title: Study of Non-Pharmacological Interventions on COVID-19 Spread

text: COVID-19 disease has emerged as one of the life threatening threat to the society. It is caused by a novel beta coronavirus. It began as unidentified pneumonia of unknown aetiology in Wuhan City, Hubei province in China emerged in December 2019. No vaccine has been produced till now. Mathematical models are used to study impact of different measures used to decrease pandemic. Mathematical models have been designed to estimate the numbers of spreaders in different scenarios in the present manuscript. In the present manuscript, three different mathematical models have been proposed with different scenarios such as screening, quarantine and NPIs for estimating number of virus spreaders. the analysis shows that the numbers of COVID-19 patients will be more without screening the peoples coming from other countries. Since, every people suffering with COVID-19 disease are spreaders. The screening and quarantine with NPIs have been implemented to study their impact on the spreaders. It has been found that NPI measures are able to reduce number of spreaders. The NPI measures reduces the growth of the spread function and providing decision makers more time to prepare with in dealing of the disease.


title: The de-financialization of housing: towards a research agenda

text: Housing financialization, or the increased dominance of financial markets in the housing sector, has not stopped in the wake of the crisis. Rather, it has reinforced and rescaled itself, expanding into new market segments and urban territories. However, while academic scholarship has convincingly exposed the reconfiguration of financialization processes, it has paid surprisingly little attention to how these processes are also contested from within society and the economy. In response to this gap in the literature, I propose in this contribution a threefold research agenda, calling out for more research on (i) financial market reforms aimed at dismantling finance-led housing accumulation; (ii) policy focused on strengthening the public and affordable housing sector; and (iii) changing modes of urban governance and ‘anti-political’ social movements which can contest housing financialization locally. Taking into account these three fields of inquiry, I invite housing scholars to explore how–and if –de-financializing tendencies can become ecologically dominant in post-crisis urban housing markets.


title: COVIDTrach; the outcomes of mechanically ventilated COVID-19 patients undergoing tracheostomy in the UK: Interim Report 22nd May 2020

text: COVIDTrach is a UK multidisciplinary collaborative project that aims to evaluate the outcomes of tracheostomy in COVID-19 patients. It also examines the implementation of national guidance in COVID-19 tracheostomies and the incidence of COVID-19 infections amongst those health care workers involved in the procedure. An invitation to participate in an online survey tool (REDCap) was disseminated to all UK NHS departments involved in tracheostomy in mechanically ventilated COVID-19 patients via the Federation of Surgical Specialty Associations, it's subsidiary organisations and the Intensive Care Society. To date 78 hospitals have submitted 564 COVID-19 tracheostomy cases. Fifty-two percent (n=219/465) of patients who had undergone tracheostomy and were still alive, had been successfully weaned from mechanical ventilation at the point of completing the survey. The all cause in-hospital mortality following tracheostomy was 12% (n=62/530), with 3% of these (n=2/62) due to tracheostomy related complications and the remaining deaths due to COVID-19 related complications. Amongst 400 cases submitting data two weeks after the tracheostomy, no instance of COVID-19 infection amongst operators was recorded. FFP3 masks or Powered Air Purifying Respirators were used by operators in 100% of tracheostomies and a face visor or hood with face shield was available in 99% of cases. This interim report highlights early outcomes following tracheostomy in mechanically ventilated COVID-19 patients. Future reporting from COVIDTrach will include more detailed analysis at later timepoints using comparator groups in order to provide a more comprehensive assessment of tracheostomy in COVID-19.


title: Characterisation of Acute Kidney Injury in Critically Ill Patients with Severe Coronavirus Disease-2019 (COVID-19)

text: Background: COVID19-associated acute kidney injury frequency, severity and characterisation in critically ill patients has not been reported. Methods: Single-center cohort performed from March 3, 2020, to April 14, 2020 in 4 intensive care units in Bordeaux University Hospital, France. All patients with COVID19 and pulmonary severity criteria were included. AKI was defined using KDIGO criteria. A systematic urinary analysis was performed. The incidence, severity, clinical presentation, biological characterisation (transient vs. persistent acute kidney injury; proteinuria, hematuria and glycosuria), and short-term outcomes was evaluated. Results: 71 patients were included, with basal serum creatinine of 69 +/- 21 micromol/L. At admission, AKI was present in 8/71 (11%) patients. Median follow-up was 17 [12-23] days. AKI developed in a total of 57/71 (80%) patients with 35% Stage 1, 35% Stage 2, and 30% Stage 3 acute kidney injury; 10/57 (18%) required renal replacement therapy. Transient AKI was present in only 4/55 (7%) patients and persistent AKI was observed in 51/55 (93%). Patients with persistent AKI developed a median urine protein/creatinine of 82 [54-140] (mg/mmol) with an albuminuria/proteinuria ratio of 0.23 +/- 20 indicating predominant tubulo-interstitial injury. Only 2 (4%) patients had glycosuria. At Day 7 onset of after AKI, six (11%) patients remained dependent on renal replacement therapy, nine (16%) had SCr > 200 micromol/L, and four (7%) died. Day 7 and day 14 renal recovery occurred in 28% and 52 % respectively. Conclusion: COVID19 associated AKI is frequent, persistent severe and characterised by an almost exclusive tubulo-interstitial injury without glycosuria


title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine

text: SARS-CoV-2 is known to infect the neurological, respiratory, enteric, and hepatic systems of human and has already become an unprecedented threat to global healthcare system. COVID-19, the most serious public condition caused by SARS-CoV-2 leads the world to an uncertainty alongside thousands of regular death scenes. Unavailability of specific therapeutics or approved vaccine has made the recovery of COVI-19 more troublesome and challenging. The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins (S, E, M and N) reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and Normal Mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. The development of preventive measures to combat COVID-19 infections might be aided the present study. However, the in vivo and in vitro validation might be ensured with wet lab trials using model animals for the implementation of the presented data.


title: COVID-19 Implications on Clinical Clerkships and the Residency Application Process for Medical Students

text: The coronavirus disease 2019 (COVID-19) pandemic has caused significant disruption to undergraduate medical education (UME). Although the immediate scheduling challenges are being addressed, there has been less discourse regarding how this pandemic will impact medical students in their preparation for and application to residency programs. While some historical disasters and pandemics provide a loose precedent for UME response during COVID-19, the impact of the current pandemic has surpassed any other events. COVID-19 will likely impact UME in the suspension of clinical rotations, alterations in grading, suspension or elimination of away rotations, changes in medical licensing exams, and ramifications on mental health. This review assesses governing medical bodies’ recommendations regarding UME during the COVID-19 pandemic and how this may impact preparation for residency. In particular, residency programs will likely have to create new guidelines for assessing applicants during this unique cycle.


title: A Method to Model Outbreaks of New Infectious Diseases with Pandemic Potential such as COVID-19

text: The emergence of the novel coronavirus (a.k.a. COVID-19, SARS-CoV-2) out of Wuhan, Hubei Province, China caught the world by surprise. As the outbreak began to spread outside of China, too little was known about the virus to model its transmission with any acceptable accuracy. World governments responded to rampant misinformation about the virus leading to collateral disasters, such as plunging financial markets, that could have been avoided if better models of the outbreak had been available. This is an engineering approach to model the spread of a new infectious disease from sparse data when little is known about the infectious agent itself. The paper is not so much about the model itself - because there are many good scientific approaches to model an epidemic - as it is about crunching numbers when there are barely any numbers to crunch. The coronavirus outbreak in USA is used to illustrate the implementation of this modeling approach. A Monte Carlo approach is implemented by using incubation period and testing efficiency as variables. Among others it is demonstrated that imposing early travel restrictions from infected countries slowed down the outbreak in the USA by about 26 days.


title: The competing risk between in-hospital mortality and recovery: A pitfall in COVID-19 survival analysis research

text: Background Many studies investigating mortality and recovery in COVID-19 have been published recently. The majority of these studies used the standard Cox Proportional Hazards (Cox PH) model without taking into account the presence of competing risks. This study investigates, through extensive simulations, the bias in estimating the hazard ratio (HR) of death due to COVID-19 and the absolute risk reduction (ARR) when competing risks are not taken into consideration, and suggests an alternative method. Methods We simulated data for a fictive clinical trial in COVID-19 patients, to mimic recent trials involving the use of Hydroxychloroquine, Remdesivir, and convalescent plasma therapy for example. The primary outcome is the time from randomization until death due to COVID-19. Six scenarios representing different situations of the effect of treatment on death and its competing event recovery were considered. The HR of death and the 28-day ARR were estimated using the Cox PH model and the Fine and Gray (FG) model which takes competing risks into account. The estimates were then compared to their corresponding true values and the magnitude of misestimation quantified. Results The Cox PH model misestimated the true HR of death in the majority of the scenarios. The magnitude of this misestimation increased when the process of recovery was faster and/or the chance of recovery was higher. In some cases, this model has also incorrectly shown a harmful effect of treatment when it was in fact beneficial. The true 28-day ARR of death was also misestimated, and this misestimation increased in magnitude when the process of recovery was faster. The results obtained from the FG competing risks model are all consistent and show no misestimation or changes in direction for both the HR and the 28-day ARR of death. Conclusion There is a substantial risk of misleading results in COVID-19 research if recovery and death are not considered as competing risk events. We strongly suggest the use of a competing risk approach to re-analyze relevant published data that have used the Cox PH model.


title: Improved and Simplified Diagnosis of Covid-19 using TE Extraction from Dry Swabs

text: Rigorous testing is the way forward to fight the Covid-19 pandemic. Here we show that the currently used and most reliable RT-PCR based SARS-CoV-2 procedure can be further simplified to make it faster, safer and economical by bypassing the RNA isolation step. The modified method is not only fast and convenient but also at par with the traditional method in terms of accuracy, and therefore, can be used for mass screening. Our method takes about half the time and is cheaper by about 40% compared to current most widely used method. We also provide a variant of the new method that increases the efficiency of detection by about 20% compared to the currently used method. Taken together, we demonstrate a more effective and reliable method of SARS-CoV-2 detection.


title: An interpretable mortality prediction model for COVID-19 patients - alternative approach

text: The pandemic spread of coronavirus leads to increased burden on healthcare services worldwide. Experience shows that required medical treatment can reach limits at local clinics and fast and secure clinical assessment of the disease severity becomes vital. In L. Yan et al. a model is presented for predicting the mortality of COVID-19 patients from their biomarkers. Three biomarkers have been selected by ranking with a supervised Multi-tree XGBoost classifier. The prediction model is built up as a binary decision tree with depth three and achieves AUC scores of up to 97.84 pm 0.37 and 95.06 pm 2.21 for training and external test data sets, resp. In human assessment and decision making influencing parameters usually are not considered as sharp numbers but rather as Fuzzy terms, and inferencing primarily yields Fuzzy terms or continuous grades rather than binary decisions. Therefore, I examined a Sugeno-type Fuzzy classifier for disease assessment and decision support. In addition, I used an artificial neural network (SOM, [4]) for selecting the biomarkers. Modelling and validation was done with the identical data base provided by L. Yan et al.. With the complete training and test data sets, the Fuzzy prediction model achieves improved AUC scores of up to 98.59 or 95.12 The improvements with the Fuzzy classifier obviously become clear as physicians can inter- pret output grades to belong to positive or negative class more or less strongly. An extension of the Fuzzy model, which takes into account the trend in key features over time, provides excellent results with the training data, which, however, could not be finally verified due to the lack of suitable test data. The generation and training of the Fuzzy models was fully automatic and without additional adjustment with the help of ANFIS from Matlab(c).


title: The local stability of a modified multi-strain SIR model for emerging viral strains

text: We study a novel multi-strain SIR epidemic model with selective immunity by vaccination. A newer strain is made to emerge in the population when a preexisting strain has reached equilibrium. We assume that this newer strain does not exhibit cross-immunity with the original strain, hence those who are vaccinated and recovered from the original strain become susceptible to the newer strain. Recent events involving the COVID-19 virus demonstrates that it is possible for a viral strain to emerge from a population at a time when the influenza virus, a well-known virus with a vaccine readily available for some of its strains, is active in a population. We solved for four different equilibrium points and investigated the conditions for existence and local stability. The reproduction number was also determined for the epidemiological model and found to be consistent with the local stability condition for the disease-free equilibrium.


title: Evaluation of COVID 19 infection in 279 cancer patients treated during a 90-day period in 2020 pandemic

text: Background: The aim of this study was investigation of COVID-19 disease and its outcome in cancer patients who needed treatment, in a 90-day period. Methods: Cancer patient who required treatment, were evaluated for potential COVID-19 infection in a 90-day period, starting from beginning of this epidemic in Iran, January, to April 19, 2020. For treatment of solid tumor patients, if they did not have symptoms related to COVID-19, just chest X-ray was requested. If they showed COVID-19 related symptoms, High Resolution CT scan of lungs was requested. For hematology cancer patients, PCR test for COVID-19 infection was requested as well. Protection measures were considered for personnel of oncology wards. Results: In this study, 279 patients were followed up in this 90-day period. No COVID-19 infection was observed in 92 cases of breast cancer, 72 cases of colon cancer, 14 cases of gastric cancer and 12 cases of pancreaticobiliary cancer .However, in 11 cases of lung cancer, 5 cases brain tumors and 12 cases ovarian cancer; 3 case of COVID-19 were observed. In the hematology cancers group, which included 14 cases of Hodgkin Lymphoma, 23 cases of lymphoproliferative disorder, 12 cases of acute leukemia and 12 cases of multiple myeloma; three of COVID-19 were observed. Conclusion: Patients with cancer who need treatment can be treated by taking some measures. These measures include observing individual and collective protection principles in patients and health-care personnel, increasing patients awareness particularly about self-care behavior, performing a COVID-19 test, and taking a chest X ray, before the treatment starts


title: 11 Ways to Stop Misinformation

text: Following the wrong advice in these difficult times could be dangerous Martin Cooper MBCS RIT Tech looks at 11 ways we can all help to combat the rising tide of misinformation on the web


title: Evaluating the Efficacy of Stay-At-Home Orders: Does Timing Matter?

text: BACKGROUND: The many economic, psychological, and social consequences of pandemics and social distancing measures create an urgent need to determine the efficacy of non-pharmaceutical interventions (NPIs), and especially those considered most stringent, such as stay-at-home and self-isolation mandates. This study focuses specifically on the efficacy of stay-at-home orders, both nationally and internationally, in the control of COVID-19. METHODS: We conducted an observational analysis from April to May 2020 and included countries and US states with known stay-at-home orders. Our primary exposure was the time between the date of the first reported case of COVID-19 to an implemented stay-at-home mandate for each region. Our primary outcomes were the time from the first reported case to the highest number of daily cases and daily deaths. We conducted simple linear regression analyses, controlling for the case rate of the outbreak. RESULTS: For US states and countries, a larger number of days between the first reported case and stay-at-home mandates was associated with a longer time to reach the peak daily case and death counts. The largest effect was among regions classified as the latest 10% to implement a mandate, which in the US, predicted an extra 35.3 days to the peak number of cases (95 % CI: 18.2, 52.5), and 38.3 days to the peak number of deaths (95 % CI: 23.6, 53.0). CONCLUSIONS: Our study supports the potential beneficial effect of earlier stay-at-home mandates, by shortening the time to peak case and death counts for US states and countries. Regions in which mandates were implemented late experienced a prolonged duration to reaching both peak daily case and death counts.


Active smoking is associated with severity of coronavirus disease 2019 (COVID-19): An update of a meta-analysis


Development of a Portuguese COVID-19 imaging repository and database: Learning and sharing knowledge during a pandemic


Learning From the COVID-19 Pandemic


title: Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations

text: Background: SARS-CoV-2 virus testing for persons with COVID-19 symptoms, and contact tracing for those testing positive, will be critical to successful epidemic control. Willingness of persons experiencing symptoms to seek testing may determine the success of this strategy. Methods: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. Instructions clarified that home-collected specimens would be mailed to a laboratory for testing. We presented similar willingness questions regarding testing during follow-up care. Results: Of 1435 participants, comprising a broad range of sociodemographic groups, 92% were willing to test with a home saliva specimen, 88% with home swab, 71% with drive-through swab, and 60% with clinic collected swab. Moreover, 68% indicated they would be more likely to get tested if there was a home testing option. There were no significant differences in willingness items across sociodemographic variables or for those currently experiencing COVID-19 symptoms. Results were nearly identical for willingness to receive testing for follow-up COVID-19 care. Conclusions: We observed a hierarchy of willingness to test for SARS-CoV-2, ordered by the degree of contact required. Home specimen collection options could result in up to one-third more symptomatic persons seeking testing, facilitating contact tracing and optimal clinical care. Remote specimen collection options may ease supply chain challenges and decrease the likelihood of nosocomial transmission. As home specimen collection options receive regulatory approval, they should be scaled rapidly by health systems.


title: Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

text: Stopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans. Bullet points We generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19. ACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2. ACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities. We unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry.


title: FIRST DETECTION OF SARS-COV-2 IN UNTREATED WASTEWATERS IN ITALY

text: Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewer systems for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection occurred in volumes of 250 mL of wastewaters collected in both areas at high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study shows that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.


title: Evidence for anti-viral effects of complete Freund’s adjuvant in the mouse model of enterovirus infection

text: Group B Coxsackieviruses belonging to the genus, Enterovirus, contain six serotypes that induce various diseases, whose occurrence may involve the mediation of more than one serotype. We recently identified immunogenic epitopes within CVB3 viral protein 1 that induce anti-viral T cell responses in mouse models of CVB infections. In our investigations to determine the protective responses of the viral epitopes, we unexpectedly noted that animals immunized with complete Freund’s adjuvant (CFA) alone and later challenged with CVB3 were completely protected against myocarditis. Similarly, the pancreatitis-inducing ability of CVB3 was remarkably reduced to only 10% in the CFA group as opposed to 73.3% in the control group that received no CFA. Additionally, no mortalities were noted in the CFA group, whereas 40% of control animals died during the course of 21 days post-infection with CVB3. Taken together, our data suggest that the adjuvant effects of CFA may be sufficient for protection against CVB infections. These observations may provide new insights into our understanding of the occurrence of viral infections. One example is Coronavirus disease-19 (COVID-19) as individuals suffering from COVID-19 who have been vaccinated with Bacillus Calmette–Guérin appear to have fewer morbidities and mortalities than unvaccinated individuals.


title: Coronavirus Disease 2019 State Guidelines on Elective Surgery: Considerations for Plastic and Reconstructive Surgeons

text: Background: Vague recommendations regarding elective surgery have been proposed by national organizations in an attempt to conserve personal protective equipment and to protect healthcare workers during the coronavirus disease 2019 pandemic In response, some states have attempted to provide more clear guidance Methods: An internet search was performed to identify and analyze what guidance each state published through government websites through April 10, 2020 Results: Thirty-five states and the District of Columbia published guidance in the form of either a recommendation or a mandate Procedures relating to cosmetics and malignancy were found to be mentioned in 4 and 12 states, respectively, but ultimately lacked case-specific information Conclusions: Current government and state recommendations do not provide clear guidance on how plastic and reconstructive surgeons should approach elective surgeries Ultimately, it is the responsibility of all plastic and reconstructive surgeons to operate under appropriate law while individualizing their practices to best suit the needs of their patients while being mindful of resource limitations and exposure risks


title: Risk of secondary infection waves of COVID-19 in an insular region: the case of the Balearic Islands, Spain

text: The Spanish government declared the lockdown on March 14th, 2020 to tackle the fast-spreading of COVID-19. As a consequence the Balearic Islands remained almost fully isolated due to the closing of airports and ports, These isolation measures and the home-based confinement have led to a low incidence of COVID-19 in this region. We propose a compartmental model for the spread of COVID-19 including five compartments (Susceptible, Latent, Infected, Diseased, and Recovered), and the mobility between municipalities. The model parameters are calibrated with the temporal series of confirmed cases provided by the Spanish Ministry of Health. After calibration, the proposed model captures the trend of the official confirmed cases before and after the lockdown. We show that the estimated number of cases depends strongly on the initial dates of the local outbreak onset and the number of imported cases before the lockdown. Our estimations indicate that the population has not reached the level of herd immunization necessary to prevent future outbreaks. While the low incidence, in comparison to mainland Spain, has prevented the saturation of the health system, this low incidence translates into low immunization rates, therefore facilitating the propagation of new outbreaks that could lead to secondary waves of COVID-19 in the region. These findings warn about scenarios regarding after-lockdown-policies and the risk of second outbreaks, emphasize the need for widespread testing, and could potentially be extrapolated to other insular and continental regions.


title: Elective Surgery during SARS-Cov-2/Covid-19 Pandemic: Safety Protocols with Literature Review

text: BACKGROUND: Health care systems worldwide have been affected by the novel SARS-Cov-2 emergence since December 2019 The Covid-19 pandemic produced a deep decrease on elective surgery scheduling, to the extent of complete cancellation without future planning of safely development PURPOSE: We performed a review of the literature and diagnosis data analysis with the aim to reduce the risk of operating a patient infected with SARS-Cov-2/Covid-19 during the incubation period METHODS: We searched for specific words and phrases about SARS-Cov-2 and Covid-19 in The PubMed database (U S National Library of Medicine) from December 2019 to April 2020 A detailed analysis of the clinical picture and existing diagnostic tests for COVID-19 was performed to achieve the desired objectives RESULTS: 1,273 out of 5,930 articles about COVID-19/SARS-Cov-2 did meet the criteria for the searched terms We reviewed 105 papers and 60 were selected for analysis Specific recommendations were described based on our revision CONCLUSIONS: With the combination of Ig-M and Ig-G Antibody tests + real-time RT-PCR for SARS-Cov-2 implemented in different time periods by taking into account the natural history of the disease, it is possible to decrease the risk of operating a patient during the incubation period higher than 93% Adding other security measures can further increase this percentage As long as there is no immunity to COVID-19, these measures will help us to perform safer elective surgeries Financial disclosure and products: The authors have no conflict of interest to declare in relation to the content of this article, we didn’t receive any financing for the realization of this work Corresponding Author, Contact Information: Lázaro Cárdenas-Camarena MD, INNOVARE Cirugía Plástica Especializada, Av Verona 7412 Col Villa Verona, Zapopan, Jalisco, México 45019, drlazaro@drlazarocardenas com This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4 0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited The work cannot be changed in any way or used commercially without permission from the journal Copyright © 2020 The Authors Published by Wolters Kluwer Health, Inc on behalf of the American Society of Plastic Surgeons All rights reserved


title: The efficacy of convalescent plasma for the treatment of severe influenza

text: Background. Administration of convalescent plasma may be of clinical benefit for treatment of severe acute viral respiratory infections. However, no clear evidence exists to support or oppose convalescent plasma use in clinical practice. We conducted a systematic review and meta-analysis to assess the evidence of randomized controlled trials (RCTs) in the convalescent plasma for the treatment of severe influenza. Methods. Healthcare databases were searched in February 2020. All records were screened against the eligibility criteria. Data extraction and risk of bias assessments were undertaken. The primary outcome was case fatality rates by influenza. Results. We identified 5 RCTs of severe influenza. The pooled analyses showed no evidence for a reduction in mortality (Odds Ratio (OR) 1.06; p = 0.87; I2 = 35%). We also found non significant reductions in days in ICU and hospital, and days on mechanical ventilation. There seemed to have a biological benefit of increasing HAI titer levels and decreasing influenza B virus loads and cytokines after convalescent plasma treatment. No serious adverse events was reported between two groups. Studies were commonly of low risk of bias with high quality. Conclusions. Convalescent plasma appears safe but may not reduce mortality in severe influenza. This therapy should be studied within the context of a well designed clinical trial for treatment of SARS Cov 2 infection.


title: Therapeutic Application of Chloroquine in Clinical Trials for COVID-19

text: The novel corona virus disease -2019 (COVID-19) pandemic has caused a massive global public health havoc. Recent clinical trials carried out in China has found a promising therapeutic application of chloroquine and hydroxychloroquine for COVID-19. This study meticulously evaluated the various dosages of chloroquine and hydroxychloroquine utilized in clinical trials registered in Chinese and US clinical trial registries for the treatment of pneumonia caused by SARS-CoV-2.


title: Network pharmacology studies on the effect of Chai-Ling decoction in coronavirus disease 2019

text: Background: Chai-Ling decoction (CLD), derived from a modification of Xiao-Chai-Hu (XCH) decoction and Wu-Ling-San (WLS) decoction, has been used to treat the early-stage of coronavirus disease 2019 (COVID-19). However, the mechanisms of CLD in COVID-19 remain unknown. In this study, the potential mechanisms of CLD in COVID-19 were preliminarily investigated based on network pharmacology and molecular docking method. Methods: Initially, the active components and targets of CLD were screened based on Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and PharmMapper database. The targets of COVID-19 were obtained from GeneCards database. The protein-protein interaction network was established using STRING database to analyze the key targets. Gene Oncology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes analysis were also conducted to evaluate the pathways related to the targets of CLD on COVID-19. Moreover, the compound-target-pathway network was established using Cytoscape 3.2.7. Subsequently, the molecular docking method was performed to select the active compounds with high binding affinity on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2), which is the key target of SARS-CoV-2 in entering target cells. The possible binding sites were also visualized by a three-dimensional graph. Results: Network pharmacology analysis showed that there were 106 active components and 160 targets of CLD. Additionally, 251 targets related to COVID-19 were identified, and 24 candidates of CLD on COVID-19 were selected. A total of 283 GO terms of CLD on COVID-19 were identified, and 181 pathways were screened based on GO and Kyoto Encyclopedia of Genes and Genomes analyses. CLD might alleviate the inflammatory response and improve lung injury to treat COVID-19 through interleukin 17 signaling, T helper cell 17 differentiation, tumor necrosis factor signaling, and hypoxia inducible factor-1 signaling. Besides, molecular docking indicated that beta-sitosterol, kaempferol, and stigmasterol were the top three candidates in CLD with the highest affinity to SARS-CoV-2 and ACE2. Conclusion: Our study identifies the potential mechanisms of CLD on COVID-19 and beta-sitosterol, kaempferol, and stigmasterol may be the key compounds that exert antiviral effects against SARS-CoV-2.


title: Industry call for covid-19 convalescent plasma collections

text: ABSTRACT Plasma of individuals recovered from COVID-19 is needed to address the immediate demand for treatment of SARS-CoV-2 infected patients in severe conditions This communication: highlights the need for COVID-19 convalescent plasma collections to manufacture hyperimmune immunoglobulin therapies, which take months to develop;advocates for the collection of convalescent plasma from asymptomatic donors who tested positive for SARS-CoV-2 virus but did not develop symptoms of the disease;and suggests to use convalescent plasma for transfusion as well as future hyperimmune immunoglobulins as pre- and post-exposure prophylactic treatments for individuals with high risks of exposure to the virus or contracting severe disease


title: A genome-wide haploid genetic screen for essential factors in vaccinia virus infection identifies TMED10 as regulator of macropinocytosis

text: Vaccinia virus is a promising viral vaccine and gene delivery candidate, and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to Modified Vaccinia Virus Ankara (MVA). Deep-sequencing analysis of virus-resistant cells identified host factors involved in heparan sulfate synthesis, Golgi organization, and vesicular protein trafficking. We validated EXT1, TM9SF2 and TMED10 (TMP21/p23/p24δ) as important host factors for vaccinia virus infection. The critical role of EXT1 in heparan sulfate synthesis and vaccinia virus infection was confirmed. TM9SF2 was validated as a player mediating heparan sulfate expression, explaining its contribution to vaccinia virus infection. In addition, TMED10 was found to be crucial for virus-induced plasma membrane blebbing and phosphatidylserine-induced macropinocytosis, suggesting that TMED10 regulates actin cytoskeleton remodelling necessary for virus infection. Importance Poxviruses are large DNA viruses that can infect a wide range of host species. A number of these viruses are clinically important to humans, including variola virus (smallpox) and vaccinia virus. Since the eradication of smallpox, zoonotic infections with monkeypox virus and cowpox virus are emerging. Additionally, poxviruses can be engineered to specifically target cancer cells, and are used as vaccine vector against tuberculosis, influenza, and coronaviruses. Poxviruses rely on host factors for most stages of their life cycle, including attachment to the cell and entry. These host factors are crucial for virus infectivity and host cell tropism. We used a genome-wide knock-out library of host cells to identify host factors necessary for vaccinia virus infection. We confirm a dominant role for heparin sulfate in mediating virus attachment. Additionally, we show that TMED10, previously not implicated in virus infections, modulates the host cell membrane to facilitate virus uptake.


title: Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

text: Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of cytidine to uridine in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis - for example, A3G deaminates the third cytidine in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy, which we have used to capture an A3G-ssDNA interaction. We characterized an A3G-DNA binding pocket that is important for the enzyme to scan the DNA for its hotspot. The results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.


title: THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY

text: ABSTRACT - Importance: Many COVID-19 prognostic factors for disease severity have been identified and many scores have already been proposed to predict death and other outcomes. However, hospitals in developing countries often cannot measure some of the variables that have been reported as useful. - Objective: To assess the sensitivity, specificity, and predictive values of the novel LOW-HARM score (Lymphopenia, Oxygen saturation, White blood cells, Hypertension, Age, Renal injury, and Myocardial injury). - Design: Demographic and clinical data from patients with known clinical outcomes (death or discharge) was obtained. Patients were grouped according to their outcome. The LOW-HARM score was calculated for each patient and its distribution, potential cut-off values and demographic data were compared. - Setting: Thirteen hospitals in ten different cities in Mexico. - Participants: Data from 438 patients was collected. A total of 400 (200 per group) was included in the analysis. - Exposure: All patients had an infection with SARS-CoV-2 confirmed by PCR. - Main Outcome: The sensitivity, specificity, and predictive values of different cut-offs of the LOW-HARM score to predict death. - Results: Mean scores at admission and their distributions were significantly lower in patients who were discharged compared to those who died during their hospitalization 10 (SD: 17) vs 71 (SD: 27). The overall AUC of the model was 95%. A cut-off > 65 points had a specificity of 98% and a positive predictive value of 96%. More than a third of the cases (34%) in the sample had a LOW-HARM score > 65 points. - Conclusions and relevance: The LOW-HARM score measured at admission is highly specific and useful for predicting mortality. It is easy to calculate and can be updated with individual clinical progression. The proposed cut-off can assist the decision-making process in more than a third of the hospital admissions.


title: Between Geography and Demography: Key Interdependencies and Exit Mechanisms for Covid-19

text: We develop a minimalist compartmental model to analyze policies on mobility restriction in Italy during the Covid-19 outbreak. Our findings show that a early lockdowns barely shift the epidemic in time: moreover, beyond a critical value of the lockdown strength, an epidemic that seems to be quelled fully recovers after lifting the restrictions. We investigate the effects on lockdown scenarios and exit mechanisms by introducing heterogeneities in the model. In particular, we consider Italian regions as separate administrative entities in which social interactions through different age classes occur. We find that, due to the sparsity of the mobility matrix, epidemics developed independently in different regions once the outbreak starts. Moreover, after the epidemics ha started, the influence of contacts with other regions becomes soon irrelevant. Sparsity accounts for the observed delays across different regions. Analogous arguments would apply to the international borders. We also show how disregarding the structure of social contacts could lead to severe underestimation of the post-lockdown effects. Nevertheless, age class based mechanisms can help to mitigate rebound effects with milder strategies. Finally, we point out that our results can be generalized beyond this particular model by providing a description of the effects of key parameters on non-medical mitigation strategies for epidemics.


title: An Assessment of Organizational Culture Traits Impacting Problem Solving for Lean Transformation

text: Abstract An organization’s culture is a significant contributor to its success with Lean transformations and structured problem solving practices are essential to achieving continuous improvement. This research focuses on establishing whether a relationship exists between the organization’s culture and the capability of team members to engage in structured problem solving practices. Six hypotheses were formulated based on potential relationships between steps required for structured problem solving, and critical organizational culture traits that influence an organization’s problem solving capabilities. A survey was administered to gather data as are necessary for evaluating the hypotheses. Results indicate there is a positive correlation between organizational cultural traits and the ability of team members to engage in structured problem solving practices for continuous improvement. For all hypotheses, the survey results permitted their rejection. This study examined the relationship between one organizational culture trait and one (or a few) problem solving step(s). It is, however, likely that multiple culture traits affect multiple problem solving steps and vice versa. Further studies to examine such relationships can be very useful to help ascertain how best to develop an organizational culture (traits) to succeed and sustain lean transformations. Study findings can guide organizations in their journey towards Lean transformation by helping identify organizational culture traits that must be promoted. Promoting the desired culture traits can create an environment where team members can engage in structured problem solving effectively to help continuous improvement for Lean transformations. The empirical examination of potential relationships between an organization’s cultural traits and the ability of team members to engage in continuous improvement through the problem solving for lean transformations is lacking. The work presented in this paper helps address that gap.


title: The Corona Virus and Migration Governance in South Africa: Business As Usual?/ Der Corona-Virus und Migrationspolitik in Südafrika: Weiter wie bisher?

text: The South African response in dealing with the Corona pandemic needs to speak to the realities of all people living in the country, including migrant and refugee communities. Reflecting on this in light of ongoing research on the political stakes of migration governance, we find that the virus response shows little change in the government agenda when it comes to dealing with refugees and other migrants. Veritably, we see that the pandemic may even be an excuse for pushing through already-aspired to policies. This includes the securitised agenda behind the sudden building of a border fence to close off Zimbabwe and the xenophobic-rhetorical clout behind the lockdown rules about which shops are allowed to remain open. The temporary stay on renewing asylum seekers permits counts as a perfunctory exception. We show that each of these developments very much play into politics as usual.


title: Why Do COVID-19 Fatality Rates Differ Across Countries? An Explorative Cross-country Study Based on Select Indicators

text: In this article, we analyse the factors that determine the fatality rates across 29 economies spread across both the developing and developed world. Recent emerging literature and expert opinions in popular media have indicated various factors that may explain cross-country difference in fatality rates. These factors range from access to public health infrastructure, BCG vaccination policies, demographic structure, restrictive policy interventions and the weather. In addition, articles are examining different kinds of fatality rates that can be explained. Progressing beyond fragmented databases and anecdotal evidence, we have developed a database for such factors, have explored various econometric models to test the explanatory power of these factors in explaining several kinds of fatality rates. Based on available data, our study reveals that factors such as public health system, population age structure, poverty level and BCG vaccination are powerful contributory factors in determining fatality rates. Interactions between factors such as poverty level and BCG vaccination provide interesting insights into the complex interplay of factors. Our analysis suggests that poor citizens’ access to the public healthcare system are worse in many countries irrespective of whether they are developed or developing countries.


COVID-19 Sidelines Breast Cancer Screening


title: Heterogeneous contact networks in COVID-19 spreading: the role of social deprivation

text: We have two main aims in this paper. First we use theories of disease spreading on networks to look at the COVID-19 epidemic on the basis of individual contacts -- these give rise to predictions which are often rather different from the homogeneous mixing approaches usually used. Our second aim is to look at the role of social deprivation, again using networks as our basis, in the spread of this epidemic. We choose the city of Kolkata as a case study, but assert that the insights so obtained are applicable to a wide variety of urban environments which are densely populated and where social inequalities are rampant. Our predictions of hotspots are found to be in good agreement with those currently being identfied empirically as containment zones and provide a useful guide for identifying potential areas of concern.


title: Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil

text: Background. We investigated a likely scenario of COVID-19 spreading in Brazil through the complex airport network of the country, for the 90 days after the first national occurrence of the disease. After the confirmation of the first imported cases, the lack of a proper airport entrance control resulted in the infection spreading in a manner directly proportional to the amount of flights reaching each city, following first occurrence of the virus coming from abroad. Methodology. We developed a SIR (Susceptible-Infected-Recovered) model divided in a metapopulation structure, where cities with airports were demes connected by the number of flights. Subsequently, we further explored the role of Manaus airport for a rapid entrance of the pandemic into indigenous territories situated in remote places of the Amazon region. Results. The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to the airport closeness centrality within the Brazilian air transportation network. There was a clear pattern in the expansion of the pandemic, with a stiff exponential expansion of cases for all cities. The more an airport showed closeness centrality, the greater was its vulnerability to SARS-CoV-2. Conclusions. We discussed the weak pandemic control performance of Brazil in comparison with other tropical, developing countries, namely India and Nigeria. Finally, we proposed measures for containing virus spreading taking into consideration the scenario of high poverty.


title: Excess mortality and potential undercounting of COVID-19 deaths by demographic group in Ohio

text: Background: There are significant gaps in our understanding of the mortality effects of COVID-19 due to evolving diagnosis criteria, shortages of testing supplies, and challenges faced by physicians in treating patients in crisis environments. Accurate information on the number of deaths caused by COVID-19, both population wide and for demographic subgroups, is vital for policy makers and health care providers. Methods: We performed a retrospective study of weekly data for Ohio, a large American state. To estimate expected mortality in 2020 we employed data from 2010 through 2019, adjusted for secular trends and seasonality. We estimated excess mortality as the number of observed deaths less the number of expected deaths. We conducted the analysis for the entire population and by gender, race, age, and county of residence. Findings: We estimated 1,485 (95% CI 680-2,345) excess all-cause deaths in Ohio from March 15, 2020 through May 23, 2020. When limited to deaths due to natural causes, the estimated excess number of deaths increased to 2,504 (95% CI 1,633-3,221), reflecting the countervailing effect of a decrease in deaths due to external causes. While the largest number excess of deaths was observed in the 80+ age group, excess deaths comprised 45.3% (95% CI 21.8-60.9) of observed deaths in the groups corresponding to ages between 20 and 49 years old. Our estimate of 729 (95% CI 355-966) excess deaths for this group substantially exceeds the reported number of COVID-19 deaths of 51. We found elevated excess deaths for older individuals, blacks, and males. Interpretation: Our methodology addressed some of the challenges of estimating the number of deaths caused by COVID-19. Our finding of high proportional levels of excess deaths among younger age groups suggests that increases in the infection rates for this cohort may have a greater mortality impact than expected. Funding: None.


title: Effective Heat Inactivation of SARS-CoV-2

text: The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) has quickly turned into a global pandemic. Infectious viruses had been isolated from oro- or naso-pharyngeal swabs, sputum and possibly stool samples of infected individuals. Handling these clinical specimens therefore poses a biosafety risk to both healthcare professionals and laboratory workers. In this study, we aimed to evaluate the stability of SARS-CoV-2 under different heat conditions and report that the virus is stable at 37 C for at least 24 hours. Heating at 56 C for 30 minutes, however, effectively inactivated the virus while preserved the stability of viral RNA in both human sera and sputum samples. These findings provide critical information regarding the biology of the virus as well as a practical way to inactivate infectious virus that is potentially found in clinical specimens.


title: An acceptable method to evaluate the analytical performance of real-time fluorescent RT-PCR targeting SARS-CoV-2

text: It was necessary to carry out methodologies evaluations of real-time fluorescent reverse-transcription PCR (RT-PCR) targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Considering biosafety issues and lack of positive specimens in some special locations in China, the routine specimens from healthy individuals were used to perform methodologies evaluations, in which the indexes were the differences of quantification cycle values ({Delta}Cq) between human derived internal reference control (IRC) genes of a specimen and quality control (QC). Serial experiments were carried out to evaluate various factors that might affect aforementioned methodologies, such as types of virus transport mediums, methods of specimen pretreatment and template preparation, specimen vortex strength, specimen storage temperature and duration. The results showed that using {Delta}Cq values as indexes, among various factors that might affect analytical performance, it was better to store specimens in the normal saline transport mediums, inactivate pathogens using water or metal bath, release more virus particles from swabs by vortex mixing, extract nucleic acids with centrifuge methods, and perform amplification assays timely. Aforementioned opinions and optimum conditions were further confirmed by SRAS-CoV-2 pseudovirus and clinical positive specimens. Altogether, the results of this study indicated that the routine specimens from healthy individuals could be used to evaluate the analytical performance of real-time fluorescent RT-PCR targeting SRAS-CoV-2, of which the indexes were the {Delta}Cq values between IRC genes of a specimen and QC. This acceptable method was extremely valuable in both theoretical and practical significance under current pandemic of coronavirus disease 2019 (COVID-19).


Commentary: Preparation for Pandemics Prevent Pandemonium


title: Modelling SARS-CoV-2 Dynamics: Implications for Therapy

text: The scientific community is focussed on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data collected from the same specimen (throat / nasal swabs or nasopharyngeal / sputum / tracheal aspirate), we compare within-host dynamics for patients infected in the current outbreak with analogous dynamics for MERS-CoV and SARS-CoV infections. Our quantitative analyses revealed that SARS-CoV-2 infection dynamics are more severe than those for mild cases of MERS-CoV, but are similar to severe cases, and that the viral dynamics of SARS-CoV infection are similar to those of MERS-CoV in mild cases but not in severe case. Consequently, SARS-CoV-2 generates infection dynamics that are more severe than SARS-CoV. Furthermore, we used our viral dynamics model to predict the effectiveness of unlicensed drugs that have different methods of action. The effectiveness was measured by AUC of viral load. Our results indicated that therapies that block de novo infections or virus production are most likely to be effective if initiated before the peak viral load (which occurs around three days after symptom onset on average), but therapies that promote cytotoxicity are likely to have only limited effects. Our unique mathematical approach provides insights into the pathogenesis of SARS-CoV-2 in humans, which are useful for development of antiviral therapies.


title: Fight against coronavirus disease 2019: epidemic prevention and infection control in Naval medical team camps

text: Since December 2019, many cases of pneumonia of unknown causes have been found in Wuhan and surrounding areas of Hubei Province, China With the aggravation of the epidemic, on January 24, 2020, medical team of Naval Medical University (Second Military Medical University) in Wuhan started emergency medical rescue This medical rescue was not only a treatment war, but also an antiepidemic war It is very important to have strict personal protection, disinfection and isolation measures and epidemic prevention in the camp, which are the precondition and guarantee to ensure zero infection of medical staff In this paper, we introduce our measures and experience on epidemic prevention and infection control, such as personnel management and decontamination


title: Effectiveness of COCOA, a COVID-19 contact notification application, in Japan

text: Background: COCOA, a contact reporting application in Japan, was launched at the end of June 2020. Object: We assessed effectiveness of COCOA. Method: After developing a simple susceptible-infected-recovery model with COCOA and voluntary restrictions against going out (VRG), we assumed that COCOA can reduce infectiousness by 10-50% points through self-quarantine at home after receiving notification from COCOA. Results: COCOA alone is insufficient to halt an outbreak. Even if the entire population were to use COCOA, the reproduction number would be 1.31. However, if VRG were 15%, about half of the maximum VRG effectiveness under the emergency state declaration, then 10% COCOA use by a population can reduce the reproduction number to less than one. Conclusion: Significant effects of COCOA for reducing the reproduction number were found. However, without VRG, COCOA alone is insufficient to control an outbreak.


title: Why Ignore the Dark Side of Social Media? A Role of Social Media in Spreading Corona-Phobia and Psychological Well-Being

text: Coronaviruses are a category of associated viruses that trigger disease in mammals and birds Human coronaviruses have been identified including severe acute respiratory syndrome-related coronavirus (SARS-CoV) in 2003, human coronavirus NL63 (HCoV NL63) in 2004, human coronavirus HKU1 (HKU1) in 2005, Middle East respiratory syndrome-related coronavirus (MERS-CoV) in 2012, and severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) in December, 2019 This study aims to examine whether social media at residing/admittance in quarantine ward (due to corona virus pandemic disease) affects psychological health or not? We asked questions from 250 quarantined patients infected from coronavirus (restricted to quarantine ward) about their psychological health who have accessed of different channels of social media This study concludes that social media has caused of various psychological symptoms in quarantined patients (due to coronavirus) in form of anxiety, depression, negative well-being, lack of self-control, general health and vitality This study suggests that there is an urgency to provide awareness/right information to each infected individual and their family members to create peaceful society and social rest Thus, productive use of social media is recommended while minimizing its negative impact


title: Clinical features and outcomes of 221 patients with COVID-19 in Wuhan, China

text: Rationale: In late December 2019, an outbreak of acute respiratory illness, now officially named as COVID-19, or coronavirus disease 2019, emerged in Wuhan, China, now spreading across the whole country and world. More data were needed to understand the clinical characteristics of the disease. Objectives: To study the epidemiology, clinical features and outcomes of patients with COVID-19. Methods: we performed a single center, retrospective case series study in 221 patients with laboratory confirmed SARS-CoV-2 pneumonia at a university hospital. Measurements and Main Results: The median age was 55.0 years and 48.9% were male and only 8 (3.6%) patients had a history of exposure to the Huanan Seafood Market. Compared to the non-severe pneumonia patients, the median age of the severe patients was significantly older, and they were more likely to have chronic comorbidities. Most common symptoms in severe patients were high fever, anorexia and dyspnea. On admission, 33.0% patients showed leukopenia and 73.8% showed lymphopenia. In addition, the severe patients suffered a higher rate of co-infections with bacteria or fungus and they were more likely to developing complications. As of February 15, 2020, 19.0% patients had been discharged and 5.4% patients died. 80% of severe cases received ICU care, and 52.3% of them transferred to the general wards due to relieved symptoms, and the mortality rate of severe patients in ICU was 20.5%. Conclusions: The COVID-19 epidemic spreads rapidly by human-to-human transmission. Patients with elder age, chronic comorbidities, blood leukocyte/lymphocyte count, procalcitonin level, co-infection and severe complications might increase the risk of poor clinical outcomes. Keywords: coronavirus disease 2019; clinical features; outcomes; severe patients


title: Evolution of the COVID Pandemic: A Technique for Mathematical Analysis of Data

text: The analysis of COVID-19 statistics in different regions of the world with the intention of understanding the trend of progression of the pandemic is a task of paramount importance. Publicly available data includes cumulative number of cases, new cases each day, and the mortality. Extracting information from this data necessitates mathematical modeling. In this note a simple technique is adopted to determine the trend towards stabilized elimination of the infection. Results pertaining to several representative regions of the world are presented.


title: Estimating the Case Fatality Risk of COVID-19 using Cases from Outside China

text: There is large uncertainty around the case fatality risk (CFR) for COVID-19 in China. Therefore, we considered symptomatic cases outside of China (countries/settings with 20+ cases) and the proportion who are in intensive care units (4.0%, 14/349 on 13 February 2020). Given what is known about CFRs for ICU patients with severe respiratory conditions from a meta-analysis, we estimated a CFR of 1.37% (95%CI: 0.57% to 3.22%) for COVID-19 cases outside of China.


title: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

text: Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.


title: What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?

text: A recent work (DOI 10.1101/2020.05.06.20093310) indicated that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterwards, on May 15, 2020, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper we investigate the time dynamics of coronavirus cases in Slovenia with emphasis on how efficient various containment measures act to diminish the number of COVID-19 infections. Noteworthily, the present analysis does not rely on any speculative theoretical assumption; it is solely based on raw epidemiological data. Out of the results presented here, the most important one is perhaps the finding that, while imposing drastic curfews and travel restrictions reduce the infection rate kappa by a factor of four with respect to the unrestricted state, they only improve the kappa-value by ~15 % as compared to the much bearable state of social and economical life wherein (justifiable) wearing face masks and social distancing rules are enforced/followed. Significantly for behavioral and social science, our analysis of the time dependence kappa = kappa(t) may reveal an interesting self-protection instinct of the population, which became manifest even before the official lockdown enforcement.


title: SUPERSPREADING AS A REGULAR FACTOR OF THE COVID-19 PANDEMIC

text: An impact of superspreading on the course of the COVID-19 epidemic is considered. A two-component model of the epidemic has been developed, in which all infected are divided in two groups. They are asymptomatic superspreaders spreading the infection and sensitive persons which can only get infection. Once infected the sensitive exhibit clear symptoms and become isolated. Taking into account both factors allows find the numbers of superspreaders and sensitive persons. It is shown, that the ratio of increment of the number of daily cases in the beginning of the epidemic and decrement at the end of the epidemic is equal to the ratio of numbers of the superspreaders and sensitive persons. In this way, on the base of data from 12 countries and territories, the share of asymptomatic among all infected persons is found to be (17 {+/-} 3)%. Specific measures to limit the epidemical incidence are proposed. The possibility of an allergic component in the disease is discussed.


title: LONG-TERM CLINICAL OUTCOMES IN SURVIVORS OF CORONAVIRUS OUTBREAKS AFTER HOSPITALISATION OR ICU ADMISSION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF FOLLOW-UP STUDIES

text: Objective: To determine the long-term clinical problems in adult survivors of coronavirus (CoV) infection [Coronavirus disease 2019 (COVID-19), Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS)] after hospitalisation or Intensive Care Unit (ICU) admission. Design: Systematic review and meta-analysis of the literature. Data sources: Ovid MEDLINE, EMBASE, CINAHL Plus and PsycINFO were searched using the strategy: (Coronavirus OR Coronavirus Infections OR COVID OR SARS virus OR Severe acute respiratory syndrome OR MERS OR Middle east respiratory syndrome) AND (Follow-up OR Follow-up studies OR Prevalence). Original studies reporting the clinical outcomes of adult survivors of coronavirus outbreaks two months after discharge or three months after admission were included. The quality of the studies was assessed using the Oxford Centre for Evidence-Based Medicine (OCEBM) 2009 Level of Evidence Tool. Meta-analysis was conducted to derive pooled estimates of prevalence and severity for different outcomes at time points up to 6 months follow-up and beyond 6 months follow-up. Results: The search yielded 1169 studies of which 28 were included in this review. There were 15 Level 1b, 8 Level 2b, 2 Level 3b and 3 Level 4 studies by OCEBM grading. Pooled analysis of studies revealed that complications commonly observed were impaired diffusing capacity for carbon monoxide (DLCO) [prevalence of 27.26%, 95% CI 14.87 to 44.57] and reduced exercise capacity [(6-minute walking distance (6MWD) mean 461m, 95% CI 449.66 to 472.71] at 6 months with limited improvement beyond 6 months. Coronavirus survivors had considerable prevalence of psychological disorders such as post-traumatic stress disorder (PTSD) [38.80%, CI 30.93 to 47.31], depression [33.20%, CI 19.80 to 50.02] and anxiety [30.04%, CI 10.44 to 61.26) beyond 6 months. These complications were accompanied by low Short Form 36 (SF-36) scores at 6 months and beyond indicating reduced quality of life which is present long-term. Conclusions: The long term clinical problems in survivors of CoV infections (SARS and MERS) after hospitalisation or Intensive Care Unit (ICU) admission include respiratory dysfunction, reduced exercise capacity, psychological problems such as PTSD, depression and anxiety, and reduced quality of life. Critical care, rehabilitation and mental health services should anticipate a high prevalence of these problems following COVID-19 and ensure their adequate and timely management with the aim of restoring premorbid quality of life.


title: Triplex Real Time RT-PCR for N1, N2 and RP probes from CDC EUA SARS-CoV-2 diagnosis kit.

text: CDC protocol for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include 3 targets for detection (N1, N2 and RP) labelled with FAM so 3 PCR reactions are required per sample. We developed a triplex, real-time reverse transcription PCR for SARS-CoV-2 that maintained clinical performance compared with CDC singleplex assay. This protocol could speed up detection and save reagents during current SARS-CoV-2 testing supplies shortage.


Covid-19


title: ON THE UNCERTAINTY ABOUT HERD IMMUNITY LEVELS REQUIRED TO STOP COVID-19 EPIDEMICS

text: COVID-19 evolved into a pandemic in 2020 affecting more than 150 countries. Given the absence of a vaccine, discussion has taken place on the strategy of allowing the virus to spread in a population, to increase population "herd immunity". Knowledge of the minimum proportion of a population required to have recovered from COVID-19 infection in order to attain "herd" immunity, P(crit), is important for formulating epidemiological policy. A method for measuring uncertainty about P(crit) based on a widely used package, EpiEstim, is derived. The procedure is illustrated using data from twelve countries at two early times during the COVID-19 epidemic. It is shown that simple plug-in measures of confidence on estimates of P(crit) are misleading, but that a full characterization of statistical uncertainty can be derived from EpiEstim, which reports percentiles only. Because of the important levels of uncertainty, it is risky to design epidemiological policy based on guidance provided by a single point estimate.


title: Blood glucose is a representative of the clustered indicators of multi-organ injury for predicting mortality of COVID-19 in Wuhan, China

text: OBJECTIVE Most patients with Coronavirus Disease 2019 (COVID-19) were Mild or Moderate. Severe patients progressed rapidly to Critical condition including multi-organ failure and even death. Identification of early predictive factors is urgently necessary to facilitate appropriate intensive care. METHODS We included all patient admitted to Wuhan Union Hospital and treated by the supportive medical team of Beijing Tongren Hospital as of March 20, 2020. Indicators of injuries for multiple organs, including the heart, kidney and liver, and glucose homeostasis were specifically analyzed for predicting primary outcomes (an intensive care unit (ICU) or death). RESULTS The data of 120 patients with a severity equal to or greater than Moderate, discharged or died were extracted. After excluding patients with history of diabetes, chronic heart, kidney, and liver disease, 69 patients were included in the final analysis. There were 26 cases with primary outcomes including 16 deaths. Univariable analysis indicated that fasting blood glucose (FBG), lactate dehydrogenase (LDH), hydroxybutyrate dehydrogenase (HBDH), creatine kinase and creatinine were associated with primary outcomes and death. Among patients with primary outcomes, although FBG levels were much higher on admission, they dramatically decreased subsequently, while in deceased patients they increased continuously. Multivariable Cox regression indicated that FBG≥7mmol/L was the only independent predictor for death (HR = 3.75, 95% CI 1.26-11.15). Cluster analysis found more proximities of FBG (at the time of admission) with LDH, HDDH or Creatinine (after 2-4 days of hospitalization) (r=0.43, 0.43 and 0.50, respectively, P<0.01 for all). Conclusions Blood glucose is a representative of the clustered indicators of multi-organ injury and earlier predictor for poor outcomes and death in the COVID patients. As it is easy to perform for clinical practices and self-monitoring, glucose testing will be much helpful for predicting poor outcomes to facilitate appropriate intensive care.


title: Estimating the Global Infection Fatality Rate of COVID-19

text: COVID-19 has become a global pandemic, resulting in nearly three hundred thousand deaths distributed heterogeneously across countries. Estimating the infection fatality rate (IFR) has been elusive due to the presence of asymptomatic or mildly symptomatic infections and lack of testing capacity. We analyze global data to derive the IFR of COVID-19. Estimates of COVID-19 IFR in each country or locality differ due to variable sampling regimes, demographics, and healthcare resources. We present a novel statistical approach based on sampling effort and the reported case fatality rate of each country. The asymptote of this function gives the global IFR. Applying this asymptotic estimator to cumulative COVID-19 data from 139 countries reveals a global IFR of 1.04% (CI: 0.77%,1.38%). Deviation of countries' reported CFR from the estimator does not correlate with demography or per capita GDP, suggesting variation is due to differing testing regimes or reporting guidelines by country. Estimates of IFR through seroprevalence studies and point estimates from case studies or sub-sampled populations are limited by sample coverage and cannot inform a global IFR, as mortality is known to vary dramatically by age and treatment availability. Our estimated IFR aligns with many previous estimates and is the first attempt at a global estimate of COVID-19 IFR.


title: Striking a balance between science and politics: understanding the risk-based policy-making process during the outbreak of COVID-19 epidemic in China

text: The outbreak of the COVID-19 epidemic in China is, essentially, a public health emergency. Therefore, it becomes a critical issue to make policies by using scientific knowledge in a highly uncertain and unpredictable context. The key issue of risk-based decision-making (RBDM) is how to strike a balance between science and politics. After reviewing existing literature and practice, three main approaches to risk-based decision-making (RBDM) can be summarized: politics-based, science-led, and the integration and negotiation of science and politics. On the basis of public reports from current mass media, this article focuses on the time period from the releasing of the first COVID-19 case in Wuhan to the lockdown policy made by Wuhan municipal government, and we divide important stakeholders in early stage into two groups：scientist group and politician group. It finds that the RBDM process of Wuhan municipal government against COVID-19 demonstrated that politics intertwined tightly with science. Its RBDM process could be categorized into three phases: politics-based, science-involved, and science-led. We conclude six main characteristics of RBDM mechanisms in contemporary China. Finally, we argue that Chinese governments should establish institutionalized mechanisms for the negotiation and cooperation of science and politics in its RBDM process like COVID-19 epidemic. Five policy recommendations have been discussed to improve its RBDM quality in China’s context.


title: Mathematical modeling of COVID-19 containment strategies with considerations for limited medical resources

text: The outbreak of SARS-CoV-2 in China has spread around the world, infecting millions and causing governments to implement strict policies to counteract the spread of the disease. One of the most effective strategies in reducing the severity of the pandemic is social distancing, where members of the population systematically reduce their interactions with others to limit the transmission rate of the virus. However, the implementation of social distancing can be difficult and costly, making it imperative that both policy makers and the citizenry understand the potential benefits if done correctly and the risks if not. In this work, a mathematical model is developed to study the effects of social distancing on the spread of the SARS-CoV-2 virus in Canada. The model is based upon a standard epidemiological SEIRD model that has been stratified to directly incorporate the proportion of individuals who are following social distancing protocols. The model parameters characterizing the disease are estimated from current epidemiological data on COVID-19 using machine learning techniques. The results of the model show that social distancing policies in Canada have already saved thousands of lives and that the prolonged adherence to social distancing guidelines could save thousands more. Importantly, our model indicates that social distancing can significantly delay the onset of infection peaks, allowing more time for the production of a vaccine or additional medical resources. Furthermore, our results stress the importance of easing social distancing restrictions gradually, rather than all at once, in order to prevent a second wave of infections. Model results are compared to the current capacity of the Canadian healthcare system by examining the current and future number of ventilators available for use, emphasizing the need for the increased production of additional medical resources.


title: Comparison of the coronavirus pandemic dynamics in Europe, USA and South Korea

text: The pandemic cased by coronavirus COVID-19 is of great concern. A detailed scientific analysis of this phenomenon is still to come, but now it is urgently needed to evaluate the disease dynamics in order to organize the appropriate quarantine activities, to estimate the required number of places in hospitals, the level of individual protection, the rate of isolation of infected persons, etc. South Korea has achieved the stabilization of the number of cases at rather low level. The epidemic dynamics there can be compared with its development in other countries to make some preliminary, but very important conclusions. Here we provide a simple method of data comparison that can be useful for both governmental organizations and anyone.


title: Establishment and Application of an Indirect ELISA Based on Recombinant S1 Protein for the Detection of Antibodies against Porcine Deltacoronavirus

text: This study was conducted to understand porcine deltacoronavirus (PDCoV) epidemic situation, and provide a tool for PDCoV serum antibody detection and the epidemiological investigation. Prokaryotic expression of recombinant PDCoV partial spike (S) protein was used as detection antigen, and an indirect ELISA antibody detection method based on PDCoV S1 protein was established. The method was used to detect 570 serum samples collected from some pig farms in Hebei from January to December 2017. The results showed that the established ELISA method of PDCoV IgG antibody in this study could specifically detect PDCoV antibody; no cross-reaction with antisera against porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), classical swine fever (CSF) and pseudorabies virus (PRV) was found. The coefficients of variation (CV) of repeated in-batch test was 1.9%-5.4%, CV of batch-to-batch test was 2.3%-5.1%. In 570 blood samples, 105 were positive, and the positive rate was 18.4% (105/570), which was higher than the positive rate of PDCoV IgG antibody (11%) in Hebei from January 2016 to October 2016. It is suggested that the infection rate of PDCoV in Hebei is on the rise. The ELISA method established in this study had the advantages of high sensitivity, strong specificity and good reproducibility, and can be used for the detection of clinical PDCoV serum antibodies.Copyright © 2019, Chinese Journal of Animal Science and Veterinary Medicine Co., Ltd. All right reserved.


title: Effects of misleading media coverage on public health crisis: a case of the 2019 novel coronavirus outbreak in China

text: The coronavirus outbreak in Wuhan, China has sparked a global epidemic, which the World Health Organization declared a public health emergency of international concern on 31st January 2020 (Beijing time). This crisis has attracted intense media attention. Recently, some media outlets inappropriately labelled the coronavirus by race, using such headlines as “Chinese virus pandemonium” and even suggesting “China kids stay home.” The biased and misleading coverage presented via Western media channels has incited anger throughout the Chinese community and has placed undue stress upon Chinese individuals living outside China. This post-published review takes a tourism-focused perspective to examine findings from a quantitative study (Rodriguez-Seijas, Stohl, Hasin, & Eaton, 2015) published in 2015 in JAMA Psychiatry. The current paper highlights the potential impacts of misleading and biased media coverage on Chinese individuals’ mental health. Specifically, this work considers perceived racial discrimination stemming from coronavirus as a public health crisis and the effects of such discrimination on individuals of Chinese heritage. Similarly imperative are pertinent effects on country image and destination image with respect to tourism marketing and tourist behaviour during times of crisis. By considering racism in the context of the coronavirus outbreak, this paper identifies potential avenues for relevant research in tourism and hospitality.


title: History of coronary heart disease increases the mortality rate of COVID-19 patients: a nested case-control study

text: Background: China has experienced an outbreak of a novel human coronavirus (SARS-CoV-2) since December 2019, which quickly became a worldwide pandemic in early 2020. There is limited evidence on the mortality risk effect of pre-existing comorbidities for coronavirus disease 2019 (COVID-19), which has important implications for early treatment. Objective: Evaluate the risk of pre-existing comorbidities on COVID-19 mortality, and provide clinical suggestions accordingly. Method: This study used a nested case-control design. A total of 94 publicly reported deaths in locations outside of Hubei Province, China, between December 18th, 2019 and March 8th, 2020 were included as cases. Each case was matched with up to three controls, based on gender and age (94 cases and 181 controls). The inverse-probability-weighted Cox proportional hazard model was performed. Results: History of comorbidities significantly increased the death risk of COVID-19: one additional pre-existing comorbidity led to an estimated 40% higher risk of death (p<0.001). The estimated mortality risk in patients with CHD was three times of those without CHD (p<0.001). The estimated 30-day survival probability for a profile patient with pre-existing CHD (65-year-old female with no other comorbidities) was 0.53 (95% CI [0.34-0.82]), while it was 0.85 (95% CI [0.79-0.91]) for those without CHD. Older age was also associated with increased death risk: every 5-year increase in age was associated with a 20% increased risk of mortality (p<0.001). Conclusion: Extra care and early medical intervention are needed for patients with pre-existing comorbidities, especially CHD.


title: Understanding the current status of patients with pulmonary hypertension during COVID-19 outbreak: a small-scale national survey from China

text: Pulmonary hypertension is a chronic disease developing progressively with high mortality. Pulmonary hypertension patients need persistent medical care; however, limited reports focused on them when there was an outbreak of coronavirus disease 2019 in China. This national survey was aimed to evaluate the overall condition of pulmonary hypertension patients during this period. A questionnaire regarding the living condition of pulmonary hypertension patients during coronavirus disease 2019 was designed by pulmonary hypertension diagnostic experts in Wuhan Asia Heart Hospital. Pulmonary hypertension patients and their family members were invited to participate in this survey online. One-hundred twenty pulmonary hypertension patients and 23 family members participated in the survey; 64.8% (n = 87) participants came from Hubei, and others were from 15 other provinces; 98.6% (n = 141) participants were in home quarantine; 65.8% (n = 79) were pulmonary arterial hypertension associated with congenital heart disease; and 76.7% (n = 92) patients proclaimed their heart function was well maintained at class I or II. One (0.8%) patient was confirmed severe acute respiratory syndrome coronavirus 2 infection. Two (1.7%) patients were hospitalized due to heart function worsening. Nearly 70% (n = 100) participants implied shortage in medications during coronavirus disease 2019 outbreak. A total of 24.2% (n = 29) patients indicated that medications were discontinued due to the insufficient supply. Most of the participants stayed optimistic on either coronavirus disease 2019 outbreak or their pulmonary hypertension disease, and 61.7% (n = 74) patients would go to the hospital for follow-up immediately after outbreak. These preliminary data show pulmonary hypertension patients are able to avoid severe disease when they are in home quarantine. Medication supplement is important for pulmonary hypertension patients when their heart function is well maintained. In addition, there might be increasing requirements of medical care for pulmonary hypertension patients after the outbreak.


title: Impact assessment of accreditation in primary and secondary public Healthcare Institutions in the State of Kerala, India

text: Objectives This study examines the impact of accreditation on the quality of public healthcare delivery in primary and secondary healthcare facilities in Kerala, India. Study Design A cross-sectional study. Setting Kerala State, India Participants Participants are the in-patients (621) who are admitted in medical wards at accredited (312) and non-accredited (309) public healthcare facilities. Main Outcome Measures Ten constructs used in the study, overarching the quality healthcare delivery, adapting previous studies, SERVQUAL, and Donabedian's SPO models, are Physical Facility, Admission Services, Patient centeredness, Accessibility of Medical Care, Financial Factors, Professionalism, Staff Services, Medical Quality, Diagnostic Services, and Patient Satisfaction. Methods The study employed a positivist approach using a survey questionnaire. The study was conducted from July 2017 to July 2018, using stratified random sampling consists of the four strata; GHs, W&C hospitals, THQHs/THs, and CHCs. Results Accreditation has a positive impact on patient satisfaction and other quality dimensions, overarching structural and procedural quality in primary healthcare facilities under the public sector in Kerala. Conversely, accreditation has not improved the quality dimensions in secondary healthcare facilities and, thereby, the satisfaction of patients. Conclusions It cannot be assumed that accreditation is always associated with quality care in primary healthcare facilities. The implementation process must be systematic and must be regularly monitored to make it useful. Mere structural transformation through accreditation alone cannot guarantee patient satisfaction. Secondary healthcare facilities must be transformed into quality care centers through rhetoric action of the authorities concerned through organized efforts.


title: Early dynamics of transmission and control of COVID-19: a mathematical modelling study

text: Background: An outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. Methods: We combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. Findings: We estimated that the median daily reproduction number, Rt , declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. Interpretation: Our results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.


Extremists use virus to curb opposition: Covid-19 is being used by religious militia as a recruitment tool in Yemen and Iraq. Speaking out as a secular voice is even more challenging


title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in protein translation

text: TARGET OF RAPAMYCIN (TOR) is a deeply conserved protein kinase that coordinates eukaryotic metabolism with nutrient availability. In mammals, TOR specifically promotes translation of ribosomal protein mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. Here, we took parallel global profiling approaches to define the in planta TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on the canonical 5′ oligopyrimidine tract motif (5′TOP) found in mammalian ribosomal protein mRNAs. To investigate this further, we focused on a putative TOR substrate identified in our phosphoproteome: LARP1, a eukaryotic RNA-binding protein that is proposed to mediate TOR translational control of 5′TOP mRNAs in humans and that has gained increased interest because it associates with SARS-CoV-2. By conducting parallel global profiling experiments with larp1 mutants, we discovered that the TOR-LARP1 signaling axis controls 5′TOP mRNA translation in plants and defined a set of conserved eukaryotic 5′TOP mRNAs that encode cyclins, importins/karyopherins, translation elongation factors, and TCTP1, among others. We then identified novel, plant-specific 5′TOP mRNAs involved in critical biological processes, including ribosome biogenesis, chromatin remodeling, and auxin signaling. Our study illuminates the ancestral roles of the TOR-LARP1-5′TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1 in eukaryotic cells.


title: Veno‐venous extracorporeal membrane oxygenation for severe pneumonia: COVID‐19 case in Japan

text: BACKGROUND: Veno‐venous extracorporeal membrane oxygenation (VV‐ECMO) is one of the ultimate treatments for acute respiratory failure. However, the effectiveness of ECMO in patients with novel coronavirus disease (COVID‐19) is unknown. CASE PRESENTATION: A 72‐year‐old woman who was a passenger of a cruise ship tested positive for the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) while in quarantine on board using throat swab. Three days after admission, her condition deteriorated, and she was subsequently intubated. On day 6, VV‐ECMO was introduced. Lopinavir/ritonavir was given; continuous renal replacement therapy was also introduced. On day 10, her chest radiography and lung compliance improved. She was weaned off ECMO on day 12. CONCLUSION: Treatment of severe pneumonia in COVID‐19 by ECMO should recognize lung plasticity considering time to ECMO introduction and interstitial biomarkers. In Japan, centralization of ECMO patients has not been sufficient. Thus, we suggest nationwide centralization and further research to respond to the crisis caused by COVID‐19.


title: A Primer on Biodefense Data Science for Pandemic Preparedness

text: The coronavirus outbreak is sweeping the globe with outbreaks reported on every continent except Antarctica as of March 2020. Data scientists are uniquely and diversely skilled in ways that can be highly effective in minimizing, combatting, and recovering from the impacts of the COVID-19 outbreak. In this Opinion, the basics of biodefense as well as specific opportunities for the data science community to contribute are discussed.


title: Strong Effects of Population Density and Social Characteristics on Distribution of COVID-19 Infections in the United States

text: Coronavirus disease 2019 (Covid-19) has devastated global populations and has had a large impact in the United States with the number of infections and deaths growing exponentially. Using a smooth generalized additive model with quasipoisson counts for total infections and deaths, we developed a county-level predictive model that included population demographics, social characteristics, social distancing, and testing data. This model strongly predicted the actual US distribution of Covid-19, accounting for 94.8% of spatial-temporal variation in total infections and 99.3% in Covid-19 related fatalities from March 15, 2020. US counties with higher population density, poverty index, civilian population, and minorities, especially African Americans had a higher number of confirmed infections adjusted for county population. Social distancing measured by the change in the rate of human encounter per km2 relative to pre-covid-19 national average was associated with slower rate of Covid-19 infections, whereas higher testing was associated with higher number of infections. The number of people infected was increasing, however, the rate of increase in new infections was starting to show signs of plateauing starting from the second week of April. Our model projects 2.11 million people to test positive for Covid-19 and 122,951 fatalities by June 1, 2020. Importantly, our model suggests strong social differences in the infections and deaths across US communities, and inequities in areas with larger African American minorities and higher poverty index expected to show higher rates of Covid-19 infections and deaths. Preventive steps including social distancing and community closures have been a cornerstone in stopping the transmission and potentially reducing the spread of the disease. Crucial knowledge of the role of social characteristics in the disease transmission is essential to understand current disease distribution, predict future distribution, and plan additional preventive steps.