title: Diagnostic value of skin manifestation of SARS-CoV-2 infection

text: SARS-CoV-2 causes multiple immune-related reactions at various stages of the disease. The wide variety of skin presentations has delayed linking these to the virus. Previous studies had attempted to look at the prevalence and timing of SARS-COV-2 rashes but were based on mostly hospitalized severe cases and had little follow up. Using data collected on a subset of 336,847 eligible UK users of the COVID Symptom Study app, we observed that 8.8% of the swab positive cases (total: 2,021 subjects) reported either a body rash or an acral rash, compared to 5.4% of those with a negative swab test (total: 25,136). Together, these two skin presentations showed an odds ratio (OR) of 1.67 (95% confidence interval [CI]: 1.41-1.96) for being swab positive. Skin rashes were also predictive in the larger untested group of symptomatic app users (N=54,652), as 8.2% of those who had reported at least one classical COVID-19 symptom, i.e., fever, persistent cough, and/or anosmia, also reported a rash. Data from an independent online survey of 11,546 respondents with a rash showed that in 17% of swab positive cases, the rash was the initial presentation. Furthermore, in 21%, the rash was the only clinical sign. Skin rashes cluster with other COVID-19 symptoms, are predictive of a positive swab test and occur in a significant number of cases, either alone or before other classical symptoms. Recognising rashes is important in identifying new and earlier COVID-19 cases.


title: Novel coronavirus disease 2019 and perinatal outcomes

text: BACKGROUND AND AIM: Given the prevalence of novel coronavirus disease 2019 (COVID-19) and the lack of information on coronavirus and pregnancy, the purpose of this study was to evaluate the association of COVID-19 and perinatal outcomes in pregnant women. MATERIALS AND METHODS: In the present review article, the search process was conducted on English and Persian scientific databases of PubMed, Scopus, Google Scholar, Magiran, Irandoc, Iranmedx, and SID as well as the websites of international organizations of World Health Organization and Centers for Disease Control and Prevention using the main keywords of “Pregnancy,” “Perinatal outcomes,” “Coronavirus,” “COVID-19,” “MERS-CoV,” “MERS,” “SARS-CoV-2,” and “SARS-CoV-1” and their Persian-equivalent keywords from inception until March 16 2020. RESULTS: The findings of studies on mothers with COVID-19 were limited, and insufficient information is available on the adverse pregnancy outcomes in pregnant women with COVID-19. In cases of infection with other coronaviruses such as Middle East respiratory syndrome and severe acute respiratory syndrome during pregnancy, there have been reports on adverse pregnancy outcomes such as miscarriage, stillbirth, preterm labor, low birth weight, and congenital malformations following high fever in the first trimester. CONCLUSION: Pregnant women may be more susceptible to viral respiratory infections, including COVID-19, due to immunological and physiological changes. Therefore, pregnant women should take routine preventive measures, such as washing their hands frequently and avoiding contact with infected people, to prevent infection.


docid: bxumrghg

title: Broad beans (Vicia faba) and the potential to protect from COVID-19 coronavirus infection

text: Due to its high linoleic acid concentration (41%), sesame oil has been proposed to have the potential to protect from COVID-19 coronavirus (SARS-CoV-2) infection, which was characterised by the World Health Organization as a pandemic in March 2020 Unsaturated fatty acids, in general, are active against some enveloped viruses, like COVID-19 coronavirus, due to the incorporation of the fatty acid into the lipid membrane of the viral envelope causing destabilisation of its bilayer Broad beans (Vicia faba), grown in Northern Sudan, proved to incorporate high content of unsaturated fatty acids and in particular linoleic acid (46 41%) It forms a traditional meal in Sudan and in several Middle East countries Hence, it is here recommended to be taken as the main meal in combination with sesame oil, as it is commonly practiced in Sudan Theoretically, it has the potential to protect from COVID-19 coronavirus infections This proposal needs to be confirmed by further experimental and clinical research


title: The four horsemen of fear: An integrated model of understanding fear experiences during the COVID-19 pandemic

text: In this article, we argue that fear experiences during the COVID-19 pandemic are organized on the psychological level around four interrelated dialectical domains, namely (1) fear of the body/fear for the body, (2) fear of significant others/fear for significant others, (3) fear of not knowing/fear of knowing, and (4) fear of taking action/fear of inaction. These domains represent the bodily, interpersonal, cognitive, and behavioural features of fear, respectively. We propose ways of addressing these fears and minimising their impact by improving appraisal of the body, fostering attachment security, improving emotion regulation, adopting acceptance and promoting responsibility.


title: Targeting the catecholamine-cytokine axis to prevent SARS-CoV-2 cytokine storm syndrome

text: The mortality of Coronavirus disease 2019 (COVID-19) appears to be driven by acute respiratory distress syndrome (ARDS) and a dysregulated immune response to SARS-CoV-2. Emerging evidence suggests that a subset of COVID-19 is characterized by the development of a cytokine storm syndrome (CSS), and interleukin (IL)-6 levels are predictors of COVID-19 severity and in-hospital mortality. Targeting hyper-inflammation in COVID-19 may be critical for reducing mortality. Catecholamines enhance inflammatory injury by augmenting the production of IL-6 and other cytokines through a self-amplifying feed-forward loop in immune cells that requires alpha-1 adrenergic receptor (α1-AR) signaling. Prophylactic inhibition of catecholamine synthesis with the α1-AR antagonist prazosin reduced catecholamines and cytokine responses in mice, and resulted in markedly increased survival following various hyper-inflammatory stimuli. These findings offer a rationale for studying α1-AR antagonists in the prophylaxis of patients with COVID-19-CSS and ARDS. As high infection rates threaten to overwhelm hospital capacity during this pandemic, preventative approaches that ameliorate COVID-19 severity and reduce excessive mortality are desperately needed. We hypothesize that treatment with prazosin of individuals who test positive for SARS-CoV-2 could reduce catecholamine surges, secondary cytokine dysregulation, and mortality. To investigate a potential role for α1-AR antagonists in preventing poor outcomes in ARDS, we conducted a retrospective analysis of hospitalized patients diagnosed with ARDS. Using data from the Truven Health MarketScan Research Database (2010-2017), we identified 13,125 men (age 45-64) with ARDS, of whom 655 patients (5.0%) were prescribed α1-AR antagonists in the previous year. Applying logistic regression models, we found that patients with prior use of α1-AR antagonists had lower odds of invasive mechanical ventilation compared to non-users (adjusted OR=0.75, 95% CI 0.59-0.95, p=0.019). Perhaps more importantly, those patients had a ~36% lower incidence of both being ventilated and dying in the hospital (adjusted OR=0.59, 95% CI 0.34-0.95, p=0.042). By contrast, prior use of beta-adrenergic receptor (β-AR) antagonists was not correlated with either outcome. We extended these analyses to patients admitted with pneumonia. Of 108,956 subjects in this cohort, 5,498 patients (5.0%) were taking α1-AR antagonist. Similar to ARDS, patients with pneumonia on α1-AR antagonists (but no β-AR antagonists) had a lower odds of mechanical ventilation (adjusted OR=0.83, 95% CI 0.75-0.92, p<0.001) and of both being ventilated and dying in the hospital (adjusted OR=0.77, 95% CI 0.62-0.94, p=0.014) compared to non-users. Mirroring findings from pre-clinical models, these data support a clinical rationale to study α1-AR antagonists in the prevention of severe complications of pneumonia, ARDS, and COVID-19. Prospective, randomized clinical trials of alpha-1 receptor antagonists (e.g. prazosin) administered prior to the onset of severe symptoms are needed to assess their efficacy in preventing CSS and reducing mortality in COVID-19.


COVID-19 outbreak in a large hemodialysis centre in Lombardy, Italy


title: Pseudo-Likelihood Based Logistic Regression for Estimating COVID-19 Infection and Case Fatality Rates by Gender, Race, and Age in California

text: In emerging epidemics, early estimates of key epidemiological characteristics of the disease are critical for guiding public policy. In particular, identifying high risk population subgroups aids policymakers and health officials in combatting the epidemic. This has been challenging during the coronavirus disease 2019 (COVID-19) pandemic, because governmental agencies typically release aggregate COVID-19 data as marginal summary statistics of patient demographics. These data may identify disparities in COVID-19 outcomes between broad population subgroups, but do not provide comparisons between more granular population subgroups defined by combinations of multiple demographics. We introduce a method that overcomes the limitations of aggregated summary statistics and yields estimates of COVID-19 infection and case fatality rates --- key quantities for guiding public policy related to the control and prevention of COVID-19 --- for population subgroups across combinations of demographic characteristics. Our approach uses pseudo-likelihood based logistic regression to combine aggregate COVID-19 case and fatality data with population-level demographic survey data to estimate infection and case fatality rates for population subgroups across combinations of demographic characteristics. We illustrate our method on California COVID-19 data to estimate test-based infection and case fatality rates for population subgroups defined by gender, age, and race and ethnicity. Our analysis indicates that in California, males have higher test-based infection rates and test-based case fatality rates across age and race/ethnicity groups, with the gender gap widening with increasing age. Although elderly infected with COVID-19 are at an elevated risk of mortality, the test-based infection rates do not increase monotonically with age. LatinX and African Americans have higher test-based infection rates than other race/ethnicity groups. The subgroups with the highest 5 test-based case fatality rates are African American male, Multi-race male, Asian male, African American female, and American Indian or Alaska Native male, indicating that African Americans are an especially vulnerable California subpopulation.


COVID-19: Guidelines for Myasthenia Gravis Management and other Neuromuscular Disorders


title: COVID-19 and disabled people: perspectives from Iran

text: This is a Current Issue because, at the time of writing, COVID-19 has affected many countries and territories worldwide and Iran ranked early on as one of the most seriously affected countries. As a result, this pandemic crisis poses a considerable challenge to people with disabilities in Iran. In this short article we show the different challenges people with disabilities are facing during the COVID emergency in Iran. In addition, we provide several recommendations, based on our perspective and experience in Rehabilitation and Health Policy Centres, to improve the situation in the content of the COVID-19 breakout.


title: Traffic Impacts of the COVID-19 Pandemic: Statewide Analysis of Social Separation and Activity Restriction

text: The COVID-19 pandemic resulted in significant social and economic impacts throughout the world In addition to the health consequences, the impacts on travel behavior have also been sudden and wide ranging This study describes the drastic changes in human behavior using the analysis of highway volume data as a representation of personal activity and interaction Same-day traffic volumes for 2019 and 2020 across Florida were analyzed to identify spatial and temporal changes in behavior resulting from the disease or fear of it and statewide directives to limit person-to-person interaction Compared to similar days in 2019, overall statewide traffic volume dropped by 47 5% Although decreases were evident across the state, there were also differences between rural and urban areas and between highways and arterials both in terms of the timing and extent The data and analyses help to demonstrate the early impacts of the pandemic and may be useful for operational and strategic planning of recovery efforts and for dealing with future pandemics


title: Rapid assessment of the impact of lockdown on the COVID-19 epidemic in Portugal

text: Background: Portugal took early action to control the COVID19 epidemic, imposing a lockdown on March 16 when it recorded only 62 cases of COVID-19 per million inhabitants and no reported deaths. The Portuguese people complied quickly, reducing their overall mobility by 80% . We estimate the impact of the lockdown in Portugal in terms of reducing burden on the health service. Methods: Using publicly available official data from the Portuguese Directorate-General of Health we forecasted epidemic curves for: Cases, hospital inpatients (overall and in ICU), and deaths without lockdown, assuming that the impact of containment measures would start 14 days after lockdown was implemented. We used exponential smoothing models for deaths, intensive care (ICU) and hospitalizations and an ARIMA model for number of cases. Models were selected considering fitness to the observed data to the 31st of March 2020. We then compared observed(with intervention) and forecasted curves( without intervention). Results: Between April 1 and April 15, there were 146 fewer deaths(-25%), 5568 fewer cases (-23%) and, as of April 15, there were 519 fewer ICU inpatients(-69%) and 508 fewer overall hospital inpatients(-28%) than forecasted without lockdown. On April 15 the number of ICU inpatients could have reached 748, three times higher than the observed value (229) if the intervention had been delayed. Conclusion: If the lockdown had not been implemented in mid-March, Portugal ICU capacity (528 ICU beds) would likely have been breached in the first half of April. The lockdown seems to have been effective in reducing transmission of SARS-Cov-2, serious Covid-19 illness and associated mortality, thereby decreasing demand on health services. Early action allowed time for the National Health Service to acquire protective equipment, to increase capacity to test and cope with the surge in hospital and ICU demand caused by the pandemic.


title: Metapopulation modeling of COVID-19 advancing into the countryside: an analysis of mitigation strategies for Brazil

text: Since the first case of COVID-19 was confirmed in Brazil at 19 February 2020, this epidemics has spread out throughout all states and at least 2142 of 5570 municipalities up to 30 April 2020. In order to understand this spreading, we investigate a stochastic epidemic model using a metapopulation approach. Simulations are supplied with real data for mobility, demography, and confirmed cases of COVID-19 extracted from public sources. Contagion follows a compartmental epidemic model for each municipality which, in turn, interact with each other through recurrent mobility. Considering the number of municipalities with confirmed COVID-19 cases, simulations can infer the level of mitigation (strong, moderate, or none) that each state is effectively adopting. Properties of the epidemics curves such as time and value of epidemic peak and outbreak duration have very broad distributions across different geographical locations. This outbreak variability is observed in several scales from state, passing through intermediate and immediate up to municipality levels. The epidemic waves start from several foci concentrated in highly populated regions and propagate towards countryside. Correlations between delay of the epidemic outbreak and distance from the respective capital cities are strong in several states, showing propagation towards the countryside, and weak in others, signaling strong influences of multiple centers, not necessarily within the same state. Our take home message is that the responses of different regions to a same mitigation protocol can vary enormously such that the policies of combat to COVID-19, such as quarantine or lockdown, must be engineered according to the region specificity but integrated with the overall situation. Even though we considered a single case of study, we believe that these ideas can be generalized to other countries with mainland scales and heterogeneous demographic distributions.


title: Clinical academic research in the time of Corona: a simulation study in England and a call for action

text: Background: Coronavirus (COVID-19) poses health system challenges in every country. As with any public health emergency, a major component of the global response is timely, effective science. However, particular factors specific to COVID-19 must be overcome to ensure that research efforts are optimised. We aimed to model the impact of COVID-19 on the clinical academic response in the UK, and to provide recommendations for COVID-related research. Methods: We constructed a simple stochastic model to determine clinical academic capacity in the UK in four policy approaches to COVID-19 with differing population infection rates: Italy model (6%), mitigation (10%), relaxed mitigation (40%) and do-nothing (80%) scenarios. The ability to conduct research in the COVID-19 climate is affected by the following key factors: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics). Findings: In Italy model, mitigation, relaxed mitigation and do-nothing scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, less than 400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively, with no clinical academics at all for 37 days in the do-nothing scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11,12, 30 and 26 weeks respectively. Interpretation: Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3-4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches.


title: Struggling for food in a time of crisis: Responsibility and paradox

text: Struggling for food in a time of crisis: responsibility and paradox. Responsibility is a useful lens through which to examine the current state of food poverty in the UK in the context of the Covid‐19 crisis, noting that this concept contains several paradoxes. Currently, responsibility involves the voluntary sector, the food industry and the state, a situation which the author has been exploring for the last five years in an ethnographic study of food poverty and food aid in the UK. Food aid organizations, especially food banks, have mushroomed during the period of austerity. This reveals the first paradox: namely, that the existence of food banks conveys the message that ‘something is being done’, but in actuality this is very far from being sufficient to meet the needs of either the ‘old’ or ‘new’ food insecure. The second paradox is that at the onset of the crisis, a government which had been responsible for inflicting austerity on the country for 10 years, dramatically reversed some of its policies. However, predictably, this did not change the situation vis‐à‐vis food insecurity. The third paradox is that the frequent rhetoric invoking the two world wars has not resulted in lessons being learned – notably, the creation of a ministry to deal with food and rationing, as in the Second World War. The final paradox relates to Brexit and its likely deleterious effects on food security, particularly if no ‘deal’ is achieved with the European Union, as seems likely. The voluntary food aid sector, try as it may, cannot possibly assume responsibility for the long‐standing and now hugely increased problems of food insecurity. That belongs to the state.


title: COVID-19 epidemic in Malaysia: Impact of lock-down on infection dynamics

text: COVID-19 epidemic in Malaysia started as a small wave of 22 cases in January 2020 through imported cases. It was followed by a bigger wave mainly from local transmissions resulting in 651 cases. The following wave saw unexpectedly three digit number of daily cases following a mass gathering urged the government to choose a more stringent measure. A limited lock-down approach called Movement Control Order (MCO) was immediately initiated to the whole country as a way to suppress the epidemic trajectory. The lock-down causes a major socio-economic disruption thus the ability to forecast the infection dynamic is urgently required to assist the government on timely decisions. Limited testing capacity and limited epidemiological data complicate the understanding of the future infection dynamic of the COVID-19 epidemic. Three different epidemic forecasting models was used to generate forecasts of COVID-19 cases in Malaysia using daily reported cumulative case data up until 1st April 2020 from the Malaysia Ministry of Health. The forecasts were generated using a Curve Fitting Model with Probability Density Function and Skewness Effect, the SIR Model, and a System Dynamic Model. Method one based on curve fitting with probability density function estimated that the peak will be on 19th April 2020 with an estimation of 5,637 infected persons. Method two based on SIR Model estimated that the peak will be on 20th - 31st May 2020 if Movement Contro (MCO) is in place with an estimation of 630,000 to 800,000 infected persons. Method three based on System Dynamic Model estimated that the peak will be on 17th May 2020 with an estimation of 22,421 infected persons. Forecasts from each of model suggested the epidemic may peak between middle of April to end of May 2020. Keywords: COVID-19, Infection dynamic, Prediction Modeling, SIR, System Learning, Lock-down


title: Estimating COVID-19 Prevalence in the United States: A Sample Selection Model Approach

text: Background: Public health efforts to determine population infection rates from coronavirus disease 2019 (COVID-19) have been hampered by limitations in testing capabilities and the large shares of mild and asymptomatic cases. We developed a methodology that corrects observed positive test rates for non-random sampling to estimate population infection rates across U.S. states from March 31 to April 7. Methods We adapted a sample selection model that corrects for non-random testing to estimate population infection rates. The methodology compares how the observed positive case rate vary with changes in the size of the tested population, and applies this gradient to infer total population infection rates. Model identification requires that variation in testing rates be uncorrelated with changes in underlying disease prevalence. To this end, we relied on data on day-to-day changes in completed tests across U.S. states for the period March 31 to April 7, which were primarily influenced by immediate supply-side constraints. We used this methodology to construct predicted infection rates across each state over the sample period. We also assessed the sensitivity of the results to controls for state-specific daily trends in infection rates. Results The median population infection rate over the period March 31 to April 7 was 0.9% (IQR 0.64 1.77). The three states with the highest prevalence over the sample period were New York (8.5%), New Jersey (7.6%), and Louisiana (6.7%). Estimates from models that control for state-specific daily trends in infection rates were virtually identical to the baseline findings. The estimates imply a nationwide average of 12 population infections per diagnosed case. We found a negative bivariate relationship (corr. = -0.51) between total per capita state testing and the ratio of population infections per diagnosed case. Interpretation The effectiveness of the public health response to the coronavirus pandemic will depend on timely information on infection rates across different regions. With increasingly available high frequency data on COVID-19 testing, our methodology could be used to estimate population infection rates for a range of countries and subnational districts. In the United States, we found widespread undiagnosed COVID-19 infection. Expansion of rapid diagnostic and serological testing will be critical in preventing recurrent unobserved community transmission and identifying the large numbers individuals who may have some level of viral immunity.


title: Readability of selected governmental and popular health organization websites on Covid-19 public health information: A descriptive analysis

text: Background: The U.S. Department of Health & Human Services (USDHHS) recommends that health material be written at or below a sixth-grade reading level to ensure readability. The aim of this study was to examine the readability of international and national health organizations on Covid-19 information in their websites employing a previously validated tool. Methods: A purposive sample of publicly accessible governmental and popular international health organization websites was selected. The readability of the websites Covid-19 public health information was estimated using the previously validated SMOG readability formula, which determined reading level by correlating the number of polysyllabic words. Results: Of the 10 websites included in the analysis, none had Covid-19 public health information at the USDHHS recommended reading level. The material ranged in reading level at undergraduate level or above. Discussion: The findings indicate that the online Covid-19 materials need to be modified in order to reach recommended reading levels. This study can be of practical use to policy makers and public health government officials when designing, modifying, and evaluating Covid-19 materials. We recommend using simple, non-polysyllable words to ensure that Covid-19 public health information materials are written at the recommended reading levels.


Health Care Disparities, Neurologic Risk Factors, and COVID-19


title: Fertility Preservation in Cancer Patients During the Coronavirus (COVID-19) Pandemic

text: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also identified as Corona virus disease 19 (COVID-19), has recently produced a dramatic and widespread sanitary emergency. However, despite the necessity to assist a substantial number of affected patients, it is also essential to, at the same time, guarantee the usual clinical care, particularly to cancer patients, including fertility preservation (FP) strategies before the beginning of the anti-cancer treatments. The FP techniques for adult female patients include oocyte and embryo cryopreservation, which require both adequate ovarian reserve (OR) and controlled ovarian stimulation (COS) to promote multiple follicular growth. However, ovarian tissue cryopreservation is an additional FP practice suitable when an anti-cancer treatment is urgently required, whereas, for male patients, sperm cryopreservation is a simple and well-adopted procedure. Here, we focus on the current conditions in terms of agreements and rules of FP procedures during this COVID-19 pandemic to achieve and provide useful recommendations for the adoption of these techniques in patients with cancer.


title: A data first approach to modelling Covid-19

text: The primary data for Covid-19 pandemic is in the form of time series for the number of confirmed, recovered and dead cases. This data is updated every day and is available for most countries from multiple sources. In this work we present a two step procedure for model fitting to Covid-19 data. In the first step, time dependent transmission coefficients are constructed directly from the data and, in the second step, measures of those (minimum, maximum, mean, median etc.,) are used to set priors for fitting models to data. We call this approach a "data driven approach" or "data first approach". This scheme is complementary to Bayesian approach and can be used with or without that for parameter estimation. We use the procedure to fit a set of SIR and SIRD models, with time dependent contact rate, to Covid-19 data for a set of 45 most affected countries. We find that SIR and SIRD models with constant transmission coefficients cannot fit Covid-19 data for most countries (mainly because social distancing, lockdown etc., make those time dependent). We find that any time dependent contact rate, which falls gradually with time, can help to fit SIR and SIRD models for most of the countries. We also present constraints on transmission coefficients and basic reproduction number R0~ as well as effective reproduction number R(t). The main contributions of our work are as follows. (1) presenting a two step procedure for model fitting to Covid-19 data (2) constraining transmission coefficients as well as R0~ and R(t), for a set of most affected countries and (3) releasing a python package PyCov19 that can used to fit a set of compartmental models with time varying coefficients to Covid-19 data.


title: Development and simulation of fully glycosylated molecular models of ACE2-Fc fusion proteins and their interaction with the SARS-CoV-2 spike protein binding domain

text: We develop fully glycosylated computational models of ACE2-Fc fusion proteins which are promising targets for a COVID-19 therapeutic. These models are tested in their interaction with fragments of the binding domain of the Spike Protein S1 of the SARS-CoV-2 virus. We see that some ACE2 glycans interact with S1 and glycans are influencing the conformation of the ACE2 receptor. Additionally, we optimize algorithms for protein glycosylation modelling in order to expedite future model development. All models and algorithms are openly available.


docid: zhfrgaxf

title: Systematic benefit-risk assessment for the use of chloroquine or hydroxychloroquine as a treatment for COVID-19: Establishing a framework for rapid decision-making

text: Objectives: Given the current pandemic, there is an urgent need to identify effective, safe treatments for COVID-19 (coronavirus disease). A systematic benefit-risk assessment was designed and conducted to strengthen the ongoing monitoring of the benefit-risk balance for chloroquine and hydroxychloroquine in COVID-19 treatment. Methods: The overall benefit-risk of the use of chloroquine or hydroxychloroquine as a treatment for COVID-19 compared to standard of care, placebo or other treatments was assessed using the Benefit-Risk Action Team (BRAT) framework. We searched PubMed and Google Scholar to identify literature reporting clinical outcomes in patients taking chloroquine or hydroxychloroquine for COVID-19. A value tree was constructed and key benefits and risks were ranked by two clinicians in order of considered importance. Results: Several potential key benefits and risks were identified for use of hydroxychloroquine or chloroquine in COVID-19 treatment. For the benefit of virological clearance, three studies were identified. A significant risk difference (RD) between hydroxychloroquine and the comparator group (standard of care) was found for only one study (RD=0.58, 95% CI: 0.17, 0.98). The risk difference was not significant for the other two studies (RD=-0.07, 95% CI:-0.75, 0.61 and RD=0.08, 95% CI:-0.74, 0.91). In addition, no significant risk difference between hydroxychloroquine and the comparator group (standard of care) was identified for the risk of abnormal liver function tests (LFTs) (RD=0.07, 95% CI: -0.28, 0.41). Conclusions: Overall, no conclusion can be made on the benefit-risk profile of hydroxychloroquine or chloroquine in the treatment of COVID-19 compared to standard of care, placebo or other treatments at this time. Whilst the availability of comparative data are limited, the current framework summarises the key anticipated benefits and risks. As further data from clinical trials and real world use on these benefits and risks becomes available, this can be incorporated into the framework for an ongoing benefit-risk assessment.


title: Noncanonical junctions in subgenomic RNAs of SARS-CoV-2 lead to variant open reading frames

text: SARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused the current worldwide pandemic, known as coronavirus disease 2019 or COVID-19. The definition of SARS-CoV-2 open reading frames is a key step in delineating targets for vaccination and treatment for COVID-19. Here, we report an integrative analysis of three independent direct RNA sequencing datasets of the SARS-CoV-2 transcriptome. We find strong evidence for variant open reading frames (ORFs) encoded by SARS-CoV-2 RNA. A variant transcript for the matrix protein (M) lacking its N-terminal transmembrane domain, initiated by a TTG start codon, is produced by a strong transcriptional regulatory sequence (TRS)-mediated junction within the M ORF and represents up to 19% of all M ORFs. Sporadic non-canonical junctions in the spike (S) ORF lead to N-terminal truncations that remove the N-terminal and receptor-binding domains from up to 25% of S ORFs. Surprisingly, nearly all ORFs from ORF1a identified in these transcriptome sequences were variant. These ORFs contain the first 200-800 amino acids of ORF1a and may represent a mechanism to regulate the relative abundance of ORF1a nonstructural proteins. We show there is strong transcriptome and junctional support for variant ORF1a ORFs in independent direct RNA sequencing and short-read RNA sequencing datasets, and further show that up to 1/3 of these ORFs are expected to have C-terminal fusions with downstream genes. Finally, we show that currently unannotated ORFs are abundant in the SARS-CoV-2 transcriptome. Together, these analyses help to elucidate the diverse coding potential of SARS-CoV-2.


title: On the true numbers of COVID-19 infections: behind the available data

text: In December-2019 China reported several cases of a novel coronavirus later called COVID-19. In this work, we will use a probabilistic method for approximating the true daily numbers of infected. Based on two distribution functions to describe the spontaneous recovered cases on the one hand and the detected cases on the other hand. The impact of the underlying variables of these functions is discussed. The detected rate is predicted to be between 5.3% and 10,8%, which means that there would be about 38 million infected until now (10-May 2020), rather than the officially declared number of 3.99 million worldwide cases.


title: A Study of Different Deposition Strategies in Direct Energy Deposition (DED) Processes

text: Abstract The stepover of adjacent deposition lines (or beads), when stacking layers to build a 3D-solid shape, is found to be of great importance to minimize voidage and so, improving density of parts produced by the Directed Energy Deposition (DED) process. During such process, in which the stacking of layers occurs, the complex thermal activity of metal deposition affects the part geometry, microstructure, physical and mechanical properties. The correlation between deposition path, bead stepover, and the direct effect on the part density, microstructure and geometry distortions are yet to be found in the literature. Therefore, the aim of this study is to evaluate the effect of deposition paths and bead stepover on the final part geometry form, microhardness and density. In order to do so, four deposition paths (linear, zigzag, chessboard and contour) and beads stepover of 0.44 mm and 0.55 mm were performed on the production of Stainless Steel 316L cubes by a 5-axis laser based DED BeAM Machine Magic800 with laser spot size of 0.80 mm. The paths shown considerable influence on the variation of both final part geometry and density. Contour (spiral-like) was the path, which produced workpieces with finer form and finishing, with density and microhardness closer to the conventional AISI 316L material. The bead stepover was also found to influence the surface finishing, as larger critical valleys between adjacent beads were noticed when using the higher stepover value.


title: Coronavirus Disease (COVID-19) Pandemic: An Overview of Systematic Reviews

text: Background: Navigating the rapidly growing body of scientific literature on the SARS-CoV-2 pandemic is challenging and ongoing critical appraisal of this output is essential. We aimed to collate and summarize all published systematic reviews on the coronavirus disease (COVID-19). Methods: Nine databases (Medline, EMBASE, Cochrane Library, CINAHL, Web of Sciences, PDQ-Evidence, WHO's Global Research, LILACS and Epistemonikos) were searched from December 1, 2019 to March 24, 2020. Systematic reviews analyzing primary studies of COVID-19 were included. Two authors independently undertook screening, selection, extraction (data on clinical symptoms, prevalence, pharmacological and non-pharmacological interventions, diagnostic test assessment, laboratory and radiological findings) and quality assessment (AMSTAR 2). Meta-analysis on prevalence of clinical outcomes was performed. Results: Eighteen systematic reviews were included; one was empty. Using AMSTAR 2, confidence in the results of 13 reviews was rated as "critically low", one as "low", one as "moderate" and two as "high". Symptoms of COVID-19 were (range values of point estimates): fever (82-95%), cough with or without sputum (58-72%), dyspnea (26-59%), myalgia or muscle fatigue (29-51%), sore throat (10-13%), headache (8-12%) and gastrointestinal complaints (5-9%). Severe symptoms were more common in men. Elevated C-reactive protein (associated with lymphocytopenia) and lactate dehydrogenase, and slightly elevated aspartate and alanine aminotransferase, were commonly described. Thrombocytopenia and elevated levels of procalcitonin and cardiac troponin I were associated with severe disease. Chest imaging described a frequent pattern of uni- or bilateral multilobar ground-glass opacity. Only one review investigated the impact of medication (chloroquine) but found no verifiable clinical data. All-cause mortality ranged from 0.3% to 14%. Conclusions: Confidence in the results of most reviews was "critically low". Future studies and systematic reviews should adhere to established methodologies. The majority of included systematic reviews were hampered by imprecise search strategy and no previous protocol submission. Protocol registration: This is an extension of a PROSPERO protocol (CRD42020170623); protocol available on Open Science Framework (https://osf.io/6xtyw).


title: Can a century-old TB vaccine steel the immune system against the new coronavirus?

text: Researchers in four countries will soon start a clinical trial of an unorthodox approach to the new coronavirus They will test whether a century-old vaccine against tuberculosis (TB), a bacterial disease, can rev up the human immune system in a broad way, allowing it to better fight the virus that causes coronavirus disease 2019 and, perhaps, prevent infection with it altogether The studies will be done in physicians and nurses, who are at higher risk of becoming infected with the respiratory disease than the general population, and in the elderly, who are at higher risk of serious illness if they become infected


title: Proposal on Application of the Multi-Wire Proportional Chambers of the LHCb MUON Detector at Very High Rates for the Future Upgrades

text: The MUON Detector (MD) of LHCb is one of the largest instruments of this kind worldwide, and one of the most irradiated. It has performed exceptionally well during the RUN1 and RUN2 of the LHC at an instantaneous luminosity of 4$\times$10$^{32}$ cm$^{-2}$s$^{-1}$, with tracking inefficiencies at the level of 1$\%$ and 2.6$\%$, respectively. Looking forward for the future LHCb Upgrade 2 (U2) planned in 2031 and aiming in running the detector at increased luminosity by a factor $\sim$50, and at the same time keeping a very high ($\sim$99$\%$) detection efficiency, an option with reuse significant part of the present Multi-Wire Proportional Chambers (MWPC) in a new Muon System is presented. In addition, the first idea of new Front End Electronics (FEE) and an existing test setup applicable for designing both: new MWPCs with a higher granularity of the cathode readout pads and new FEE are described.


High Risk of COVID-19 Infection for Head and Neck Surgeons


title: Statistics associated with the lethality of COVID-19 by age group and gender in Mexico

text: We analyzed outcomes of 34,686 SARS-CoV-2 confirmed cases of patients attending the IMSS (Mexican Institute for National Insurance) from January 2 to June 23, 2020. We calculated relative IFR by age group and gender and introduced the concept of adjusted lethalities, that can be used to project the burden of the disease for a population with different demographic characteristics.


title: Risk Factors Associated With Long-Term Hospitalization in Patients With COVID-19: A Single-Centered, Retrospective Study

text: Background: The coronavirus disease 19 (COVID-19) pandemic has become a global threat. Few studies have explored the risk factors for the recovery time of patients with COVID-19. This study aimed to explore risk factors associated with long-term hospitalization in patients with COVID-19. Methods: In this retrospective study, patients with laboratory-confirmed COVID-19 hospitalized in a hospital in Wuhan by March 30, 2020, were included. Demographic, clinical, laboratory, and radiological data from COVID-19 patients on hospital admission were extracted and were compared between the two groups, defined as short- and long-term hospitalization, respectively according to the median hospitalization time. Univariable and multivariable logistic regression methods were performed to identify risk factors associated with long-term hospitalization in patients with COVID-19. Results: A total of 125 discharged patients with COVID-19 were reviewed, including 123 general patients and two severe patients. The median hospitalization time was 13.0 days (IQR 10.0–17.0). Among them, 66 patients were discharged <14 days (short-term group) and 59 patients were discharged ≥14 days (long-term group). Compared with the short-term group, patients in the long-term group had significantly higher levels of C-reactive protein (P = 0.000), troponin I (P = 0.002), myoglobin (P = 0.037), aspartate aminotransferase (P = 0.005), lactic dehydrogenase (P = 0.000), prothrombin time (P = 0.030), fibrinogen (P = 0.000), and D-dimer (P = 0.006), but had significantly lower levels of lymphocyte count (P = 0.001), platelet count (P = 0.017), albumin (P = 0.001), and calcium (P = 0.000). Additionally, the incidences of hypocalcemia (P = 0.001), hyponatremia (P = 0.021), hypochloremia (P = 0.019), and bilateral pneumonia (P = 0.000) in the long-term group were significantly higher than those in the short-term group. Multivariable regression showed that hypocalcemia (P = 0.007, OR 3.313, 95% CI 1.392–7.886), hypochloremia (P = 0.029, OR 2.663, 95% CI 1.104–6.621), and bilateral pneumonia (P = 0.009, OR 5.907, 95% CI 1.073–32.521) were independent risk factors associated with long-term hospitalization in patients with COVID-19. Furthermore, a ROC curve where the area under the ROC was 0.766 for retained variables is presented. Conclusions: Hypocalcemia, hypochloremia, and bilateral pneumonia on hospital admission were independent risk factors associated with long-term hospitalization in patients with COVID-19. To the best of our knowledge, this is the first study to highlight the importance of electrolyte imbalance in predicting the hospitalization time of patients with COVID-19.


title: Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans

text: Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic spread2,3. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 Spike (S) glycoprotein, we demonstrate the presence of pre-existing immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies, exclusively of the IgG class, were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals with recent HCoV infection and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, as well as concomitant IgM and IgA antibodies throughout the observation period of 6 weeks since symptoms onset. HCoV patient sera also variably reacted with SARS-CoV-2 S and nucleocapsid (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, HCoV patient sera exhibited specific neutralising activity against SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for serology, seroprevalence and vaccine studies, as well as for our understanding of susceptibility to and natural course of SARS-CoV-2 infection.


title: Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19

text: Background: The coronavirus disease 2019 (COVID-19) has become a global pandemic currently. Many drugs showed potential for COVID-19 therapy. However, genetic factors which can lead to different drug efficiency and toxicity among populations are still undisclosed in COVID-19 therapy. Methods: We selected 67 potential drugs for COVID-19 therapy (DCTs) from clinical guideline and clinical trials databases. 313 pharmaco-genes related to these therapeutic drugs were included. Variation information in 125,748 exomes were collected for racial differences analyses. The expression level of pharmaco-genes in single cell resolution was evaluated from single-cell RNA sequencing (scRNA-seq) data of 17 healthy adults. Results: Pharmacogenes, including CYP3A4, ABCB1, SLCO1B1, ALB, CYP3A5, were involved in the process of more than multi DCTs. 224 potential drug-drug interactions (DDI) of DCTs were predicted, while 112 of them have been reported. Racial discrepancy of common nonsynonymous mutations was found in pharmacogenes including: VDR, ITPA, G6PD, CYP3A4 and ABCB1 which related to DCTs including ribavirin, -interferon, chloroquine and lopinavir. Moreover, ACE2, the target of 2019-nCoV, was only found in parts of lung cells, which makes drugs like chloroquine that prevent virus binding to ACE2 more specific than other targeted drugs such as camostat mesylate. Conclusions: At least 17 drugs for COVID-19 therapy with predictable pharmacogenes should be carefully utilized in risk races which are consisted of more risk allele carriers. At least 29 drugs with potential of DDIs are reported to be affected by other DDIs, they should be replaced by similar drugs without interaction if it is possible. Drugs which specifically targeted to infected cells with ACE2 such as chloroquine are preferred in COVID-19 therapy.


docid: pmqqemku

title: In-flight Transmission Cluster of COVID-19: A Retrospective Case Series

text: Objectives: No data were available about in-flight transmission of SARS-CoV-2. Here, we report an in-flight transmission cluster of COVID-19 and describe the clinical characteristics of these patients. Methods: After a flight, laboratory-confirmed COVID-19 was reported in 12 patients. Ten patients were admitted to the designated hospital. Data were collected from 25th January to 28th February 2020. Clinical information was retrospectively collected. Results: All patients are passengers without flight attendants. The median age was 33 years, and 70% were females. None was admitted to intensive care unit, and no patients succumbed through 28th February. The median incubation period was 3.0 days and from illness onset to hospital admission was 2 days. The most common symptom was fever. Two patients were asymptomatic and negative for chest CT scan throughout the disease course. On admission, initial RT-PCR were positive in 9 patients, however initial chest CT were positive in only half patients. The median lung total severity score of chest CT was 6. Notably, Crazy-Paving pattern, pleural effusion, and ground-glass nodules were also seen. Conclusion: It is potential for COVID-19 transmission by airplane, but the symptoms are mild. Passengers and attendants must be protected during the flight.


Putting abuse on the map: The coronavirus crisis has seen a huge rise in media attacks. Index has launched a map to track these


title: Use of inhibitors of the renin angiotensin system and COVID-19 prognosis: a systematic review and meta-analysis

text: Background: controversy has arisen in the scientific community on whether the use of renin angiotensin system (RAS) inhibitors in the context of COVID-19 would be of benefit or harmful. A meta-analysis of eligible studies comparing the occurrence of severe and fatal COVID-19 in infected patients who were under treatment with angiotensin converting enzyme inhibitors (ACEI) or angiotensin receptor blockers (ARB) vs no treatment or other antihypertensives was conducted. Methods: PubMed, Google Scholar, the Cochrane Library, MedRxiv and BioRxiv were searched for relevant studies. Fixed-effect models or random-effect models were used depending on the heterogeneity between estimates. Results: a total of fifteen studies with 21,614 patients were included. The use of RAS inhibitors was associated with a non-significant 20% decreased risk of the composite outcome (death, admission to intensive care unit, mechanical ventilation requirement or progression to severe or critical pneumonia): RR 0.81 (95%CI: 0.63-1.04), p=0.10, I2=82%. In a subgroup analysis that included hypertensive subjects only, ACEI/ARB were associated with a 27% significant decrease in the risk of the composite outcome (RR 0.73 (95%CI: 0.56-0.96), p=0.02, I2=65%). Conclusion: the results of this pooled analysis suggest that the use of ACEI/ARB does not worsen the prognosis, and could even be protective in hypertensive subjects. Patients should continue these drugs during their COVID-19 illness.


title: An artificial intelligence system reveals liquiritin inhibits SARS-CoV-2 by mimicking type I interferon

text: The pandemic COVID-19 has spread to all over the world and greatly threatens safety and health of people. COVID-19 is highly infectious and with high mortality rate. As no effective antiviral treatment is currently available, new drugs are urgently needed. We employed transcriptional analysis to uncover potential antiviral drugs from natural products or FDA approved drugs. We found liquiritin significantly inhibit replication of SARS-CoV-2 in Vero E6 cells with EC50 = 2.39 μM. Mechanistically, we found liquiritin exerts anti-viral function by mimicking type I interferon. Upregulated genes induced by liquiritin are enriched in GO categories including type I interferon signaling pathway, negative regulation of viral genome replication and etc. In toxicity experiment, no death was observed when treated at dose of 300 mg/kg for a week in ICR mice. All the organ indexes but liver and serum biochemical indexes were normal after treatment. Liquiritin is abundant in licorice tablet (~0.2% by mass), a traditional Chinese medicine. Together, we recommend liquiritin as a competitive candidate for treating COVID-19. We also expect liquiritin to have a broad and potent antiviral function to other viral pathogens, like HBV, HIV and etc.


title: Chloroquine Kills Hair Cells in Zebrafish Lateral Line and Murine Cochlear Cultures: Implications for Ototoxicity

text: Hearing and balance deficits have been reported during and following treatment with the antimalarial drug chloroquine. However, experimental work examining the direct actions of chloroquine on mechanoreceptive hair cells in common experimental models is lacking. This study examines the effects of chloroquine on hair cells using two common experimental models: the zebrafish lateral line and neonatal mouse cochlear cultures. Zebrafish larvae were exposed to varying concentrations of chloroquine phosphate or hydroxychloroquine for 1 hr or 24 hr, and hair cells assessed by antibody staining. A significant, dose-dependent reduction in the number of surviving hair cells was seen across conditions for both exposure periods. Hydroxycholroquine showed similar toxicity. In mouse cochlear cultures, chloroquine damage was specific to outer hair cells in tissue from the cochlear basal turn, consistent with susceptibility to other ototoxic agents. These findings suggest a need for future studies employing hearing and balance monitoring during exposure to chloroquine and related compounds, particularly with interest in these compounds as therapeutics against viral infections including coronavirus.


docid: gytebbua

title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex

text: The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) emergence in 2003 introduced the first serious human coronavirus pathogen to an unprepared world. To control emerging viruses, existing successful anti(retro)viral therapies can inspire antiviral strategies, as conserved viral enzymes (eg., viral proteases and RNA-dependent RNA polymerases) represent targets of choice. Since 2003, much effort has been expended in the characterization of the SARS-CoV replication/transcription machinery. Until recently, a pure and highly active preparation of SARS-CoV recombinant RNA synthesis machinery was not available, impeding target-based high throughput screening of drug candidates against this viral family. The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. This phylogenetic relatedness highlights the potential use of conserved replication enzymes to discover inhibitors against this significant pathogen, which in turn, contributes to scientific preparedness against emerging viruses. Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. The screening of a small (1,520 compounds) chemical library of FDA-approved drugs demonstrates the robustness of our assay and will allow to speed-up drug repositioning or novel drug discovery against the SARS-CoV-2. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights - A new SARS-CoV non radioactive RNA polymerase assay is described - The robotized assay is suitable to identify RdRp inhibitors based on HTS


title: Novel Coronavirus (COVID-19) and Dentistry–A Comprehensive Review of Literature

text: The novel coronavirus (COVID-19) pandemic has become a real challenge for healthcare providers around the world and has significantly affected the dental professionals in practices, universities and research institutions. The aim of this article was to review the available literature on the relevant aspects of dentistry in relation to COVID-19 and to discuss potential impacts of COVID-19 outbreak on clinical dentistry, dental education and research. Although the coronavirus pandemic has caused many difficulties for provision of clinical dentistry, there would be an opportunity for the dental educators to modernize their teaching approaches using novel digital concepts in teaching of clinical skills and by enhancement of online communication and learning platforms. This pandemic has also highlighted some of the major gaps in dental research and the need for new relevant knowledge to manage the current crisis and minimize the impact of such outbreaks on dentistry in the future. In conclusion, COVID-19 has had many immediate complications for dentistry of which some may have further long-term impacts on clinical practice, dental education and dental research.


title: Challenges in Abdominal Organ Transplantation During the COVID-19 Pandemic

text: As the coronavirus disease 2019 (COVID-19) outbreak has rapidly evolved into a global pandemic, abdominal organ transplantation programs are currently facing multiple challenges. Transplant candidates and recipients are considered high-risk populations for severe disease and death due to COVID-19 as a result of their numerous underlying comorbidities, advanced age and impaired immune function. Emerging reports of atypical and delayed clinical presentations in these patients generate further concerns for widespread disease transmission to medical personnel and the community. The striking similarities between COVID-19 and other outbreaks that took place over the past two decades, like Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome, highlight the severity of the situation and dictate that extra measures should be taken by the transplant programs to avoid adverse outcomes. Transplant organizations are currently calling for strict screening and isolation protocols to be established in all transplant programs, for both organ donors and recipients. As the situation escalates, more radical measures might be necessary, including a temporary hold on non-urgent transplantations, resulting in serious ethical dilemmas between the survival of these patients and the safety of the community. Further data about these special populations could result in more individualized guidelines for abdominal organ transplantation in the era of COVID-19.


title: Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus

text: World Health Organization (WHO) declared COVID-19 as a pandemic disease on March 11, 2020. Comparison of genome sequences from diverse locations allows us to identify the genetic diversity among viruses which would help in ascertaining viral virulence, disease pathogenicity, origin and spread of the SARS-CoV-2 between countries. The aim of this study is to ascertain the genetic diversity among Indian SARS-CoV-2 isolates. Initial examination of the phylogenetic data of SARS-CoV-2 genomes (n=3123) from different continents deposited at GISAID (Global Initiative on Sharing All Influenza Data) revealed multiple origin for Indian isolates. An in-depth analysis of 449 viral genomes derived from samples representing countries from USA, Europe, China, East Asia, South Asia, Oceania, Middle East regions and India revealed that most Indian samples are divided into two clusters (A and B) with cluster A showing more similarity to samples from Oceania and Kuwait and the cluster B grouping with countries from Europe, Middle East and South Asia. Diversity analysis of viral clades, which are characterized by specific non-synonymous mutations in viral proteins, discovered that the cluster A Indian samples belong to I clade (V378I in ORF1ab), which is an Oceania clade with samples having Iran connections and the cluster B Indian samples belong to G clade (D614G in Spike protein), which is an European clade. Thus our study identifies that the Indian SARS-CoV-2 viruses belong to I and G clades with potential origin to be countries mainly from Oceania, Europe, Middle East and South Asia regions, which strongly implying the spread of virus through most travelled countries. The study also emphasizes the importance of pathogen genomics through phylogenetic analysis to discover viral genetic diversity and understand the viral transmission dynamics with eventual grasp on viral virulence and disease pathogenesis.


title: How Many Lives Has Lockdown Saved in the UK?

text: We compare the trajectory of deaths (both in hospitals and care homes) on a daily basis in Sweden and England and Wales (which constitute 90 per cent of the UK population) from 11 March to 12 June 2020, the latest date at which the relevant data is available for England and Wales. Deaths in both Sweden and England and Wales peaked on 8 April. The build up to the peak was very similar in both. Given the time lag between infection and death, the lockdown would have had little effect on the peak number of deaths. By 12 June, the deaths are virtually the same in both. However, from early May the decline in England and Wales has been much sharper. We estimate that to 12 June, lockdown saved just under 6,000 lives in England and Wales, or around 6,500 extrapolating to a UK level.


title: Analysing recovery from pandemics by Learning Theory: the case of CoVid-19

text: We present a method for predicting the recovery time from infectious diseases outbreaks such as the recent CoVid-19 virus. The approach is based on the theory of learning from errors, specifically adapted to the control of the virus spread by reducing infection rates using countermeasures such as medical treatment, isolation, social distancing etc. When these are effective, the infection rate, after reaching a peak, declines following a given recovery rate curve. We use presently available data from China, South Korea and others to make actual predictions of the time needed for securing minimum infection rates in the future.


title: Neurologic Manifestations of Severe Respiratory Viral Contagions

text: Endemic and pandemic viral respiratory infections have recently emerged as a critical topic of investigation given the recent severe acute respiratory syndrome coronavirus-2 outbreak. Data from such outbreaks indicate that severe systemic comorbidities including acute neurologic illness are associated with illness and lead to significant outcome differences. Herein, we will discuss the neurologic manifestations of severe viral respiratory infections including coronavirus, influenza, respiratory syncytial virus, metapneumovirus, and enterovirus. DATA SOURCES: PubMed and EMBASE were searched by two independent investigators up to March 2020. STUDY SELECTION: Data selection included preclinical and clinical studies detailing neurologic manifestations of viral respiratory infections. DATA EXTRACTION AND SYNTHESIS: Two independent investigators reviewed and extracted the data. CONCLUSIONS: Neurologic manifestations including seizures, status epilepticus, encephalitis, critical illness neuromyopathy, acute disseminated encephalomyelitis, acute necrotizing encephalitis, Guillan-Barré syndrome, transverse myelitis, and acute flaccid myelitis have all been associated with severe viral respiratory infections. Having an understanding of the direct neurotropism of such viruses is imperative to understanding pathogenesis, clinical presentation, and potential treatment paradigms aimed at improving morbidity and mortality.


title: Forecasting the Peak of Novel Coronavirus Disease in Egypt Using Current Confirmed Cases and Deaths

text: The first case of coronavirus disease 2019 (COVID-19) in Egypt was reported on 14 February 2020 and the number of reported cases has increased daily. The purpose of this study is to describe the current situation of Covid-19 in Egypt and to predict the expected timing of the peak of this epidemic using current confirmed cases and deaths. We used one of the online tools; the Epidemic Calculator that utilizes, the well-known SEIR compartmental model. We utilized the daily reports published by the Egyptian Ministry of Health & Population from 14 February to 11 May 2020. Given the highest calculated case fatality rate (7.7%), the number of hospitalized individuals is expected to peak in the middle of June with a peak of hospitalized cases of 20,126 individuals and total expected deaths 12,303. We recommend strengthening of the Egyptian preventive and control measures so as to decrease the CFR and the number of cases to the least possible as we approach the epidemic peak. It is most important that appropriate quarantine measures are retained., the quarantine measures should not be relaxed before the end of June, 2020.


title: Subsequent waves of viral pandemics, a hint for the future course of the SARS-CoV-2 pandemic.

text: Background It is unknown if the SARS-CoV-2 pandemic will have a second wave. We analysed published data of five influenza pandemics (such as the Spanish Flu and the Swine Flu) and the SARS-CoV-1 pandemic to describe whether there were subsequent waves and how they differed. Methods We reanalysed literature and WHO reports on SARS-CoV-1 and literature on five influenza pandemics. We report frequencies of second and third waves, wave heights, wavelengths and time between subsequent waves. From this, we estimated peak-to-peak ratios to compare the wave heights, and wave-length-to-wave-length ratios to compare the wavelengths differences in days. Furthermore, we analysed the seasonality of the wave peaks and the time between the peak values of two waves. Results Second waves, the Spanish Flu excluded, were usually about the same height and length as first waves and were observed in 93% of the 57 described epidemic events of influenza pandemics and in 42% of the 19 epidemic events of the SARS-CoV-1 pandemic. Third waves occurred in 54% of the 28 influenza and in 11% of the 19 SARS-CoV-1 epidemic events. Third waves, the Spanish Flu excluded, usually peaked higher than second waves with a peak-to-peak ratio of 0.5. Conclusion While influenza epidemics are usually accompanied by 2nd waves, this is only the case in the minority of SARS-Cov1 epidemics.


title: Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting

text: The use of saliva collection for SARS-CoV-2 diagnostics in the ambulatory setting provides several advantages when compared to nasopharyngeal swabs (NPS), including ease of self-collection and reduced use of personal protective equipment (PPE). In addition saliva collection could be advantageous in advising if a convalescent patient is able to return to work after a period of self-quarantine. We investigated the utility of saliva collection in the community setting at Renown Health in a prospective Diagnostic Cohort of 88 patients and in a Convalescent Cohort of 24 patients. In the Diagnostic Cohort, we find that saliva collection has reduced sensitivity (~15% less) relative than NPS. And in our convalescent cohort of patients greater than 8 days and less than 21 days from first symptom, we find that saliva has ~ 50% sensitivity relative to NPS. Our results suggest that rigorous studies in the intended populations should be performed before large-scale screening using saliva as the test matrix is initiated.


title: Early surveillance and public health emergency disposal measures between novel coronavirus disease 2019 and avian influenza in China: a case-comparison study

text: Background: The novel coronavirus disease 2019 (COVID-19) outbreak is spreading rapidly throughout China and the world. Hence, early surveillance and public health emergency disposal are considered crucial to curb this emerging infectious disease. However, studies that investigated the early surveillance and public health emergency disposal for the prevention and control of the COVID-19 outbreak in China are relatively few. We aimed to compare the strengths and weaknesses of early surveillance and public health emergency disposal for prevention and control between COVID-19 and H7N9 avian influenza, which was commended by the international community, in China. Methods: A case-comparison study was conducted using a set of six key time nodes to form a reference framework for evaluating early surveillance and public health emergency disposal between H7N9 avian influenza (2013) in Shanghai, China and COVID-19 in Wuhan, China. Findings: A report to the local Center for Disease Control and Prevention, China, for the first hospitalized patient was sent after 6 and 20 days for H7N9 avian influenza and COVID-19, respectively. In contrast, the pathogen was identified faster in the case of COVID-19 than in the case of H7N9 avian influenza (12 days vs. 31 days). The government response regarding COVID-19 was 10 days later than that regarding avian influenza. The entire process of early surveillance and public health emergency disposal lasted 5 days longer in COVID-19 than in H7N9 avian influenza (46 days vs. 41 days). Conclusions: The identification of the unknown pathogen improved in China between the outbreaks of avian influenza and COVID-19. The longer emergency disposal period in the case of COVID-19 could be attributed to the government's slower response to the epidemic. Improving public health emergency management could lessen the adverse social effects of emerging infectious diseases and public health crisis in the future.


title: Evidence-based, cost-effective interventions to suppress the COVID-19 pandemic: a rapid systematic review

text: Background: Countries vary in their response to the COVID-19 pandemic. Some emphasise social distancing, while others focus on other interventions. Evidence on the effectiveness and cost-effectiveness of these interventions is urgently needed to guide public health policy and avoid unnecessary damage to the economy and other harms. We aimed to provide a comprehensive summary of the evidence on epidemic control, with a focus on cost-effectiveness. Methods: MEDLINE (1946 to March week 3, 2020) and Embase (1974 to March 27, 2020) were searched using a range of terms related to epidemic control. Reviews, randomized trials, observational studies, and modelling studies were included. Articles reporting on the effectiveness or cost-effectiveness of at least one intervention were included and grouped into higher-quality (randomized trials) and lower-quality evidence (other study designs). Findings: We found 1,653 papers; 34 were included. Higher-quality evidence was only available to support the effectiveness of hand washing and face masks. Modelling studies suggested that these measures are highly cost-effective. For other interventions, only evidence from observational and modelling studies was available. A cautious interpretation of this body of lower-quality evidence suggests that: (1) the most cost-effective interventions are swift contact tracing and case isolation, surveillance networks, protective equipment for healthcare workers, and early vaccination (when available); (2) home quarantines and stockpiling antivirals are less cost-effective; (3) social distancing measures like workplace and school closures are effective but costly, making them the least cost-effective options; (4) combinations are more cost-effective than single interventions; (5) interventions are more cost-effective when adopted early and for severe viruses like SARS-CoV-2. For H1N1 influenza, contact tracing was estimated to be 4,363 times more cost-effective than school closures ($2,260 vs. $9,860,000 per death prevented). Conclusions: A cautious interpretation of this body of evidence suggests that for COVID-19: (1) social distancing is effective but costly, especially when adopted late and (2) adopting as early as possible a combination of interventions that includes hand washing, face masks, swift contact tracing and case isolation, and protective equipment for healthcare workers is likely to be the most cost-effective strategy.


title: Potential modes of COVID-19 transmission from human eye revealed by single-cell atlas

text: There is a pressing urgency to understand the entry route of SARS-CoV-2 viruses into the human body. SARS-CoV-2 viruses enter through ACE2 receptors after the S proteins of the virus are primed by proteases such as TMPRSS2. Most studies focused on the airway epithelial and lung alveolar cells as the route of infection, while the mode of transmission through the ocular route is not well established. Here, we profiled the presence of SARS-CoV-2 receptors and receptor-associated enzymes at single-cell resolution of thirty-three human ocular cell types. We identified unique populations of corneal cells with high ACE2 expression, among which the conjunctival cells co-expressed both ACE2 and TMPRSS2, suggesting that they could serve as the entry points for the virus. Integrative analysis further models the signaling and transcription regulon networks involved in the infection of distinct corneal cells. Our work constitutes a unique resource for the development of new treatments and management of COVID-19.


title: Reproduction ratio and growth rates: measures for an unfolding pandemic

text: The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates {lambda}(t) of tested positive COVID-19 cases have crossed the threshold in many countries, with negative numbers as surrogate for disease transmission deceleration, lockdowns lifting are linked to the behavior of the momentary reproduction numbers r(t), often called R0. Important to note that this concept alone can be easily misinterpreted as it is bound to many internal assumptions of the underlying model and significantly affected by the assumed recovery period. Here we present our experience, as part of the Basque Country Modeling Task Force (BMTF), in monitoring the development of the COVID-19 epidemic, by considering not only the behaviour of r(t) estimated for the new tested positive cases - significantly affected by the increased testing capacities, but also the the momentary growth rates for hospitalizations, ICU admissions, deceased and recovered cases, in assisting the Basque Health Managers and the Basque Government during the lockdown lifting measures. Two different data sets, collected and then refined during the COVID-19 responses, are used as an exercise to estimate the momentary growth rates and reproduction numbers over time in the Basque Country, and the implications of using those concepts to make decisions about easing lockdown and relaxing social distancing measures are discussed. These results are potentially helpful for task forces around the globe which are now struggling to provide real scientific advice for health managers and governments while the lockdown measures are relaxed.


title: Coronavirus Disease 2019 (COVID-19) in a Renal Transplant Patient

text: Coronavirus disease 2019 (COVID-19) has resulted in significant morbidity and mortality worldwide. Transplant patients are particularly at a higher risk of contracting COVID-19 because of their immunosuppressed state, and they have the propensity to develop opportunistic infections. The pre-immunosuppressed state, along with other existing comorbidities, can influence the outcomes of COVID-19 in transplant patients. We describe a case of a renal transplant patient who developed COVID-19. Real-time nucleic acid testing (NAT) should be done in deceased and living donors. The most common management strategy is the modification of immunosuppression along with current experimental strategies for COVID-19.


title: Erratum to: Transmission risk of patients with COVID-19 meeting discharge criteria should be interpreted with caution

text: The original version of this article unfortunatelycontained a mistake. For Fig. 1a in p.409, the citationof a reference, as well as the permission to reprint thispicture, was missing. The correct version and thecorresponding reference are given below: (a) Chest computed tomography (CT) image of Patient 1 onadmission presents multiple ground-glass opacities distributedin the periphery of inferior lobe of both lungs. Reprinted fromZhang et al. (2020), with kind permission from SpringerNature.


title: A machine learning-based model for survival prediction in patients with severe COVID-19 infection

text: The sudden increase of COVID-19 cases is putting a high pressure on healthcare services worldwide. At the current stage, fast, accurate and early clinical assessment of the disease severity is vital. To support decision making and logistical planning in healthcare systems, this study leverages a database of blood samples from 404 infected patients in the region of Wuhan, China to identify crucial predictive biomarkers of disease severity. For this purpose, machine learning tools selected three biomarkers that predict the survival of individual patients with more than 90% accuracy: lactic dehydrogenase (LDH), lymphocyte and high-sensitivity C-reactive protein (hs-CRP). In particular, relatively high levels of LDH alone seem to play a crucial role in distinguishing the vast majority of cases that require immediate medical attention. This finding is consistent with current medical knowledge that high LDH levels are associated with tissue breakdown occurring in various diseases, including pulmonary disorders such as pneumonia. Overall, this paper suggests a simple and operable formula to quickly predict patients at the highest risk, allowing them to be prioritised and potentially reducing the mortality rate.


title: Creating Virtual Presence During a Pandemic

text: This article describes ways in which telemedicine has reshaped the doctor–patient relationship, and how we may face the challenge of maintaining a clinician’s presence in the virtual environment.


title: Telepsychotherapy: a leaflet for psychotherapists in the age of COVID-19. A review of the evidence

text: COVID-19 outbreak imposes the adoption of extraordinary containment measures, including the strict necessity to limit interpersonal contact. Face-to-face psychotherapy collides with this requirement and, above all, it might endanger both therapists and patients’ safety. Telepsychotherapy might come to the aid, ensuring therapeutic continuity and the possibility to reach people who might benefit of extra psychological support. Infectious outbreaks have been indeed associated with major psychopathological outcomes. The aim of the present work is to review the most recent experimental evidence about telepsychotherapy, focusing on its effectiveness, possible determinants of efficacy and therapists/patients’ attitudes, to rapidly inform psychotherapists. Out of the 857 records found, 18 studies have been included in the review. Our results show that, despite therapists and public’s skepticism, telepsychotherapy is a trustworthy alternative to be adopted, which can be used efficaciously to treat common mental-health disorders such as anxiety, depression and post-traumatic distress. As well as in the traditional setting, a higher number of sessions and the proper management of patients’ expectations seem to be associated with better outcomes. On the contrary, low familiarity with web-based means of communication and technical issues might reduce specifically the effectiveness of telepsychotherapy.


title: COVID-19: An updated review/ COVID-19: ОБНОВЛЕННЫЙ ВЗГЛЯД

text: COVID-19 is a zoonotic disease that showed higher levels of transmissibility in humans. Coronavirus has the largest recognized genome (28–33 kb) of a positive-sense single stranded RNA. The genome composed of 5′-end, the translationable mRNA sequences for the key proteins; replicase, spike, envelop membrane, and nucleocapsid and 3′-end (polyA tail). This highly contagious virus may impair the immune system in the early phase of the disease, hence the symptoms of the disease appear very rapidly. Importantly until now, there is no efficient strategy for containing the disease. So, all the world scientists today are in a race against time to find a vaccine or treatment to COVID-19, which requires a deeper understanding.


title: The spatial and temporal pattern of COVID-19 and its effect on humans development in China

text: The coronavirus disease 2019 (COVID-19) has been identified as the main cause of the outbreak of the respiratory disease in Wuhan, Hubei Province of China in December 2019 Since then, the epidemic has spread rapidly throughout China and many other countries in the world This study, therefore, examines the spatiotemporal distribution of the confirmed cases of COVID-19 and its effect on human development in China, and suggested social and non-pharmaceutical preventive interventions to help curb the further spread of the disease The public open data available from January to February 2020, from the National Health Commission of the People's Republic of China and a medical knowledge sharing website were used, and spatial analysis was performed to visualize the spatial distribution pattern of COVID-19 in China The results showed among others that COVID-19 had entered a dispersed spatial pattern, resulting in increased pressure to control the spread of the disease In early March, there was a significant reduction in the existing number of cases, and the number of deaths also decreased At the provincial level, the spatial distribution of the number of cumulative confirmed cases in China was divided into four patterns: Hubei was the initial core region;the eastern provinces adjacent to Hubei formed the second concentrated pattern;the western provinces adjacent to Hubei and the northeastern and southeastern provinces which were separated from Hubei by one province belonged to the third distribution pattern;while the rest of the provinces in the north, south and west showing sporadic distribution patterns formed the fourth It has been estimated that about 80% of students' online learning at all schools were not effective due to lack of access to reliable and uninterrupted internet services especially in the rural areas of China (C) 2020 GJESM All rights reserved


title: COVID-SGIS: A smart tool for dynamic monitoring and temporal forecasting of Covid-19

text: Objective The new kind of coronavirus SARS-Cov2 spread to countries in all continents in the World. The coronavirus disease 2019 (Covid-19) causes fever, cough, sore throat, and in severe cases shortness of breath and death. To evaluate strategies, it is necessary to forecast the number of cases and deaths, in order to aid the stakeholders in the process of making decisions against the disease. We propose a system for real-time forecast of the cumulative cases of Covid-19 in Brazil. Study Design Monitoring of all Brazilian cities using oficial information from the National Notification System, from March to May 2020, concentrated on Brazil.io databases. Training and evaluation of ARIMA and other machine learning algorithms for temporal forecasting using correlation indexes (Pearson's, Spearman's, and Kendall's) and RMSE(%). Validation from the relative errors of the following six days. Methods Our developed software, COVID-SGIS, captures information from the 26 states and the Distrito Federal at the Brazil.io database. From these data, ARIMA models are created for the accumulation of confirmed cases and death cases by Covid-19. Finally, six-day forecasts graphs are available for Brazil and for each of its federative units, separately, with a 95% CI. In addition to these predictions, the worst and best scenarios are also presented. Results ARIMA models were generated for Brazil and its 27 federative units. The states of Bahia, Maranhao, Piaui, Rio Grande do Norte, Amapa, Rondonia every day of the predictions were in the projection interval. The same happened to the states of Espirito Santo, Minas Gerais, Parana and Santa Catarina. In Brazil, the percentage error between the predicted values and the actual values varied between 2.56% and 6.50%. For the days when the forecasts outside the prediction interval, the percentage errors in relation to the worst case scenario were below 5%. The states of Bahia, Maranhao, Piaui, Rio Grande do Norte, Amapa, and Rondonia every day of the predictions were in the projection interval. The same happened to the states of Espirito Santo, Minas Gerais, Parana and Santa Catarina. Conclusion The proposed method for dynamic forecasting may be used to guide social policies and plan direct interventions in a robust, flexible and fast way. Since it is based on information from multiple databases, it can be adapted to the different realities, becoming an important tool to guide the course of politics and action against Covid-19 pandemic worldwide.


title: Dynamic coupling between the COVID epidemic timeline and the behavioral response to PAUSE in New York State counties

text: By many expert opinions, the COVID 19 epidemic is still much in its developing stages. While awaiting for effective clinical answers for the outbreak, the best approach remains that of social distancing. This raises a few crucial questions related to the extent to which social distancing measures were (1) well timed, (2) necessary and (3) efficient. By investigating correlations between epidemic measures such as daily infection rate, and social mobility measures (as reported by Apple and Google), our study aims to establish whether data identifies social distancing measures as a primary player in controlling the outbreak in New York State.


title: Herding Effect based Attention for Personalized Time-Sync Video Recommendation

text: Time-sync comment (TSC) is a new form of user-interaction review associated with real-time video contents, which contains a user's preferences for videos and therefore well suited as the data source for video recommendations. However, existing review-based recommendation methods ignore the context-dependent (generated by user-interaction), real-time, and time-sensitive properties of TSC data. To bridge the above gaps, in this paper, we use video images and users' TSCs to design an Image-Text Fusion model with a novel Herding Effect Attention mechanism (called ITF-HEA), which can predict users' favorite videos with model-based collaborative filtering. Specifically, in the HEA mechanism, we weight the context information based on the semantic similarities and time intervals between each TSC and its context, thereby considering influences of the herding effect in the model. Experiments show that ITF-HEA is on average 3.78\% higher than the state-of-the-art method upon F1-score in baselines.


title: Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19

text: Background. The outbreak of the 2019 novel coronavirus (COVID-19) has attracted global attention. In the early stage of the outbreak, the most important question concerns some meaningful milepost moments, including (1) the time when the number of daily confirmed cases decreases, (2) the time when the number of daily confirmed cases becomes smaller than that of the daily removed (recovered and death), (3) the time when the number of daily confirmed cases becomes zero, and (4) the time when the number of patients treated in hospital is zero, which indicates the end of the epidemic. Intuitively, the former two can be regarded as two important turning points which indicate the alleviation of epidemic to some extent, while the latter two as two ``zero" points, respectively. Unfortunately, it is extremely difficult to make right and precise prediction due to the limited amount of available data at a early stage of the outbreak. Method. To address it, in this paper, we propose a flexible framework incorporating the effectiveness of the government control to forecast the whole process of a new unknown infectious disease in its early-outbreak. Specially, we first establish the iconic indicators to characterize the extent of epidemic spread, yielding four periods of the whole process corresponding to the four meaningful milepost moments: two turning points and two ``zero" points. Then we develop the tracking and forecasting procedure with mild and reasonable assumption. Finally we apply it to analyze and evaluate the COVID-19 using the public available data for mainland China beyond Hubei Province from the China Centers for Disease Control (CDC) during the period of Jan 29th, 2020, to Feb 29th, 2020, which shows the effectiveness of the proposed procedure. Results. Results show that our model can clearly outline the development of the epidemic at a very early stage. The first prediction results on Jan 29th reveal that the first and second milepost moments for mainland China beyond Hubei Province would appear on Jan 31st and Feb 14th respectively, which are only one day and three days behind the real world situations. Forecasting results indicate that the number of newly confirmed cases will become zero in the mid-late March, and the number of patients treated in the hospital will become zero between mid-March and mid-April in mainland China beyond Hubei Province. The framework proposed in this paper can help people get a general understanding of the epidemic trends in counties where COVID-19 are raging as well as any other outbreaks of new and unknown infectious diseases in the future.


title: Early experience with COVD-19 patients at tertiary care teaching hospital in southwestern United states

text: Abstract Importance: There is limited information about presenting characteristics, treatment and outcomes of patients requiring hospitalization for coronavirus disease 2019 (COVID-19) serving underserved population in southwestern United states. Objective: To describe the clinical characteristics and outcomes of patients with COVID-19, hospitalized in a tertiary care teaching hospital in southwestern United states serving Underserved population. Methods: Case series of first 50 adults admitted at the University of New Mexico (UNM) Health Science center, the only tertiary care teaching hospital in the state of New Mexico between Jan 19th to April 24th 2020 via retrospective and prospective chart review. Main outcomes and measures: Clinical outcomes during hospitalization, such as invasive mechanical ventilation, kidney replacement therapy and death. Demographics, baseline comorbidities, presenting vital signs, and test results were also collected. Results: A total of 50 patients were included (median age, 55.5; 20-85-year-old, 54% were female). Obesity was the most common comorbidity in 20/39 (51%), followed by diabetes in 18/50 (36%) and hypertension 17/50(34%). Mean onset of symptoms duration before admission 7.39 days (range 1-21days). Most common symptoms on presentation included subjective fevers 40/42 (95.2%), cough 43/46 (93%) 43/46 and shortness of breath 40/46(87%). At triage only 24% were febrile and 46% patient did not have a single febrile episode throughout hospitalization, 56% had respiratory rate > 20 and 66% had a heart rate > 90. 80% patients required oxygen and 20%required intubation on presentation. On differential analysis 46% had elevated neutrophil counts, and 48% had low lymphocytes counts. Median D dimer, Ferritin, CRP, LDH were all elevated at presentation. 10% of patients had a negative initial chest x ray. 19.3% patients have coinfection with another respiratory viral pathogen. 34 (68%) patient required ICU level of care at some point during hospitalization. More than 70% of patients were treated with antibiotics mainly directed towards community acquired pneumonia but 97.5% patient has negative blood culture and 93.3% has negative sputum cultures. Of admitted patients, 34% (17/50) were directly admitted to ICU and. Of these ICU patients 82.4% (28/34) required invasive mechanical ventilation. Patients spent a median of 2 days on the floor prior to ICU transfer, median length of stay in the ICU was 7 days. On comparing characteristics of patients, patients with diabetes, and higher lactate dehydrogenase on admission were more likely to require ICU level of care. No patient deaths were reported on the floor. Of 34 patients in the ICU 13 died while 6 are still receiving care in the hospital, with an overall mortality of 30.2% (13/43). Out of 13 patients who died, 2 were on HD, 11/13(84%) patients had acute kidney injury and required CRRT or HD. The median length of stay is 7 days (Range 1-31days), for floor patients 4 days and ICU patients 13 days. Out of 43 patients who completed their clinical course 24/43(58.1%) were discharged home, 5/43(11.6%) went to rehabilitation facilities and 30.2% died. 16/30(53.3%) required oxygen on discharge. Conclusion: This case series provides characteristics and early experience in treating patient admitted to tertiary care teaching hospital in state of NEW Mexico.


title: The role of asymptomatic SARS-CoV-2 infections: rapid living systematic review and meta-analysis

text: Background: There is substantial disagreement about the level of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in a population. The disagreement results, in part, from the interpretation of studies that report a proportion of asymptomatic people with SARS-CoV-2 detected at a single point. Review questions: 1. Amongst people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? 2. Amongst people with SARS-CoV-2 infection who are asymptomatic when diagnosed, what proportion will develop symptoms later? 3. What proportion of SARS-CoV-2 transmission is accounted for by people who are either asymptomatic throughout infection, or pre-symptomatic? Methods: Rapid living systematic review (protocol https://osf.io/9ewys/). We searched Pubmed, Embase, bioRxiv and medRxiv using a living evidence database of SARS-CoV-2 literature on 25.03.2020. We included studies of people with SARS-CoV-2 diagnosed by reverse transcriptase PCR (RT-PCR) that documented follow-up and symptom status at the beginning and end of follow-up and modelling studies. Study selection, data extraction and bias assessment were done by one reviewer and verified by a second, with disagreement resolved by discussion or a third reviewer. We used a common-effect model to synthesise proportions from comparable studies. Results: We screened 89 studies and included 11. We estimated an upper bound for the proportion of asymptomatic SARS-CoV-2 infections of 29% (95% confidence interval 23 to 37%) in eight studies. Selection bias and likely publication bias affected the family case investigation studies. One statistical modelling study estimated the true proportion of asymptomatic infections at 18% (95% credibility interval 16 to 20%). Estimates of the proportions of pre-symptomatic individual in four studies were too heterogeneous to combine. In modelling studies, 40-60% of all SARS-CoV-2 infections are the result of transmission from pre-symptomatic individuals, with a smaller contribution from asymptomatic individuals. Conclusions: An intermediate contribution of pre-symptomatic and asymptomatic infections to overall SARS-CoV-2 transmission means that combination prevention, with enhanced hand and respiratory hygiene, testing tracing and isolation strategies and social distancing, will continue to be needed. The findings of this systematic review of publications early in the pandemic suggests that most SARS-CoV-2 infections are not asymptomatic throughout the course of infection.


title: Immunization Dynamics on a 2-layer Network Model

text: We introduce a 2-layer network model for the study of the immunization dynamics in epidemics. Spreading of an epidemic is modeled as an excitatory process in a small-world network (body layer) while immunization by prevention for the disease as a dynamic process in a scale-free network (head layer). It is shown that prevention indeed turns periodic rages of an epidemic into small fluctuation. The study also reveals that, in a certain situation, prevention actually plays an adverse role and helps the disease survive. We argue that the presence of two different characteristic time scales contributes to the immunization dynamics observed.


Compassion, the vulnerable and COVID-19


title: COVID‐19 and its effects on the digestive system and endoscopy practice

text: The Coronavirus Disease 2019 (COVID‐19) is a respiratory illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and has been classified as a pandemic by the World Health Organization in March 2020. Several studies have demonstrated that the gastrointestinal (GI) tract is also a potential route. As the pandemic is continuously evolving, and more data are made available, this article highlights the best evidence and practices regarding the effects of the SARS‐CoV‐2 virus relevant to GI practice. Published clinical studies have supported that SARS‐CoV‐2 affects the GI tract and the liver. The largest published dataset comprised of 4243 patients and showed a pooled prevalence of GI symptoms at 17.6%. GI symptoms varied and usually preceded pulmonary symptoms by 1–2 days. These include anorexia (26.8%), nausea and vomiting (10.2%), diarrhea (12.5%), and abdominal pain (9.2%). Incidence of liver injury ranges from 15 to 53%. Evidence shows that the severity of COVID‐19 infection is compounded by its effects on nutrition, most especially for the critically ill. As such, nutrition societies have recommended optimization of oral diets and oral nutritional supplements followed by early enteral nutrition if nutritional targets are not met, and parenteral nutrition in the distal end of the spectrum. In addition to possible fecal–oral transmission, GI endoscopy procedures, which are considered to be aerosol‐generating procedures, contribute to increased risk to GI health‐care professionals. Infection prevention measures and guidelines are essential in protecting both patients and personnel.