publication describes experimental testing of the Protection and Isolation System for Patients with COVID-19 (PISP/COVID-19). Method PISP/COVID-19 is a disposable transparent polyethylene plastic that covers the patient's entire hospital bed, with its internal air aspirated by the hospital's vacuum system attached to a microparticle filter. Experiments validated PISP/COVID-19's ability to block aerosolized microparticles dissemination. Caffeine was used as a molecular marker, with leakage evaluation through sensors analysis using nuclear magnetic resonance spectroscopy. The biological marker was synthetic SARS-CoV-2 RNA, using Reverse Transcription Polymerase Chain Reaction (RT-PCR) as the detection method. Results PISP/COVID-19 was effective against molecular and biological markers environmental dispersion in simulations of non-invasive ventilation, high-flow nasal cannula oxygen and mechanical ventilation isolation. Caffeine was not detected in any of the sensors positioned at points outside the PISP/COVID-19. The ability of PISP/COVID-19 to retain virus particles and protect the surrounding environment was confirmed by detection and gradients quantification of synthetic SARS-CoV-2 RNA by RT-PCR. Conclusion PISP/COVID-19 was effective in the retention of the molecular and biological markers in all tested simulations. Considering the current pandemic, PISP/COVID-19 might increase the use of non-invasive ventilation, high-flow nasal cannula oxygen and provide additional protection to healthcare professionals.


docid: qjolkwsd

title: Are COVID-19 infected children with gastrointestinal symptoms different from those without symptoms? A comparative study of the clinical characteristics and epidemiological trend of 244 pediatric cases from Wuhan

text: Objective: COVID-19 patients presenting with gastrointestinal (GI) symptoms occur in both adults and children. To date, however, no large sample size study focusing on gastrointestinal symptoms in pediatric cases has been published. We analyzed COVID-19 infected children in Wuhan who presented with initial GI symptoms to determine the GI characteristics and epidemiological trend of the disease. Design: We retrospectively analyzed 244 children patients confirmed with COVID-19 at Wuhan Children's Hospital from 21 Jan to 20 Mar 2020. Symptomatic cases were divided into two groups according to whether the patients presented with or without GI symptoms on admission. Demographic, epidemiological, symptoms, and laboratory data were compared. We also analyzed the respective trends of case number changes of GI cases and asymptomatic cases. Results: 34 out of 193 symptomatic children had GI symptoms. They had lower median age and weight, a higher rate of fever, a longer length of stay and more hematological and biochemical abnormalities than patients without GI symptoms. There was no significant difference in chest CT findings or stool SARS-CoV-2 test positive percentages between the two groups. The number of patients admitted with GI symptoms showed an overall downward trend with time. At the time of writing, 242 patients were discharged, one died, and one critically ill patient was still in the intensive care unit. Conclusion: COVID-19 infected children with GI symptoms are prone to presenting with more clinical and laboratory abnormalities than patients without GI symptoms. More attention and timely hospital admission are needed for these patients.


title: Intensive COVID-19 testing associated with reduced mortality - an ecological analysis of 108 countries

text: Background Intensive screening and testing for COVID-19 could facilitate early detection and isolation of infected persons and thereby control the size of the epidemic. It could also facilitate earlier and more targeted therapy. These factors could plausibly reduce attributable mortality which was the hypothesis tested in this study. Methods Linear regression was used to assess the country-level association between COVID-19 attributable mortality per 100 000 inhabitants (mortality/capita) and COVID-19 tests/capita (number of tests/100 000 inhabitants) controlling for the cumulative number of COVID-19 infections/100 000 inhabitants (cases/capita), the age of the epidemic (number of days between first case reported and 8 April), national health expenditure per capita and WHO world region. Results The COVID-19 mortality rate varied between 0.3 and 3110 deaths/100 000 inhabitants (median 30, IQR 8-105). The intensity of testing per 100 000 also varied considerably (median 21,970, IQR 2,735-89,095) as did the number of COVID-19 cases per 100 000 (median 1,600, IQR 340-4,760 cases/100 000). In the multivariate model, the COVID-19 mortality rate was negatively associated with tests/capita (Coef. -0.036, 95% CI -0.047- -0.025) and positively associated with cases/capita (Coef. 0.093, 95% CI 0.819- 1.034). Conclusions The results are compatible with the hypothesis that intensive testing and isolation could play a role in reducing COVID-10 mortality rates.


title: Comparison of 12 molecular detection assays for SARS-CoV-2

text: Molecular testing for SARS-CoV-2 is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. All the assays showed a specificity of 100% (95% confidence interval, 95.8 to 100). The N2 assay kit of the US Centers for Disease Control and Prevention (CDC) and the N2 assay of the Japanese National Institute of Infectious Disease (NIID) were the most sensitive assays with 100% sensitivity (95% confidence interval, 94.7 to 100), followed by the CDC N1 kit, E assay by Corman, and NIID N2 assay multiplex with internal control reactions. These assays are reliable as first-line molecular assays in laboratories when combined with appropriate internal control reactions.


title: A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

text: Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. To achieve this goal, several Immune Epitope Database (IEDB) tools, molecular docking, and safety prediction servers were used. According to the results, The Spike peptide peptides SQCVNLTTRTQLPPAYTNSFTRGVY is predicted to have the highest binding affinity to the B-Cells. The Spike peptide FTISVTTEI has the highest binding affinity to the MHC I HLA-B1503 allele. The Nucleocapsid peptides KTFPPTEPK and RWYFYYLGTGPEAGL have the highest binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1- *06:02, HLA-DRB1, respectively. Furthermore, those peptides were predicted as non-toxic and non-allergen. Therefore, the combination of those peptides is predicted to stimulate better immunological responses with respectable safety.


title: On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model

text: Measures to reduce the impact of COVID19 require a mix of logistic, political and social capacity. Depending on the country, different capacities to increase of hospitalization or to properly apply lockdowns are observed. In order to better understand the impact of these measures we have developed a compartmental model which, on the one hand allows to calibrate the reduction of movement of people within and among different areas, and on the other hand it incorporates a hospitalization dynamics that differentiates the available kinds of treatment that infected people can receive. By bounding the hospitalization capacity, we are able to study in detail the interplay between mobility and hospitalization capacity.


title: Analysis of the COVID-19 epidemic in french overseas department Mayotte based on a modified deterministic and stochastic SEIR model

text: In order to anticipate a future trends in the development of the novel coronavirus COVID-19 epidemic starting early at march 13, in the french overseas department Mayotte, we study in this paper a deterministic and stochastic epidemic model through several possible states: susceptible, exposed, infected including symptomatics and asymptomatics cases, simple or mild removed, severe removed (including hospitalized) and death cases. We first fit the constant transmission rate parameter to the epidemic data in Mayotte during an early exponential growth phase using an algorithm with a package of software R and based on a Likewook Maximum estimator. Thus, after the intervention and control measures imposed by the gouvernement, we introduce a simple temporally varying and exponentially decreasing transmission rate with a control parameter. This allows us to understand wheter these interventions are having the desired impact of controlling the epidemic by pointing out some percentages to maintain control which is critical in Mayotte given the fragility of its health infrastructure and the significant fraction of the population without access to water.


title: The politics of policing a pandemic panic

text: This essay was completed in early April 2020 and begun during the first week of the official pandemic panic in Canada. The world-wide plague caused by the COVID-19 virus precipitated the first global police event presenting an occasion for researchers and scholars to apply existing theory and empirical understanding to extra-ordinary circumstances. Consideration of the politics of the police during the plague reveals a tectonic shift in the world system. The transnational and comparative study of police and policing reveals the contours of the emerging system of world power all the more clearly in a moment of crisis. The pandemic panic presents an historical moment during which, figuratively speaking, policing power crystalizes and can be seen clearly. On the global stage, in response to the pandemic panic authoritarian and totalitarian policing practices are demonstrated alongside those in putative democracies. Emerging and observable practices of rule by law are antithetical to democratic policing in the general social interest, and rule of law rhetoric justifying militarized law enforcement action in many places continues to bring police into further disrepute. The coming era will continue to be a time where, in most places “the strong do what they will, and the weak suffer what they must”—as the ancient historian Thucydides observed in the aftermath of the fratricidal Peloponnesian War more than two millennia ago. The pandemic panic shows in the starkest statistical numbers that, where social justice is achieved, the outcome of the politics of the police is not the command of the sovereign.