title: Analysis of the time evolution of SARS-CoV-2 lethality rate in Italy: Evidence of an unaltered virus potency

text: In recent months, the entire world is facing a dramatic health emergency caused by the diffusion of a hitherto unknown coronavirus (SARS-CoV-2). Despite the efforts, the understanding of the many facets of the pandemic is still rather limited. In the present manuscript, we have monitored the evolution of the lethality rate in Italy by using the data collected over the last three months. Our data indicate that there is a striking correlation between the number of infected people of a certain week and the deaths of the following one. Despite the overall simplicity of the applied approach and its many approximations, the analysis of the Italian scenario provides some interesting insights into the pandemic. Indeed, we have found that the lethality rate is virtually unchanged over the last two months. This implies that the reduction of the deaths is strictly connected to the decrease of cases. Unfortunately, the present study does not support the idea that the virus potency has lowered in the last weeks, as our data demonstrate that the likelihood of a fatal outcome after the infection has not decreased in the recent outbreak evolution. Moreover, we show that the lethality rate is still very high in the country ({approx}13.5%). Since this number is remarkably higher if compared to the actual lethality estimates made worldwide, this finding suggests that the number of detected cases may be a gross underestimation of the actual infected people, likely due to the presence of a significant number of non-symptomatic or paucisymptomatic individuals in the population.


title: Temporal evolution of COVID-19 in the states of India using SIQR Model

text: COVID 19 entered during the last week of April 2020 in India has caused 3,546 deaths with 1,13,321 number of reported cases. Indian government has taken many proactive steps, including strict lockdown of the entire nation for more than 50 days, identification of hotspots, app-based tracking of citizens to track infected. This paper investigated the evolution of COVID 19 in five states of India (Maharashtra, UP, Gujrat, Tamil Nadu, and Delhi) from 1st April 2020 to 20th May 2020. Variation of doubling rate and reproduction number (from SIQR) with time is used to analyse the performance of the majorly affected Indian states. It has been determined that Uttar Pradesh is one of the best performers among five states with the doubling rate crossing 18 days as of 20th May. Tamil Nadu has witnessed the second wave of infections during the second week of May. Maharashtra is continuously improving at a steady rate with its doubling rate reaching to 12.67 days. Also these two states are performing below the national average in terms of infection doubling rate. Gujrat and Delhi have reported the doubling rate of 16.42 days and 15.49 days respectively. Comparison of these states has also been performed based on time-dependent reproduction number. Recovery rate of India has reached to 40 % as the day paper is written


title: Risk assessment via layered mobile contact tracing for epidemiological intervention

text: There is strong interest globally amidst the current COVID-19 pandemic in tracing contacts of infectious patients using mobile technologies, both as a warning system to individuals and as a targeted intervention strategy for governments. Several governments, including India, have introduced mobile apps for this purpose, which give a warning when the individual's phone establishes bluetooth contact with the phone of an infected person. We present a methodology to probabilistically evaluate risk of infection given the network of contacts that individuals are likely to encounter in real life. Instead of binary "infected" or "uninfected" statuses, an infection risk probability is maintained which can be efficiently calculated based on probabilities of recent contacts, and updated when a recent contact is diagnosed with a disease. We demonstrate on realistic networks that this method sharply outperforms a naive immediate-contact method even in an ideal circumstance that all infected persons are known to the naive method. We demonstrate robustness to missing contact information (such as when phones fail to make bluetooth contact or the app is not installed). We show, within our model, a strong flattening of the infectious peak when even a small fraction of cases are identified, tested and isolated. In the real world, where most known-infected persons are isolated or quarantined and where many individuals may not carry their mobiles in public, we believe the improvement offered by our method warrants consideration. Importantly, in view of widespread concerns on privacy and contact-tracing, our method relies mainly on direct contact data that can be stored locally on users' phones, and uses limited communication via intermediary servers only upon testing, mitigating privacy concerns.


docid: mqgzpjea

title: Effectiveness of Tocilizumab in a COVID-19 Patient with Cytokine Release Syndrome

text: Cytokine release syndrome (CRS) is a systemic inflammatory response that can be triggered by many factors such as infections. CRS in patients with coronavirus disease 2019 (COVID-19) is life-threatening and can occur very rapidly after COVID-19 diagnosis. Tocilizumab (TCZ), an interleukin-6 (IL-6) inhibitor, may ameliorate the CRS associated with severe COVID-19 and thus improve clinical outcomes. We present a case of life-threatening CRS caused by COVID-19 infection successfully treated with TCZ. LEARNING POINTS: Cytokine release syndrome (CRS) is a systemic inflammatory response that can be triggered by COVID-19. CRS can be life-threatening in severe COVID-19. Tocilizumab may have a role in treating severe COVID-19 patients with CRS.


title: The Political Economy of the SARS Epidemic: The Impact on Human Resources in East Asia, Grace O.M. Lee, Malcolm Warner, Routledge London and New York, 2008, xxii+168 pp. $19.95, ISBN: 0-415-39498-8.

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title: CoroNet: A Deep Network Architecture for Semi-Supervised Task-Based Identification of COVID-19 from Chest X-ray Images

text: In late 2019, a new Coronavirus disease, referred to as Corona virus disease 2019 (COVID-19), emerged in Wuhan city, Hubei, China, and resulted in a global pandemic---claiming a large number of lives and affecting billions all around the world. The current global standard used in diagnosis of COVID-19 in suspected cases is the real-time polymerase chain reaction (RT-PCR) test. Although the RT-PCR remains the standard reference for diagnosis purposes, it is a time-consuming and expensive test, and moreover, it usually suffers from high rates of false-negatives. Several early works have reported that the sensitivity of the chest Computed Tomography (CT) and the chest X-ray imaging are noticeably greater than that of the RT-PCR test at the initial representations of the disease, making them great candidates for developing new and sophisticated methodologies for analysis and classification of COVID-19 cases. In this paper, we establish the use of a rapid, non-invasive and cost-effective X-ray-based method as a key diagnosis and screening tool for COVID-19 at early and intermediate stages of the disease. To this end, we develop a novel and sophisticated deep learning-based signal and image processing technique as well as classification methodology for analyzing X-ray images specific to COVID-19 disease. Specifically, we consider a semi-supervised learning methodology based on AutoEncoders to first extract the infected legions in chest X-ray manifestation of COVID-19 and other Pneumonia-like diseases (as well as healthy cases). Then, we utilize this highly-tailored deep architecture to extract the relevant features specific to each class (i.e., healthy, non-COVID pneumonia, and COVID-19) and train a powerful yet efficient classifier to perform the task of automatic diagnosis. Furthermore, the semi-supervised nature of the proposed framework enables us to efficiently exploit the limited available dataset on COVID-19 while exploiting the vast amount of available X-ray dataset for healthy and non-COVID classes. Moreover, such a semi-supervised approach does not require an expert-annotated lesion area for each class. Our numerical investigations demonstrate that the proposed framework outperforms the state-of-the-art methods for COVID-19 identification while employing approximately ten times fewer training parameters as compared to other existing methodologies for classification of the COVID-19 from X-ray images (facilitating efficient training in a limited data regime). We further develop explainable artificial intelligence tools that can explain the diagnosis by using attribution maps while providing an indispensable tool for the radiologist in triage state. We have made the codes of our proposed framework publicly available to the research and healthcare community.


title: Risk management in Canada's agricultural sector in light of COVID-19

text: The unexpected introduction and spread of COVID-19 has presented significant challenges for every aspect of Canadian society. Although the food and agricultural sector is positioned better than most, there are many risks that will need to be managed in the coming months. The suite of Federal-Provincial-Territorial Business Risk Management (BRM) programs delivered under the Canadian Agricultural Policy framework are meant to assist farmers in managing risks; however, there are no corresponding specialized programs for agribusinesses. The underlying structure of the BRM program was developed decades ago and certainly not with any thought to the possibility of a global pandemic. This article considers to what extent the BRM program and, more broadly, government programming will assist farmers in managing new risks. By default, the article is speculative in nature given that we are currently at the onset of the pandemic in Canada.


Challenges of tackling non covid-19 emergencies during the unprecedent pandemic


title: Observer agreement and clinical significance of chest CT reporting in patients suspected of COVID-19

text: Objectives: To assess inter-observer agreement and clinical significance of chest CT reporting in patients suspected of COVID-19. Methods: From 16th to 24th March 2020, 241 consecutive patients addressed to hospital for COVID-19 suspicion had both chest CT and SARS-CoV-2 RT-PCR. Eight observers (2 thoracic and 2 general senior radiologists, 2 junior radiologists and 2 emergency physicians) retrospectively categorized each CT into one out of 3 categories (evocative, compatible for COVID-19 pneumonia, and not evocative or normal). Observer agreement for categorization between all readers and pairs of readers with similar experience was evaluated with the Kappa coefficient. The results of a consensus categorization were correlated to RT-PCR. Results: Observer agreement across the 3 categories was good between all readers (kappa value 0.68 95%CI 0.67-0.70) and good to very good between pairs of readers (0.64-0.85). It was very good (0.81 95%CI 0.79-0.83), fair (0.32 95%CI 0.29-0.34) and good (0.74 95%CI 0.71-0.76) for the categories evocative, compatible and not evocative or normal, respectively. RT-PCR was positive in 97%, 50% and 27% of cases classified in the respective categories. Observer agreement was lower (p=0.045) and RT-PCR positive cases were less frequently categorized evocative in presence of an underlying pulmonary disease (p<0.001). Conclusion: Inter-observer agreement for chest CT reporting using categorization of findings is good in patients suspected of COVID-19. Among patients considered for hospitalization in an epidemic context, CT categorized evocative is highly predictive of COVID-19, whereas the predictive value of CT decreases between the categories compatible and not evocative.


title: Cross-reactivity of neutralizing antibody and its correlation with circulating T follicular cells in recovered COVID-19 individuals

text: Seroconversion appeared early after COVID-19 onset, and convalescent sera therapy benefit some critical patients. However, neutralizing antibody (nAb) in convalescents is largely unknown. We found that 97.01% (65/67) of COVID-19 convalescents maintained IgG antibodies with high binding and avidity to SARS-CoV-2 spike subunits S1 and S2, and 95.52% (64/67) had neutralization activity against SARS-CoV-2 pesudovirus, one month after discharge (median ID50, 2.75; IQR, 2.34-3.08). Some sera exhibited cross-neutralization against SARS-CoV (76.12%), MERS-CoV (17.91%), or both (10.45%). Interestingly, individuals recovered from severe disease (severe group) had nAbs with binding and neutralization titers higher than non-severe group. Severe group appeared a rapid increase of lymphocytes and a high proportion of circulating CXCR3+ Tfh cells. Interestingly, the later were spike-specific and positively correlated with SARS-CoV-2 nAb titers. All subjects had no autoimmunity. Our findings provide novel insights into nAb responses in COVID-19 convalescents and facilitate treatment and vaccine development for SARS-CoV-2 infection.


title: Acceptance and preference for COVID-19 vaccination in health-care workers (HCWs)

text: The objective of the present study is to reveal the acceptance and preference for the 2019 novel coronavirus disease (COVID-19) vaccination in health-care workers (HCWs). We performed an internet-based, region-stratified survey among 352 HCWs and 189 individuals in the general population enrolled on March 17th and 18th 2020 from 26 Chinese provinces. The HCWs developed a more in-depth understanding of SARS-Coronavirus-2 infection and showed a higher tolerance to the future vaccination than the general population. 76.4% of HCWs (vs. 72.5% in the general) showed their willingness to receive vaccination. Potential benefits from COVID-19 outbreak such as seeking influenza (65.3%) or pneumonia (55.7%) vaccination can be gained in HCWs. To estimate the relative effects of attributes influencing vaccination choice in the discrete choice experiment, 7 attributes (3 disease-relevant, 3 vaccine-relevant, and 1 of social acceptance) were identified as key determinants. Among them, disease trend (odds ratio, OR: 4.367 (95%CI, 3.721-5.126) for seasonal epidemic, OR: 3.069 (2.612-3.605) for persistent epidemic, with reference to disappearance in summer), social contacts decisions (0.398: 0.339-0.467 for refusal, 0.414: 0.353-0.487 for neutral, with reference to acceptance) and high possibility of being infected (2.076: 1.776-2.425 for infection probability of 30%+ ) were significantly associated with increased probability of choosing vaccination in the HCWs. In contrast, for the general population, vaccine safety and social contacts decisions were the most important predictors. For COVID-19 vaccination, education in HCWs should be taken as a priority, and further benefits of its recommendation to the general public will also be anticipated.


docid: ysbopqqq

title: Clinical features and management of severe COVID-19: A retrospective study in Wuxi, Jiangsu Province, China

text: Objective: We aimed to investigate clinical features and management of 55 COVID-19 patients in Wuxi, especially severe COVID-19. Methods: Epidemiological, demographic, clinical, laboratory, imaging, treatment, and outcome data of patients were collected. Follow-up lasted until April 6, 2020. Results: All 55 patients included 47 (85.5%) non-severe patients and 8 (14.5%) severe patients. Common comorbidities were hypertension and diabetes. Common symptoms were fever, cough and sputum. Lymphopenia was a common laboratory finding, and ground-glass opacity was a common chest CT feature. All patients received antiviral therapy of α-interferon inhalation and lopinavir-ritonavir tablets. Common complications included acute liver injury and respiratory failure. All patients were discharged. No death was occurred and no medical staff got infected. Patients with severe COVID-19 showed significantly older age, decreased lymphocytes, increased C reactive protein, and higher frequency of bilateral lung infiltration compared to non-severe patients. Significantly more treatments including antibiotic therapy and mechanical ventilation, longer hospitalization stay and higher cost were shown on severe patients. Conclusions: Our study suggested that patients with severe COVID-19 may be more likely to have an older age, present with lymphopenia and bilateral lung infiltration, receive multiple treatments and stay longer in hospital.


docid: bghnhblh

title: Modeling the COVID-19 epidemic in Okinawa

text: We analyze current data on the COVID-19 spreading in Okinawa, Japan. We find that the initial spread is characterized by a doubling time of about 5 days. We implement a model to forecast the future spread under different scenarios. The model predicts that, if significant containment measures are not taken, a large fraction of the population will be infected with COVID-19, with the peak of the epidemic expected at the end of May and intensive care units having largely exceeded capacity. We analyzed scenarios implementing strong containment measures, similar to those imposed in Europe. The model predicts that an immediate implementation of strong containment measures (on the 19th of April) will significantly reduce the death count. We assess the negative consequences of these measure being implemented with a delay, or not being sufficiently stringent.


title: BeepTrace: Blockchain-enabled Privacy-preserving Contact Tracing for COVID-19 Pandemic and Beyond

text: The outbreak of COVID-19 pandemic has exposed an urgent need for effective contact tracing solutions through mobile phone applications to prevent the infection from spreading further. However, due to the nature of contact tracing, public concern on privacy issues has been a bottleneck to the existing solutions, which is significantly affecting the uptake of contact tracing applications across the globe. In this paper, we present a blockchain-enabled privacy-preserving contact tracing scheme: BeepTrace, where we propose to adopt blockchain bridging the user/patient and the authorized solvers to desensitize the user ID and location information. Compared with recently proposed contract tracing solutions, our approach shows higher security and privacy with the additional advantages of being battery friendly and globally accessible. Results show viability in terms of the required resource at both server and mobile phone perspectives. Through breaking the privacy concerns of the public, the proposed BeepTrace solution can provide a timely framework for authorities, companies, software developers and researchers to fast develop and deploy effective digital contact tracing applications, to conquer COVID-19 pandemic soon. Meanwhile, the open initiative of BeepTrace allows worldwide collaborations, integrate existing tracing and positioning solutions with the help of blockchain technology.


title: Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts

text: Background Rapid spread of SARS-CoV-2 in Wuhan prompted heightened surveillance in Shenzhen and elsewhere in China. The resulting data provide a rare opportunity to measure key metrics of disease course, transmission, and the impact of control. Methods The Shenzhen CDC identified 391 SARS-CoV-2 cases from January 14 to February 12, 2020 and 1286 close contacts. We compare cases identified through symptomatic surveillance and contact tracing, and estimate the time from symptom onset to confirmation, isolation, and hospitalization. We estimate metrics of disease transmission and analyze factors influencing transmission risk. Findings Cases were older than the general population (mean age 45) and balanced between males (187) and females (204). Ninety-one percent had mild or moderate clinical severity at initial assessment. Three have died, 225 have recovered (median time to recovery is 21 days). Cases were isolated on average 4.6 days after developing symptoms; contact tracing reduced this by 1.9 days. Household contacts and those travelling with a case where at higher risk of infection (ORs 6 and 7) than other close contacts. The household secondary attack rate was 15%, and children were as likely to be infected as adults. The observed reproductive number was 0.4, with a mean serial interval of 6.3 days. Interpretation Our data on cases as well as their infected and uninfected close contacts provide key insights into SARS-CoV-2 epidemiology. This work shows that heightened surveillance and isolation, particularly contact tracing, reduces the time cases are infectious in the community, thereby reducing R. Its overall impact, however, is uncertain and highly dependent on the number of asymptomatic cases. We further show that children are at similar risk of infection as the general population, though less likely to have severe symptoms; hence should be considered in analyses of transmission and control.


title: Mental healthcare for psychiatric inpatients during the COVID-19 epidemic

text: During this 2019 coronavirus disease (COVID-19) pneumonia epidemic, some experts have expressed concern for the mental healthcare of different types of population groups. However, hospitalised patients with severe mental illness are seemingly overlooked. Psychiatric patients are still a vulnerable group who need to obtain more attention and respect, particularly during the COVID-19 outbreak in China. In this commentary, we briefly introduce the situation of hospitalized patients with severe mental illness and suggest some effective measures that should be rapidly undertaken to reverse current challenges.


title: Binding of the SARS-CoV-2 Spike Protein to Glycans

text: The pandemic of SARS-CoV-2 has caused a high number of deaths in the world. To combat it, it is necessary to develop a better understanding of how the virus infects host cells. Infection normally starts with the attachment of the virus to cell-surface glycans like heparan sulfate (HS) and sialic acid-containing oligosaccharides. In this study, we examined and compared the binding of the subunits and spike (S) proteins of SARS-CoV-2 and SARS-CoV, MERS-CoV to these glycans. Our results revealed that the S proteins and subunits can bind to HS in a sulfation-dependent manner, the length of HS is not a critical factor for the binding, and no binding with sialic acid residues was detected. Overall, this work suggests that HS binding may be a general mechanism for the attachment of these coronaviruses to host cells, and supports the potential importance of HS in infection and in the development of antiviral agents against these viruses.


COVID-19 and water resources management: reframing our priorities as a water sector


title: Bio-informed Protein Sequence Generation for Multi-class Virus Mutation Prediction

text: Viral pandemics are emerging as a serious global threat to public health, like the recent outbreak of COVID-19. Viruses, especially those belonging to a large family of +ssRNA viruses, have a high possibility of mutating by inserting, deleting, or substituting one or multiple genome segments. It is of great importance for human health worldwide to predict the possible virus mutations, which can effectively avoid the potential second outbreak. In this work, we develop a GAN-based multi-class protein sequence generative model, named ProteinSeqGAN. Given the viral species, the generator is modeled on RNNs to predict the corresponding antigen epitope sequences synthesized by viral genomes. Additionally, a Graphical Protein Autoencoder (GProAE) built upon VAE is proposed to featurize proteins bioinformatically. GProAE, as a multi-class discriminator, also learns to evaluate the goodness of protein sequences and predict the corresponding viral species. Further experiments show that our ProteinSeqGAN model can generate valid antigen protein sequences from both bioinformatics and statistics perspectives, which can be promising predictions of virus mutations.


title: Diet and physical activity during the COVID-19 lockdown period (March-May 2020): results from the French NutriNet-Sante cohort study

text: Background: Since December 2019, the coronavirus disease (COVID-19) has massively spread, with overwhelming of health care systems and numerous deaths worldwide. To remedy this, several countries, including France, have taken strict lockdown measures, requiring the closure of all but essential places. This unprecedented disruption of daily routines has a strong potential for disrupting nutritional behaviours. Nutrition being one of the main modifiable risk factors for chronic disease risk, this may have further consequences for public health. Our objective was therefore to describe nutritional behaviours during the lockdown period and to put them in light of individual characteristics. Methods: 37,252 French adults from the web-based NutriNet-Sante cohort filled lockdown-specific questionnaires in April-May 2020 (nutritional behaviours, body weight, physical activity, 24h-dietary records). Nutritional behaviours were compared before and during lockdown using Student paired t-tests and associated to individual characteristics using multivariable logistic or linear regression models. Clusters of nutritional behaviours were derived from multiple correspondence analysis and ascending hierarchical classification. Results: During the lockdown, trends for unfavourable nutritional behaviours were observed: weight gain (for 35%; +1.8kg on average), decreased physical activity (53%), increased sedentary time (63%), increased snacking, decreased consumption of fresh food products (especially fruit and fish), increased consumption of sweets, biscuits and cakes. Yet, opposite trends were also observed: weight loss (for 23%, -2kg on average), increased home-made cooking (40%), increased physical activity (19%). These behavioural trends related to sociodemographic and economic position, professional situation during the lockdown (teleworking or not), initial weight status, having children at home, anxiety and depressive symptoms, as well as diet quality before the lockdown. Modifications of nutritional practices mainly related to routine change, food supply, emotional reasons but also to voluntary changes to adjust to the current situation. Conclusion: These results suggest that the lockdown led, in a substantial part of the population, to unhealthy nutritional behaviours that, if maintained in the long term, may increase the nutrition-related burden of disease and also impact immunity. Yet, the lockdown situation also created an opportunity for some people to improve their nutritional behaviours, with high stakes to understand the leverages to put these on a long-term footing.


Medical workers in traditional medicine who sacrificed their lives in the battle against COVID-19 deserve to be remembered forever


title: Risk assessment of progression to severe conditions for patients with COVID-19 pneumonia: a single-center retrospective study

text: Background: Management of high mortality risk due to significant progression requires prior assessment of time-to-progression. However, few related methods are available for COVID-19 pneumonia. Methods: We retrospectively enrolled 338 adult patients admitted to one hospital between Jan 11, 2020 to Feb 29, 2020. The final follow-up date was March 8, 2020. We compared characteristics between patients with severe and non-severe outcome, and used multivariate survival analyses to assess the risk of progression to severe conditions. Results: A total of 76 (31.9%) patients progressed to severe conditions and 3 (0.9%) died. The mean time from hospital admission to severity onset is 3.7 days. Age, body mass index (BMI), fever symptom on admission, co-existing hypertension or diabetes are associated with severe progression. Compared to non-severe group, the severe group already demonstrated, at an early stage, abnormalities in biomarkers indicating organ function, inflammatory responses, blood oxygen and coagulation function. The cohort is characterized with increasing cumulative incidences of severe progression up to 10 days after admission. Competing risks survival model incorporating CT imaging and baseline information showed an improved performance for predicting severity onset (mean time-dependent AUC = 0.880). Conclusions: Multiple predisposition factors can be utilized to assess the risk of progression to severe conditions at an early stage. Multivariate survival models can reasonably analyze the progression risk based on early-stage CT images that would otherwise be misjudged by artificial analysis.


title: The impact of physical distancing measures against COVID-19 transmission on contacts and mixing patterns in the Netherlands: repeated cross-sectional surveys

text: Background During the current pandemic of coronavirus (COVID-19) many countries have taken drastic measures to reduce transmission of SARS-CoV2. The measures often include physical distancing that aims to reduce the number of contacts in the population. Little is known about the actual reduction in number of contacts as a consequence of physical distancing measures. Methods In the Netherlands, a cross-sectional survey was carried out in 2016/2017 in which 8179 participants retrospectively reported the number, age and gender of different persons they had contacted (spoken to in person or touched) during the previous day. The survey was repeated among 2830 of the original participants, using the same questionnaire, in March and April 2020 after physical distancing measures had been implemented. Results The average number of contacts in the community was reduced from on average 12.5 (interquartile range: 2-17) to 3.7 (interquartile range: 0-4) different persons per participant, a reduction of 71% (95% confidence interval: 71-71). The reduction in the number of community contacts was highest for children and adolescents (between 5 and 20 years) and smallest for elderly persons of 80 years and older. The reduction in the effective number of total contacts, measured as the largest eigenvalue of the matrix with community and household contacts, was 62% (95% confidence interval: 48 - 72). Conclusion The substantial reduction in contacts has contributed greatly in halting the COVID-19 epidemic. This reduction was unevenly distributed over age groups, household sizes and occupations. These findings offer guidance for the lifting of age-group targeted measures.


docid: txuthqgo

title: Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site

text: Direct RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.


title: Monitoring the evolution of the COVID-19 pandemic in China, South Korea, Italy and USA through the net relative rate of infection of the total number of confirmed cases

text: Managing the COVID-19 pandemic in the middle of the events requires real-time monitoring of its evolution to perform analyses of containment actions and to project near future scenarios. This work proposes a scheme to monitor the temporal evolution of the COVID-19 pandemic using the time series of its total number of confirmed cases in a given region. The monitored parameter is the spread rate obtained from this time series (day-1) expressed in %/day. The scheme's capability is verified using the epidemic data from China and South Korea. Its projection capability is shown for Italy and United States with scenarios for the ensuing 30 days from April 2nd, 2020. The spread rate (relative rate of change of the time series) is very sensitive to sudden changes in the epidemic evolution and can be used to monitor in real-time the effectiveness of containment actions. The logarithm of this variable allows identifying clear trends of the evolution of the COVID-10 epidemic in these countries. The spread rate calculated from the number of confirmed cases of infection is interpreted as a probability per unit of time of virus infection and containment actions. Its product with the number of confirmed cases of infections yields the number of new cases per day. The stabilization and control of the epidemic for China and South Korea appear to occur for values of this parameter below 0.77 %/day (doubling time of 90 days).


title: Main Clinical Features of COVID-19 and Potential Prognostic and Therapeutic Value of the Microbiota in SARS-CoV-2 Infections

text: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), has become a pandemic, infecting more than 4,000,000 people worldwide. This review describes the main clinical features of COVID-19 and potential role of microbiota in COVID-19. SARS-CoV and SARS-CoV-2 have 79.5% nucleotide sequence identity and use angiotensin-converting enzyme 2 (ACE2) receptors to enter host cells. The distribution of ACE2 may determine how SARS-CoV-2 infects the respiratory and digestive tract. SARS and COVID-19 share similar clinical features, although the estimated fatality rate of COVID-19 is much lower. The communication between the microbiota and SARS-CoV-2 and the role of this association in diagnosis and treatment are unclear. Changes in the lung microbiota were identified in COVID-19 patients, and the enrichment of the lung microbiota with bacteria found in the intestinal tract is correlated with the onset of acute respiratory distress syndrome and long-term outcomes. ACE2 regulates the gut microbiota by indirectly controlling the secretion of antimicrobial peptides. Moreover, the gut microbiota enhances antiviral immunity by increasing the number and function of immune cells, decreasing immunopathology, and stimulating interferon production. In turn, respiratory viruses are known to influence microbial composition in the lung and intestine. Therefore, the analysis of changes in the microbiota during SARS-CoV-2 infection may help predict patient outcomes and allow the development of microbiota-based therapies.


title: Is nasopharyngeal swab comparable with nasopharyngeal aspirate to detect SARS-CoV-2 in children?

text: The tests currently used for the direct identification of SARS-CoV-2 include specimens taken from the upper and the lower respiratory tract. In our paediatric department all children undergo both nasopharyngeal swab and nasopharyngeal aspirate, performed from both nostrils, on admission and after 24 hours. We decided to compare these two methods of detection of SARS-CoV-2. Considering nasopharyngeal aspirate as the gold standard, we calculated sensitivities and specificities of nasopharyngeal swab. Based on our results, we suggest to prefer the collection of aspirates whenever possible.


docid: wltsgiqc

title: The challenges in colorectal cancer management during COVID-19 epidemic

text: It has been over 2 months since the start of the Coronavirus disease 2019 (COVID-19) outbreak. The epidemic stage of COVID-19 has brought great challenges to the diagnosis and management of colorectal cancer (CRC) patients. Symptoms, such as fever and cough caused by cancer, and the therapeutic process (including chemotherapy and surgery) should be differentiated from some COVID-19 related characteristics. Besides, clinical workers should not only consider the therapeutic strategy for cancer, but also emphasize COVID-19's prevention. Moreover, the detailed therapeutic regimens of CRC patients may be different from the usual. Also, treatment principles may various for CRC patients with or without severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as well as patients with or without an emergency presentation. In this paper, we want to discuss the above-mentioned problems based on previous guidelines, the current working status and our experiences, to provide a reference for medical personnel.


title: Population-level COVID-19 mortality risk for non-elderly individuals overall and for non-elderly individuals without underlying diseases in pandemic epicenters

text: OBJECTIVE: To evaluate the relative risk of COVID-19 death in people <65 years old versus older individuals in the general population, to provide estimates of absolute risk of COVID-19 death at the population level, and to understand what proportion of COVID-19 deaths occur in non-elderly people without underlying diseases in epicenters of the pandemic. ELIGIBLE DATA: Countries and US states or major cities with at least 250 COVID-19 deaths as of 4/4/2020 and with information available on death counts according to age strata, allowing to calculate the number of deaths in people with age <65. Data were available for Belgium, Germany, Italy, Netherlands, Portugal, Spain, Sweden, and Switzerland, as well as Louisiana, Michigan, Washington states and New York City as of April 4, 2020. MAIN OUTCOME MEASURES: Proportion of COVID-19 deaths that occur in people <65 years old; relative risk of COVID-19 death in people <65 versus ≥65 years old; absolute risk of death in people <65 and in those ≥80 years old in the general population as of 4/4/2020; absolute death risk expressed as equivalent of death risk from driving a motor vehicle. RESULTS: Individuals with age <65 account for 5%-9% of all COVID-19 deaths in the 8 European epicenters, and approach 30% in three US hotbed locations. People <65 years old had 34- to 73-fold lower risk than those ≥65 years old in the European countries and 13- to 15-fold lower risk in New York City, Louisiana and Michigan. The absolute risk of COVID-19 death ranged from 1.7 per million for people <65 years old in Germany to 79 per million in New York City. The absolute risk of COVID-19 death for people ≥80 years old ranged from approximately 1 in 6,000 in Germany to 1 in 420 in Spain. The COVID-19 death risk in people <65 years old during the period of fatalities from the epidemic was equivalent to the death risk from driving between 9 miles per day (Germany) and 415 miles per day (New York City). People <65 years old and not having any underlying predisposing conditions accounted for only 0.3%, 0.7%, and 1.8% of all COVID-19 deaths in Netherlands, Italy, and New York City. CONCLUSIONS: People <65 years old have very small risks of COVID-19 death even in the hotbeds of the pandemic and deaths for people <65 years without underlying predisposing conditions are remarkably uncommon. Strategies focusing specifically on protecting high-risk elderly individuals should be considered in managing the pandemic.


title: Crowding and the epidemic intensity of COVID-19 transmission

text: The COVID-19 pandemic is straining public health systems worldwide and major non-pharmaceutical interventions have been implemented to slow its spread. During the initial phase of the outbreak the spread was primarily determined by human mobility. Yet empirical evidence on the effect of key geographic factors on local epidemic spread is lacking. We analyse highly-resolved spatial variables for cities in China together with case count data in order to investigate the role of climate, urbanization, and variation in interventions across China. Here we show that the epidemic intensity of COVID-19 is strongly shaped by crowding, such that epidemics in dense cities are more spread out through time, and denser cities have larger total incidence. Observed differences in epidemic intensity are well captured by a metapopulation model of COVID-19 that explicitly accounts for spatial hierarchies. Densely-populated cities worldwide may experience more prolonged epidemics. Whilst stringent interventions can shorten the time length of these local epidemics, although these may be difficult to implement in many affected settings.


title: Conflicts with diarrheal pathogens trigger rapid evolution of an intestinal signaling axis

text: The pathogenesis of infectious diarrheal diseases is largely attributed to enterotoxin proteins that disrupt intestinal water absorption, causing severe dehydration. Despite profound health consequences, the impacts of diarrhea-causing microbes on the evolutionary history of host species are largely unknown. We investigated patterns of genetic variation in mammalian Guanylate Cyclase-C (GC-C), an intestinal receptor frequently targeted by bacterial enterotoxins, to determine how hosts might adapt in response to diarrheal infections. Under normal conditions, GC-C interacts with endogenous guanylin peptides to promote water secretion in the intestine, but signaling can be hijacked by bacterially-encoded heat-stable enterotoxins (STa) during infection, which leads to overstimulation of GC-C and diarrhea. Phylogenetic analysis in mammals revealed evidence of recurrent positive selection in the GC-C ligand-binding domain in primates and bats, consistent with selective pressures to evade interactions with STa. Using in vitro assays and transgenic intestinal organoids to model STa-mediated diarrhea, we show that GC-C diversification in these lineages results in substantial variation in toxin susceptibility. In bats, we observe a unique pattern of compensatory coevolution in the endogenous GC-C ligand uroguanylin, reflecting intense bouts of positive selection at the receptor-ligand interface. These findings demonstrate control of water physiology as a previously unrecognized interface for genetic conflict and reveal diarrheal pathogens as a source of selective pressure among diverse mammals.


title: SARS-CoV-2 in wastewater treatment plants

text: As for the SARS coronavirus in the 2003 epidemic, the presence of SARS-CoV-2 has been demonstrated in faeces and, in some cases, urine of infected people, as well as in wastewater. This paper proposes a critical review of the state of the art regarding studies on the presence of SARS-CoV-2 in wastewater and sewage sludge, the factors affecting its inactivation and the main proposed treatments, with the aim to provide useful information at operative level in order to better and safer manage wastewater and sewage sludge. Given the lack of literature on SARS-CoV-2, studies involving other HCoVs such as SARS-CoV and HCoV-229E have been also considered. In wastewater, the resistance of SARS-CoV has proven to be very limited, especially at temperatures above 20 {degrees}C, and the virus has been easily removed with the use of chlorine (> 0.5 mg L-1 for 30 min). For sewage sludge, based on in vitro experiments, it is suggested to increase the retention times before a possible reuse in agriculture only for precautionary purposes, since SARS-CoV-2 is unlikely to occur in the sludge. SARS-CoV-2 in wastewater might track the epidemic trends: although being extremely promising, an effective and wide application of this approach requires a deeper knowledge of the amounts of viruses excreted through the faeces and the actual detectability of viral RNA in sewage.


title: Effects of tourism CSR on employee psychological capital in the COVID-19 crisis: from the perspective of conservation of resources theory

text: The main purpose of this research was to illustrate how companies contributed to employee psychological capital in tourism during the COVID-19 crisis based on the conservation of resources theory (CoR). Psychological capital including self-efficacy, hope, resilience and optimism is a key source of support at work, especially during challenging events. With threats to health and job security, employee psychological capital was unlikely to recover on its own naturally. However, tourism companies can augment employee psychological capital through corporate social responsibility (CSR). The effects of CSR on employee psychological capital remains unclear. This research examined differing effects of CSR on self-efficacy, hope, resilience and optimism. Based on a survey of 430 employees in tourism in China, the results showed that CSR had positive impacts on employee self-efficacy, hope, resilience and optimism through employee satisfaction with corporate COVID-19 responses. In addition, individual loss orientation strengthened the effects of CSR on employee self-efficacy, hope, resilience and optimism.


title: Response to the COVID-19 epidemic: a report from Shenzhen, China

text: The whole world is now facing an unprecedented pandemic with over 1 8 million confirmed cases and more than one hundred thousand deaths To counter the pandemic, Shenzhen created a central command and control structure based on the only designated hospital- Shenzhen Third People's Hospital which is a large general hospital specialized on infectious diseases in the bay area The hospital has taken many decisive and effective actions to respond to the epidemic Here, we will describe and share healthcare experiences from Shenzhen and call for international cooperation and collaboration


title: Hospital admissions in inflammatory rheumatic diseases during the COVID-19 pandemic: incidence and role of disease modifying agents

text: Background: In this pandemia, it is essential for rheumatologist and patients to know the relationship between COVID-19 and inflammatory rheumatic diseases (IRD). We want to assess the role of targeted synthetic or biologic disease modifying antirheumatic drugs (ts/bDMARDs) and other variables in the development of moderate-severe COVID-19 disease in IRD. Methods: An observational longitudinal study was conducted (1stMar to 15thApr 2020). All patients from the rheumatology outpatient clinic from a hospital in Madrid with a medical diagnosis of IRD were included. Main outcome: hospital admission related to COVID-19. Independent variable: ts/bDMARDs. Covariates: sociodemographic, comorbidities, type of IRD diagnosis, glucocorticoids, NSAIDs and conventional synthetic DMARDs (csDMARDs). Incidence rate (IR) of hospital admission related to COVID-19, was expressed per 1,000 patients-month. Cox multivariate regression analysis was run to examine the influence of ts/bDMARDs and other covariates on IR. Results: 3,591 IRD patients were included (5,896 patients-month). Concerning csDMARDs, methotrexate was the most used followed by antimalarials. 802 patients were on ts/bDMARDs, mainly anti-TNF agents, and rituximab. Hospital admissions related to COVID-19 occurred in 54 patients (1.36%) with an IR of 9.15 [95%CI: 7-11.9]. In the multivariate analysis, older, male gender, presence of comorbidities and specific systemic autoimmune conditions (Sjoegren, polychondritis, Raynaud and mixed connective tissue disease) had more risk of hospital admissions regardless other factors. Exposition to ts/bDMARDs did not achieve statistical signification. Use of glucocorticoids, NSAIDs, and csDMARDs dropped from the final model. Conclusion: This study provides additional evidence in IRD patients regarding susceptibility to moderate-severe infection related to COVID-19.


title: Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions

text: Since first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. using a transmission model, we estimate a basic reproductive number of 3.11 (95%CI, 2.39-4.13); 58-76% of transmissions must be prevented to stop increasing; Wuhan case ascertainment of 5.0% (3.6-7.4); 21022 (11090-33490) total infections in Wuhan 1 to 22 January.


title: Rapid Detection of SARS-CoV-2 Using Reverse transcription RT-LAMP method

text: Corona Virus Disease 2019 (COVID-19) is a recently emerged life-threatening disease caused by SARS-CoV-2. Real- time fluorescent PCR (RT-PCR) is the clinical standard for SARS-CoV-2 nucleic acid detection. To detect SARS-CoV-2 early and control the disease spreading on time, a faster and more convenient method for SARS-CoV-2 nucleic acid detecting, RT-LAMP method (reverse transcription loop-mediated isothermal amplification) was developed. RNA reverse transcription and nucleic acid amplification were performed in one step at 63 ℃ isothermal conditions, and the results can be obtained within 30 minutes. ORF1ab gene, E gene and N gene were detected at the same time. ORF1ab gene was very specific and N gene was very sensitivity, so they can guarantee both sensitivity and specificity for SARS-CoV-2. The sensitivity of RT-LAMP assay is similar to RT-PCR, and specificity was 99% as detecting 208 clinical specimens. The RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection, which is useful for the rapid and reliable clinical diagnosis of SARS-CoV-2.


title: Comprehensive physiotherapy management in COVID-19 – A narrative review/ Tratamento fisioterápico na COVID-19 - Uma revisão narrativa

text: The 2019 novel coronavirus officially named as coronavirus disease 2019 (COVID-19) pandemic by the World Health Organization, has spread to more than 180 countries. The ongoing global pandemic of severe acute respiratory syndrome coronavirus, which causes COVID-19, spread to the United Kingdom (UK) in January 2020. Transmission within the UK was confirmed in February, leading to an epidemic with a rapid increase in cases in March. As on April 25- 2020, there have been 148,377 confirmed cases of COVID-19 in the UK and 20,319 people with confirmed infection have died. Survival of critically ill patients is frequently associated with significant functional impairment and reduced health-related quality of life. Early physiotherapy and community rehabilitation of COVID-19 patients has recently been identified as an essential therapeutic tool and has become a crucial evidence-based component in the management of these patients. This comprehensive narrative review aims to describe recent progress in the application of physiotherapy management in COVID 19 patients. Assessment and evidence-based treatment of these patients should include prevention, reduction of adverse consequences in immobilization, and long-term impairment sequelae. A variety of techniques and modalities of early physiotherapy in intensive care unit are suggested by clinical research. They should be applied according to the stage of the disease, comorbidities, and patient’s level of cooperation.


title: SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolution

text: COVID-19 has quickly become a worldwide pandemic, which has significantly impacted the economy, education, and social interactions. Understanding the humoral antibody response to SARS-CoV-2 proteins may help identify biomarkers that can be used to detect and treat COVID-19 infection. However, no immuno-proteomics platform exists that can perform such proteome-wide analysis. To address this need, we created a SARS-CoV-2 proteome microarray to analyze antibody interactions at amino acid resolution by spotting peptides 15 amino acids long with 5-amino acid offsets representing full-length SARS-CoV-2 proteins. Moreover, the array processing time is short (1.5 hours), the dynamic range is ~2 orders of magnitude, and the lowest limit of detection is 94 pg/mL. Here, the SARS-CoV-2 proteome array reveals that antibodies commercially available for SARS-CoV-1 proteins can also target SARS-CoV-2 proteins. These readily available reagents could be used immediately in COVID-19 research. Second, IgM and IgG immunogenic epitopes of SARS-CoV-2 proteins were profiled in the serum of ten COVID-19 patients. Such epitope biomarkers provide insight into the immune response to COVID-19 and are potential targets for COVID-19 diagnosis and vaccine development. Finally, serological antibodies that may neutralize viral entry into host cells via the ACE2 receptor were identified. Further investigation into whether these antibodies can inhibit the propagation of SARS-CoV-2 is warranted. Antibody and epitope profiling in response to COVID-19 is possible with our peptide-based SARS-COV-2 proteome microarray. The data gleaned from the array could provide invaluable information to the scientific community to understand, detect, and treat COVID-19.


title: Catch and kill airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system

text: Airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via air-conditioning systems poses a significant threat for the continued escalation of the current coronavirus disease (COVID-19) pandemic. Considering that SARS-CoV-2 cannot tolerate temperatures above 70 °C, here we designed and fabricated efficient air disinfection systems based on heated nickel (Ni) foam to catch and kill SARS-CoV-2. Virus test results revealed that 99.8% of the aerosolized SARS-CoV-2 was caught and killed by a single pass through a Ni-foam-based filter when heated up to 200 °C. Additionally, the same filter was also used to catch and kill 99.9% of Bacillus anthracis, an airborne spore. This study paves the way for preventing transmission of SARS-CoV-2 and other highly infectious airborne agents in closed environments. One Sentence Summary Heated Ni-foam filters are capable of effectively catching and killing airborne SARS-CoV-2 and Bacillus anthracis spores.


title: COVID-19-Associated Acute Disseminated Encephalomyelitis: A Case Report

text: We present the first described case of Acute disseminated encephalomyelitis (ADEM) in a COVID-19 patient. The clinical features with head CT and brain MRI changes were described. Our described case is an atypical presentation of the novel coronavirus in a young patient and is illustrative of the possible approaches to explore the treatable differential etiologies.


title: Number of International Arrivals Predicts Severity of the first Global Wave of the COVID-19 Pandemic

text: Background: Reported death rates from different countries during the COVID-19 pandemic vary. Lack of universal testing and death underreporting make between-country comparisons difficult. The country-level determinants of COVID-19 mortality are unknown. Objective: Derive a measure of COVID-related death rates that is comparable across countries and identify its country-level predictors. Methods: An ecological study design of publicly available data was employed. Countries reporting >25 COVID-related deaths until May 1, 2020 were included. The outcome was the mean mortality rate from COVID-19, an estimate of the country-level daily increase in reported deaths during the ascending phase of the epidemic curve. Potential predictors assessed were most recently published Demographic parameters (population and population density, percentage population living in urban areas, median age, average body mass index, smoking prevalence), Economic parameters (Gross Domestic Product per capita; environmental parameters: pollution levels, mean temperature (January-April)), co-morbidities (prevalence of diabetes, hypertension and cancer), health systems parameters (WHO Health Index and hospital beds per 10,000 population and international arrivals). Multivariable linear regression was used to analyse the data. Results: Thirty-one countries were included. Of all country-level predictors included in the multivariable model, only total number of international arrivals was significantly associated with the mean death rate: Beta 0.3798 (95% Confidence Interval 0.2414, 0.5182), P <0.001. Conclusion: International travel was directly associated with the mortality slope and thus potentially the spread of COVID-19. Stopping international travel, particularly from affected areas, may be the most effective strategy to control COVID outbreak and prevent related deaths.


title: Swine viral detection by adapted Next-Generation Sequencing (NGS) for RNA and DNA species reveals first detection of porcine circovirus type 3 (PCV3) in Chile

text: The outbreak and propagation of COVID-19 have posed a significant challenge to our society, highlighting the relevance of epidemiological monitoring of animal pathogens closely related to humans due to potential zoonosis. To find previously undetected viruses inside Chilean swine farms, we collected non-invasive samples from animals suspected to undergo any viral disease. After screening by Next Generation Sequencing (NGS) adapted to identify viral species with RNA and DNA genomes simultaneously, different viral species were successfully detected. Among viruses with an RNA genome, Porcine Rotavirus A (RVA), Porcine Astrovirus type 5 (PAstV-5) and Porcine Feces-Associated IASV-like virus (PfaIV) were identified; whereas among viruses with DNA genome, Porcine Parvovirus 1 (PPV1), Porcine Circovirus type 1 (PCV1) and Porcine Circovirus type 3 (PCV3) were found. PCV3, a recently described pathogenic virus, was detected for the first time in Chile in different samples from mummified tissue of stillbirths. The whole genome sequence of PCV3 was completed using conventional PCR and Sanger sequencing and compared with previously reported genomes. To the best of our knowledge, this is the first time that an adapted NGS system is used for the screening of DNA and RNA viral species simultaneously inside the Chilean swine industry. This adapted NGS system might be useful for the detection of swine viral emerging diseases worldwide.


title: Serological Tests for SARS-CoV-2 Coronavirus by Commercially Available Point-of-Care and Laboratory Diagnostics in Pre-COVID-19 Samples in Japan

text: Serological tests for SARS-CoV-2 coronavirus in pre-COVID-19 samples in Japan showed 1.5%-1.75% positives, and previous surveys might overestimate COVID-19 seroprevalence in several population of Japan. These false negatives could be excluded by combination of different diagnostics to 0.25%.


title: Faecal immunochemical testing (FIT): Sources of analytical variation based on three years of routine testing in the context of DG30

text: Aims: To determine analytical capabilities of a commonly used faecal immunochemical test (FIT) to detect haemoglobin (Hb) in the context of NICE guidance DG30, and the likely use of FIT to reprioritise patients delayed by the COVID-19 pandemic. Methods: Data obtained from independent verification studies and clinical testing of the HM-JACKarc FIT method in routine primary care practice were analysed to derive analytical performance characteristics. Results: Detection capabilities for the FIT method were 0.5 microg/g (limit of blank), 1.1 microg/g (limit of detection) and 15.0 microg/g (limit of quantification). 31 of 33 (94%) non-homogenised specimens analysed in triplicate were consistently categorised relative to 10 microg/g compared to all 33 (100%) homogenised specimens. Imprecision in non-homogenised specimens was higher (median 27.8%, (range 20.5% - 48.6%)) than in homogenised specimens (10.2%, (7.0 to 13.5%)). Considerable variation was observed in sequential clinical specimens from individual patients but no positive or negative trend in specimen degradation was observed (p=0.26). Conclusions: The FIT method is capable of detecting Hb at concentrations well below the DG30 threshold of 10 microg/g. However, total imprecision is considerable when including sampling variation. Binary categorisation against a single defined threshold above and below 10 microg/g was more consistent and improved following specimen homogenisation. This approach may be more appropriate when reporting results for symptomatic patients tested in primary care, including those who have had definitive investigation delayed by the COVID-19 pandemic and need to be re-prioritised.


title: Risk of COVID-19 is associated with long-term exposure to air pollution

text: High risk of severe disease of COVID-19 has been associated with patients with chronic obstructive pulmonary disease, cardiovascular disease or hypertension, and long-term exposure to PM2.5 has been associated with COVID-19 mortality. We collate individual level data of confirmed COVID-19 cases during the first wave of the epidemic in mainland China by March 6, 2020. We pair these data with a mobile phone dataset, covering human movements from Wuhan before the travel ban and inner-city movements during the time of emergency response from 324 cities in China. Adjusting for socio-economic factors, an increase of 10 μg/m3 in NO2 or PM2.5 was found to be associated with a 22.41% (95%CI: 7.28%-39.89%) or 15.35% (95%CI: 5.60%-25.98%) increase in the number of COVID-19 cases, and a 19.20% (95%CI: 4.03%-36.59%) or 9.61% (95%CI: 0.12%-20.01%) increase in severe infection, respectively. Our results highlight the importance of air quality improvements to health benefits.


docid: wdfzrzkt

title: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

text: SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19. We systematically mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in a large cohort of unexposed individuals as well as exposed family members and individuals with acute or convalescent COVID-19. Acute phase SARS-CoV-2-specific T cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent phase SARS-CoV-2-specific T cells were polyfunctional and displayed a stem-like memory phenotype. Importantly, SARS-CoV-2-specific T cells were detectable in antibody-seronegative family members and individuals with a history of asymptomatic or mild COVID-19. Our collective dataset shows that SARS-CoV-2 elicits robust memory T cell responses akin to those observed in the context of successful vaccines, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19 also in seronegative individuals.


title: How susceptible is your pet to the novel coronavirus?

text: As COVID-19 keeps people at home under quarantine, many have wondered how susceptible their canine and feline companions are to the disease Scientists now report that SARS-CoV-2, the virus that causes COVID-19, doesn’t do a good job of copying itself in dogs, pigs, chickens, and ducks But cats are susceptible to the virus and can give it to one another via airborne transmission The researchers did not study whether cats could pass the virus to people Led by Hualan Chen and Zhigao Bu, of the Harbin Veterinary Research Institute, and Guizhen Wu, of China’s National Institute for Viral Disease Control and Prevention, the team also found that ferrets—animals commonly used to study viruses that cause human respiratory infections—can also get SARS-CoV-2 In ferrets, though, the virus reproduces itself only in the upper respiratory tract, not in the lungs The findings could mean that ferrets aren’t great for models for replicating


title: High Throughput Virtual Screening with Data Level Parallelism in Multi-core Processors

text: Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements, the world might find cures for incurable diseases like HIV disease and Cancer sooner. Our approach presented in this paper is to utilize a multi-core environment to introduce Data Level Parallelism (DLP) to the Autodock Vina software, which is a widely used for molecular docking software. Autodock Vina already exploits Instruction Level Parallelism (ILP) in multi-core environments and therefore optimized for such environments. However, with the results we have obtained, it can be clearly seen that our approach has enhanced the throughput of the already optimized software by more than six times. This will dramatically reduce the time consumed for the lead identification phase in drug designing along with the shift in the processor technology from multi-core to many-core of the current era. Therefore, we believe that the contribution of this project will effectively make it possible to expand the number of small molecules docked against a drug target and improving the chances to design drugs for incurable diseases.


title: COVID-19 cripples global restaurant and hospitality industry

text: The restaurant and hospitality industries are crucial socio-economic sectors that contribute immensely to the global economy. However, these sectors are vulnerable and sensitive to natural hazards such as the COVID-19 pandemic and any resultant economic downturns. This study investigates the impact of COVID-19 on the global restaurant industry using data from OpenTable and other sources. The study found that sit-in guests dropped to zero in many countries as governments across the world instituted social distancing initiatives, movement restrictions and lockdowns. COVID-19 also led to an unprecedented loss of employment and revenue, resulting in millions of jobs and billions of dollars in potential revenue lost. The work recommends extra-ordinary financial and other support measures for the sector. It further recommends a raft of safety and health protocols as the industry gradually reopens.


title: DOUBLE POWER LAW FOR COVID-19: PREDICTION OF NEW CASES AND DEATH RATES IN ITALY AND SPAIN

text: The novel corona virus SARS-CoV-2 appeared at the end of 2019, spreading rapidly and causing a severe respiratory syndrome (COVID-19) with high mortality (2-5%). Until a vaccine or therapy is found, the most effective method of prophylaxis has been to minimize transmission via rigorous social distancing and seclusion of all but essential workers. Such measures, implemented at different times and to varying degrees worldwide, have reduced the rate of transmission compared with early phases of the pandemic, resulting in flattening of the curve followed by a gradual reduction in mortality after >6 weeks of rigorous social distancing measures. The cost of rigorous social distancing has been seen in radically reduced economic activity, job losses, disruption of schooling and social institutions. A key question facing policy makers and individuals is when to resume normal economic and social activity in the face of persistent community transmission of SARS-CoV-2 . To help address this question, we have developed a model that accurately describes the entire transmission and mortality curves in Italy and Spain, two hard-hit countries that have maintained severe social distancing measures for over 2 months. Our model quantitatively describes the rapid rise and slow decay of new cases and deaths observed under stringent social distancing (the long tail effect). We predict that even when social distancing is rigorously maintained, the number of COVID-19 deaths after peak mortality may be 2-3 times larger than the total number of deaths up to the peak. Our model has important policy implications for countries currently debating how to ease social distancing measures.


title: Isolamento social e o aumento da violência doméstica: o que isso nos revela?/ The increase in domestic violence during the social isolation: what does it reveals?

text: RESUMO: O isolamento social imposto pela pandemia da COVID-19 traz à tona, de forma potencializada, alguns indicadores preocupantes sobre a violência doméstica e a violência familiar contra a mulher. As organizações voltadas ao enfrentamento da violência doméstica já observaram aumento da violência doméstica por causa da coexistência forçada, do estresse econômico e de temores sobre o coronavírus. O artigo busca estabelecer algumas relações entre o isolamento social durante a pandemia da COVID-19 e o aumento da violência contra as mulheres, levando em conta o contexto de uma sociedade patriarcal. Foram analisados dados, ainda incipientes, publicados pela imprensa de diversos países, bem como relatórios de organizações internacionais e organizações direcionadas ao enfrentamento da violência doméstica. Paralelamente, fez-se uma breve revisão de literatura com autores que discutem o papel social da mulher na sociedade.


State of the globe: The trials and tribulations of the COVID-19 pandemic: Separated but together, telemedicine revolution, frontline struggle against 'Silent Hypoxia,' the relentless search for novel therapeutics and vaccines, and the daunting prospect of 'COVIFLU'


title: Clinical evaluation of IFN beta1b in COVID-19 pneumonia: a retrospective study

text: Background COVID-19 pneumonia is associated with significant mortality and has no approved antiviral therapy. Interferon beta1 has shown in vitro studies a potent inhibition of SARS-CoV and MERS-CoV. In an in vitro study, SARS-CoV-2 had more sensitivity to IFN-I pretreatment that SARS-CoV. A combination of IFN beta1b administered subcutaneously with other antiviral treatments has been recommended in several guidelines. However, clinical trial results for the treatment of COVID-19 are pending. We aimed to assess the efficiency of IFN beta1b in COVID19 comparing the in-hospital mortality between patients who received IFN beta1b and patients did not receive. Methods In this retrospective cohort study, we included hospitalized adults with COVID-19 between February 23th and April 4th, 2020, at the Central Defense Hospital (Madrid, Spain). Subcutaneous interferon beta-1b was recommended in moderate-severe pneumonia. The primary endpoint was in-hospital mortality. Univariate and multivariate analysis was performed to identify variables associated with in-hospital mortality. Findings We analyzed 256 patients (106 patients in interferon group and 150 patients in control group). At admission, patients who did not receive interferon beta1b presented a greater number of comorbidities. The overall mortality rate was 24.6% (63/256). Twenty-two patients (20.8%) in the interferon group died and 41 (27.3%) in the control group (p=0.229). In the multivariate analysis, the predictors of in-hospital mortality were age, severity of clinical picture at admission and hydroxychloroquine treatment. Interpretation In hospitalized patients with COVID-19, interferon beta1b treatment was not associated to decrease in-hospital mortality. Further assessment of the earlier administration of this drug in randomized trials is recommended.


title: A Novel Method for the Estimation of a Dynamic Effective Reproduction Number (Dynamic-R) in the CoViD-19 Outbreak

text: The CoViD-19 outbreak has escalated to a pandemic in the last few weeks, with no signs of stopping. Pharmaceutical solutions based upon virologic studies, at this point, remain inconclusive. In contrast, this paper looks towards epidemiological models during this phase of viral growth, in particular, by providing a responsive, timely model of the R value based on the previous few days' results. Such an R value, although bearing less statistical precision due to limited sampling, could allow R to become a more effective, responsive standalone measure of infectious transmission. It demonstrates that the R value can be used as a dynamic, time-dependent indicator without the use of curve-fitting, and also estimates the most recent R-value of the CoViD-19 outbreak to be about 4.29, based on the data from the previous 3 days.


title: Heterogeneity is essential for contact tracing

text: Background: The COVID-19 pandemic is most often modelled by well-mixed models, sometimes stratified by age and work. People are, however, different from one another in terms of interaction frequency as well as in formation of social groups. This contact heterogeneity especially challenges models of contact tracing (CT), but also predictions of epidemic severity generally. We explore how heterogeneity affects CT effectiveness and overall epidemic severity, using a real-world contact network. Methods: Utilizing smartphone proximity data from Danish university students, we simulate the spread of COVID-19 on a network with realistic contact structure. Two modes of network homogenization are implemented to probe effects of heterogeneity. We then simulate a CT scheme on the network and explore the impact of heterogeneity, testing probability and contact threshold for quarantining. Results: Measuring contact heterogeneity, we find an exponential distribution which persists on a timescale of several weeks. Comparing the true network to edge-swapped and randomized versions, we find that heterogeneity decreases the severity of COVID-19 in general, and that it drastically improves CT. Conclusions: To capture heterogeneity, it is necessary to reconsider disease transmission models. Our findings show that heterogeneity is essential for CT, and that CT is effective even if only the most frequent contacts can be tracked down. We find that contact heterogeneity impedes the spread of COVID-19 in comparison with well-mixed networks. In perspective, this means that fitting traditional SEIR models to epidemic data is likely to overestimate the severity.


title: Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor

text: SARS-CoV-2 is a once-in-a-century pandemic, having emerged suddenly as a highly infectious viral pathogen. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus isolated from bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor binding domain – or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and molecular dynamics simulations to examine the Spike-RBD’s functional evolution, finding to our surprise that it has likely possessed high affinity for human cell targets since at least 2013.


docid: ktwazcrd

title: Hydroxychloroquine plus azithromycin: a potential interest in reducing in-hospital morbidity due to COVID-19 pneumonia (HI-ZY-COVID)?

text: Introduction: Hydroxychloroquine (HCQ) with or without azithromycin is currently still debated as a potential treatment for the COVID-19 epidemic. Some studies showed discrepant results. However, timing for the treatment initiation and its setting (in-hospital or out-patient) are not consistent across studies. Methods: Monocentric retrospective study conducted from 2th March to 17th April 2020, in adults hospitalized in a tertiary hospital for COVID-19. Patients characteristics were compared between groups depending on the therapy received (HCQ/azithromycin taken [≥] 48 hours or other treatment). Outcomes were evaluated from admission, by the need for intensive care unit (ICU) support and/or death. Univariate analyses were performed using non-parametric tests and confirmed by a multiple logistic regression using Pearson correlation test. Results: Among 132 patients admitted for COVID-19 in the medicine ward, 45 received HCQ/azithromycin [≥] 48 hours, with a favorable outcome in 91.1% of cases (OR=6.2, p=0.002) versus others regimen (n=87). Groups were comparable at the baseline in terms of age, sex, comorbidities, extend in thoracic imaging, and severity. Among patients that required to be transferred to ICU (n=27) (for mechanical ventilation), median delay for transfer was 2 days (IQR 1-3). We report only 1 patient that presented an adverse event (a prolonged QT interval on EKG) that required to discontinue HCQ. Conclusion: The present study suggests a potential interest of the combination therapy using HCQ/azithromycin for the treatment of COVID-19 in in-hospital patients.


docid: mvsnybbo

title: A Randomized, Single-blind, Group sequential, Active-controlled Study to evaluate the clinical efficacy and safety of Î±-Lipoic acid for critically ill patients with coronavirus disease 2019(COVID-19)

text: Object: To evaluate the clinical efficacy and safety of -Lipoic acid (ALA) for critically ill patients with coronavirus disease 2019 (COVID-19). Methods: A randomized, single-blind, group sequential, active-controlled trial was performed at JinYinTan Hospital, Wuhan, China. Between February 2020 and March 2020, 17 patients with critically ill COVID-19 were enrolled in our study. Eligible patients were randomly assigned in a 1:1 ratio to receive either ALA (1200 mg/d, intravenous infusion) once daily plus standard care or standard care plus equal volume saline infusion (placebo) for 7 days. All patients were monitored within the 7 days therapy and followed up to day 30 after therapy. The primary outcome of this study was the Sequential Organ Failure Estimate (SOFA) score, and the secondary outcome was the all-cause mortality within 30 days. Result: Nine patients were randomized to placebo group and 8 patients were randomized to ALA group. SOFA score was similar at baseline, increased from 4.3 to 6.0 in the placebo group and increased from 3.8 to 4.0 in the ALA group (P=0.36) after 7 days. The 30-day all-cause mortality tended to be lower in the ALA group (3/8, 37.5%) compared to that in the placebo group (7/9, 77.8%, P=0.09). Conclusion: In our study, ALA use is associated with lower SOFA score increase and lower 30-day all-cause mortality as compared with the placebo group. Although the mortality rate was two-folds higher in placebo group than in ALA group, only borderline statistical difference was evidenced due to the limited patient number. Future studies with larger patient cohort are warranted to validate the role of ALA in critically ill patients with COVID-19. Keywords: Pneumonia; COVID-19; SARS-CoV-2 ; -Lipoic acid


title: Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19

text: We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. Although there was moderate negative correlation, the effect cannot be separated from that of Gross Domestic Product per capita (GDP), which may well be related to the strict compliance to social distancing. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller.


title: Now casting and Forecasting of COVID-19 outbreak in the National Capital Region of Delhi

text: Objectives: The study aimed to estimate the disease burden due to COVID-19 in the scenarios of unchecked spread and with various public health interventions in New Delhi. Methods: We adopted Susceptible, Exposed, Infected and Recovered (SEIR) model to estimate the course of COVID-19 outbreak in Delhi population and effect of public health intervention on the pandemic. We first estimated the basic reproductive rate (R0) based on the evidence from Wuhan, then ran the model considering no intervention implemented, followed by case isolation, social distancing, and lockdown, each implemented in isolation and in combinations to estimate the number of cases. Markov model was used to estimate the number of cases in various clinical scenarios of the disease. Sensitivity analysis conducted to estimate the effect of asymptomatic cases on case based interventions. Results: Estimated R0 in Delhi population was 6.18 (range 4.15 to 12.2). Effective reproductive rate (Rt) was least for case isolation (3.5). Lockdown showed highest reduction (28%) in number of prevalent cases on peak day and 22% reduction in patients in need of intensive care unit (ICU). Case isolation and lockdown together resulted in 50% reduction in number of prevalent cases and 42% reduction in patients in need of ICU care. Sensitivity analysis showed that the effect of case isolation was inversely proportionate to the proportion of asymptomatic (hidden) cases. Conclusions: Interventions should be implemented in combinations of individual and community level interventions to gain better outcome. Identifying and isolation of all cases as early as possible is important to flatten the pandemic curve.


title: Coronavirus (COVID-19) infection in children at a specialist centre: outcome and implications of underlying high-risk comorbidities in a paediatric population

text: Background: There is evolving evidence of significant differences in severity and outcomes of coronavirus disease 2019 (COVID-19) in children compared to adults. Underlying medical conditions associated with increased risk of severe disease are based on adult data, but have been applied across all ages resulting in large numbers of families undertaking social shielding (vulnerable group). We conducted a retrospective analysis of children with suspected COVID-19 at a Specialist Childrens Hospital to determine outcomes based on COVID-19 testing status and underlying health vulnerabilities. Methods: Routine clinical data were extracted retrospectively from the Institutions Electronic Health Record system and Digital Research Environment for patients with suspected and confirmed COVID-19 diagnoses. Data were compared between Sars-CoV-2 positive and negative patients (CoVPos / CoVNeg respectively), and in relation to presence of underlying health vulnerabilities based on Public Health England guidance. Findings: Between 1st March and 15th May 2020, 166 children (<18 years of age) presented to a specialist childrens hospital with clinical features of possible COVID-19 infection. 65 patients (39.2%) tested positive for SARS-CoV-2 virus. CoVPos patients were older (median 9 [0.9-14] years vs median 1 [0.1-5.7.5] years respectively, p<0.001). There was a significantly reduced proportion of vulnerable cases (47.7% vs 72.3%, p=0.002), but no difference in proportion of vulnerable patients requiring ventilation (61% vs 64.3%, p = 0.84) between CoVPos and CoVNeg groups. However, a significantly lower proportion of CoVPos patients required mechanical ventilation support compared to CoVNeg patients (27.7 vs 57.4%, p<0.001). Mortality was not significantly different between CoVPos and CoVNeg groups (1.5 vs 4% respectively, p=0.67) although there were no direct COVID-19 related deaths in this highly preselected paediatric population. Interpretation: COVID-19 infection may be associated with severe disease in childhood presenting to a specialist hospital, but does not appear significantly different in severity to other causes of similar clinical presentations. In children presenting with pre-existing COVID-19 vulnerable medical conditions at a specialist centre, there does not appear to be significantly increased risk of either contracting COVID-19 or severe complications, apart from those undergoing chemotherapy, who are over-represented.


title: Trust, threats, and consequences of the COVID-19 pandemic in Norway and Sweden: A comparative survey

text: Objectives: Norway and Sweden, two neighboring countries with similar populations, health care systems and socioeconomics, have reacted differently to the COVID-19 pandemic. Norway closed all kindergartens, schools and universities, and banned sports and cultural activities, while Sweden kept most institutions and trainings facilities open. We aimed to compare peoples' attitudes towards authorities and control measures, and effects on life in Norway and Sweden. Design: Anonymous web-based surveys for individuals age 15 or older distributed through Facebook using the snowball method. Setting: Norway and Sweden, mid-March to mid-April, 2020. Participants: Altogether, 3,508 individuals participated in the survey; 3000 in Norway and 508 in Sweden. 79% of the participants were women, 60% of the Norwegians and 47% of the Swedes were between 30-49 years, and around 45% of the participants in both countries had more than 4 years of higher education. Outcome measures: Perceived threat of the pandemic, views on infection control measures, and impact on daily life. We performed descriptive analyses of the responses and compared the two countries. Results: People had high trust in the health services in both countries, but differed in the degree of trust in their government (17% had high trust in Norway and 37% in Sweden). More Norwegians than Swedes agreed that school closure was a good measure (66% Norway and 18% in Sweden), and that countries with open schools were irresponsible (65% in Norway and 23% in Sweden). About the same amount responded that COVID-19 was a large to very large threat to the population (53% in Norway and 58% in Sweden), whereas more Norwegians than Swedes responded that the threat from repercussions of the mitigation measures were large or very large (71% in Norway and 56% in Sweden). Compliance with infection preventive measures was high and similar in the two countries (more than 98%). In Norway, 69% lived a more sedentary life during the pandemic versus 50% in Sweden; and Norwegians reported they ate more than Swedes (44% in Norway and 33% in Sweden). Conclusion: Sweden, with less restrictive measures against the COVID-19 pandemic, had a higher level of trust in the authorities, while Norwegians reported a more negative lifestyle during the pandemic. The level of trust in the health care system and self-reported compliance with preventive measures was high in both countries.


title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2

text: The recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.


docid: bbumotlt

title: Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 687 Million Compounds

text: The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health with almost 90000 people infected and thousands of fatalities To conquer viral infections, the inhibition of proteases essential for proteolytic processing of viral polyproteins is a conventional therapeutic strategy To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 despite its close relation to the SARS-CoV-1 virus that caused a similar epidemic in 2003 Thus, there remains an urgent need for the development of specific antiviral therapeutics to conquer SARS-CoV-2 In order to find novel inhibitors, we computationally screened a compound library of over 687 million compounds for binding at the recently solved crystal structure of the main protease of SARS-CoV-2 A screening of such a vast chemical space for SARS-CoV-2 protease inhibitors has not been reported before After shape screening, two docking protocols were applied followed by the determination of pharmacokinetically relevant molecular descriptors to narrow down the initial hits Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies After evaluation of off-target binding, we report a list of 11 drug-like compounds with improved binding free energy to the target protease in contrast to the cocrystallized peptidomimetic lead compound that suffers from poor pharmacokinetic properties Furthermore, we identified one potent binder with comparable properties from the natural compound library


title: Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract

text: COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world and was declared a pandemic by the World Health Organization, thus leading to a rapid surge in the efforts to understand the mechanisms of transmission, methods of prevention, and potential therapies. While COVID-19 frequently manifests as a respiratory infection,1 there is evidence for infection of the gastrointestinal (GI) tract1–4 with documented viral RNA shedding in the stool of infected patients.2,4 In this study, we aimed to investigate the expression of ACE2 and TMPRSS2, which are required for SARS-CoV-2 entry into mammalian cells,5 from single-cell RNA sequencing (scRNA-seq) datasets of five different parts of the GI tract: esophagus, stomach, pancreas, small intestine, and colon/rectum.


title: Age, gender and COVID-19 infections

text: Data for ten European countries which provide detailed distribution of COVID-19 cases by sex and age show that among people of working age, women diagnosed with COVID-19 substantially outnumber infected men. This pattern reverses around retirement: infection rates among women fall at age 60-69, resulting in a cross-over with infection rates among men. The relative disadvantage of women peaks at ages 20-29, whereas the male disadvantage in infection rates peaks at ages 70-79. The elevated infection rates among women of working age are likely tied to their higher share in health- and care-related occupations. Our examination also suggests a link between women's employment profiles and infection rates in prime working ages. The same factors that determine women's higher life expectancy account for their lower fatality and higher male disadvantage at older ages.


title: The transmission of SARS-CoV-2 is likely comodulated by temperature and by relative humidity

text: Quantifying the role of temperature and humidity on the transmission of SARS-CoV-2 has been confounded by a lack of controlled experiments, the sudden rise in detection rates, and changing weather patterns. In this paper we focus our analysis on data from Colombia, which presents unique economic, demographic and geological characteristics that favor the study of temperature and humidity upon SARS-CoV-2 transmission: the weather varies dramatically across five natural regions (from the Caribbean coast and the Amazon rainforest to the Andean mountains), there are no pronounced seasons, there is a central port of entry, the use of public transportation dominates inter- and intracity travel, and indoor climate control is rare. While only controlled experiments can precisely quantify the role of temperature and humidity upon SARS-CoV-2 transmission, we observe significant attenuation of transmission in climates with sustained daily maximum temperatures above 30 degrees Celsius and simultaneous mean relative humidity below 78%. We hypothesize that temperature and relative humidity comodulate the infectivity of SARS-CoV-2 within respiratory droplets.


title: Summer vacation and COVID-19: effects of metropolitan people going to summer provinces

text: Many countries are now investigating what the effects of summer vacation might be on the COVID-19 pandemic. Here one particular such question is addressed: what will happen if large numbers of metropolitan people visit a less populated province during the summer vacation? By means of a simple epidemic model, allowing for both short and long-term visitors to the province, it is studied which features are most influential in determining if such summer movements will result in large number of infections among the province population. The method is applied to the island of Gotland off the South East coast of Sweden. It is shown that the amount of mixing between the metropolitan and province groups and the fraction of metropolitan people being infectious upon arrival are most influential. Consequently, minimizing events gathering both the province and metropolitan groups and/or reducing the number of short-term visitors could substantially decrease spreading, as could measures to lower the fraction initially infectious upon arrival.


title: Why do dozens of diseases wax and wane with the seasons—and will COVID-19?

text: On a December afternoon, 13 days before the winter solstice, six men and women checked into the Surrey Clinical Research Facility, part of the University of Surrey in the United Kingdom After having their noses swabbed to check for 16 different respiratory viruses, they walked into their own temperature-regulated rooms and, for 24 hours, each person stayed in a semirecumbent position in dim light Nurses placed a cannula into a vein of each person’s arm, allowing easy sampling of blood that flowed through a tube to portals in the wall The six subjects could press buzzers for bathroom breaks, where the stool and urine were collected, but otherwise, they were alone in the near-dark None of these people were sick And although the shortest day of the year was approaching, their ritual had nothing to do with pagan rites, Yuletide traditions, or the annual hippie gathering at nearby Stonehenge to celebrate the rebirth of the Sun Instead, they were paid volunteers in a study led by infectious disease ecologist Micaela Martinez of Columbia University to investigate a phenomenon recognized 2500 years ago by Hippocrates and Thucydides: Many infectious diseases are more common during specific seasons “It’s a very old question, but it’s not very well studied,” Martinez says


title: Molecular Diagnosis of Severe Acute Respiratory Syndrome : The State of the Art

text: Severe acute respiratory syndrome (SARS) first appeared in Guangdong Province, China, in November 2002. Although virus isolation and serology were useful early in the SARS outbreak for diagnosing new cases, these tests are not generally useful because virus culture requires a BSL-3 laboratory and seroconversion is often delayed until 2 to 3 weeks after infection. The first qualitative reverse transcriptase-polymerase chain reaction tests for SARS-coronavirus (CoV) were sensitive and capable of detecting 1 to 10 genome equivalents. These assays were quickly supplemented with quantitative real-time assays that helped elucidate the natural history of SARS, particularly the initial presence of low viral loads in the upper respiratory tract and high viral loads in the lower respiratory tract. The unique natural history of SARS-CoV infection dictates the testing of both respiratory and nonrespiratory specimens, the testing of multiple specimens from the same patient, and sending out positives to be confirmed by a reference laboratory. Commercially available reverse transcriptase-polymerase chain reaction tests for SARS have recently appeared; however, meaningful evaluations of these assays have not yet been performed and their true performance has not been determined. These and other issues related to diagnosis of SARS-CoV infection are discussed in this review.


title: Ivermectin as a potential COVID-19 treatment from the pharmacokinetic point of view

text: The broad-spectrum antiparasitic agent ivermectin has been very recently found to inhibit SARS-CoV-2 in vitro and proposed as a candidate for drug repurposing in COVID-19. In the present report the in vitro antiviral activity end-points are analyzed from the pharmacokinetic perspective. The available pharmacokinetic data from clinically relevant and excessive dosing studies indicate that the SARS-CoV-2 inhibitory concentrations are not likely to be attainable in humans.