title: High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19

text: Considering the current status of the SARS-CoV-2 pandemic, sequence variations and possibly structural changes in the rapidly evolving SARS-CoV-2 is highly expected in the coming months. The SARS-CoV-2 spike (S) protein is responsible for mediating viral attachment and fusion with cell membranes. Mutations in the receptor-binding domain (RBD) of the S-protein occur at the most variable part of the SARS-CoV-2 genome, and specific sites of S-protein have undergone positive selection impacting the viral pathogenicity. In the present work, we used high-throughput computation to design 100,000 mutants in RBD interfacial residues and identify novel affinity-enhancing and affinity-weakening mutations. Our data suggest that SARS-CoV-2 can establish a higher rate of infectivity and pathogenesis when it acquires combinatorial mutations at the interfacial residues in RBD. Mapping of the mutational landscape of the interaction site suggests that a few of these residues are the hot-spot residues with a very high tendency to undergo positive selection. Knowledge of the affinity-enhancing mutations may guide the identification of potential cold-spots for this mutation as targets for developing a possible therapeutic strategy instead of hot-spots, and vice versa. Understanding of the molecular interactions between the virus and host protein presents a detailed systems view of viral infection mechanisms. The applications of the present research can be explored in multiple antiviral strategies, including monoclonal antibody therapy, vaccine design, and importantly in understanding the clinical pathogenesis of the virus itself. Our work presents research directions for the exploitation of non-conventional solutions for COVID-19.


title: #lockdown: Network-Enhanced Emotional Profiling in the Time of COVID-19

text: The COVID-19 pandemic forced countries all over the world to take unprecedented measures, like nationwide lockdowns To adequately understand the emotional and social repercussions, a large-scale reconstruction of how people perceived these unexpected events is necessary but currently missing We address this gap through social media by introducing MERCURIAL (Multi-layer Co-occurrence Networks for Emotional Profiling), a framework which exploits linguistic networks of words and hashtags to reconstruct social discourse describing real-world events We use MERCURIAL to analyse 101,767 tweets from Italy, the first country to react to the COVID-19 threat with a nationwide lockdown The data were collected between the 11th and 17th March, immediately after the announcement of the Italian lockdown and the WHO declaring COVID-19 a pandemic Our analysis provides unique insights into the psychological burden of this crisis, focussing on—(i) the Italian official campaign for self-quarantine (#iorestoacasa), (ii) national lockdown (#italylockdown), and (iii) social denounce (#sciacalli) Our exploration unveils the emergence of complex emotional profiles, where anger and fear (towards political debates and socio-economic repercussions) coexisted with trust, solidarity, and hope (related to the institutions and local communities) We discuss our findings in relation to mental well-being issues and coping mechanisms, like instigation to violence, grieving, and solidarity We argue that our framework represents an innovative thermometer of emotional status, a powerful tool for policy makers to quickly gauge feelings in massive audiences and devise appropriate responses based on cognitive data


title: Early Awake Prone and Lateral Position in Non-intubated Severe and Critical Patients with COVID-19 in Wuhan: A Respective Cohort Study

text: Background Previous studies suggest applying prone position (PP) and lateral position (LP) in patients with severe acute respiratory distress syndrome (ARDS) for their efficacy in improving oxygenation and lung recruitment.This paper aims to share clinical experiences and outcome of using PP and LP in combination with oxygen therapy (OT) and Non-invasive ventilation (NIV) in severe and critical patients with COVID-19. Methods Clinical data of 48 severe and critical patients have been retrieved from medical records and reviewed. The primary outcome is the survival rate. Secondary outcome is the rate of patients requiring intubation. Results In total, 25 patients were finally included in the study.The mean respiratory rate of all 25 patients decreased from 28.4 breaths/min to 21.3 breaths/min. CT results showed increase in lung recruitment. All patients tolerated PP and LP well. No deterioration or severe adverse events associated with PP and LP occurred. All patients recovered and survived without intubation. Follow-up to date showed that all patients have been discharged except one with mild symptoms and positive RNA test. Conclusion: Clinical outcomes of early application of PP and LP in combination with OT and NIV in severe and critical patients with COVID-19 indicated well tolerance of the therapy and resulted in improving patients' oxygenation in a safe and effective manner. Therefore, this strategy can be explored as an early intervention in managing patients in early stage of disease development under the context of pandemic and limited medical resources.


Analysis of Possible Intermediate Hosts of the New Coronavirus SARS-CoV-2


title: COVID-19 y enfermedad cardiovascular

text: In December 2019, in Wuhan in the province of Hubei in China, there was a report on a group of 27 patients with a pneumonia of unknown origin, linked to exposure in a market with shellfish, fish, and live animals. In January 2020, a new strain of coronavirus (SARS-CoV-2) was isolated in these patients. The disease caused by this virus has been given the name of COVID-19. During the initial stages of the pandemic, and given the scarcity of studies published about this, it was believed that this coronavirus only caused respiratory symptoms. However, as the number of patients increased, it was observed that cardiovascular disease had a fundamental role in the development and prognosis of the infection. The most important risk factors associated with mortality are age and the presence of comorbidities, particularly cardiovascular ones. The increase in the levels of troponin, natriuretic peptides, and D-dimer are of prognostic values in patients with an infection due to SARS-CoV-2. Patients with COVID-19 have an increased risk of acute myocardial infarction, myocarditis, heart failure, shock, arrhythmias, and sudden death, in relation to the systematic response to the virus and to the treatments needed in the acute phase. A review is presented in this article of the cardiovascular involvement due to SARS-CoV-2 (COVID-19).


title: Ethnicity and risk of death in patients hospitalised for COVID-19 infection: an observational cohort study in an urban catchment area

text: Objectives. To determine if specific ethnic groups are at higher risk of mortality from COVID19 infection. Design. Retrospective cohort study Setting. University Hospitals Birmingham NHS Foundation Trust (UHB) in Birmingham, UK Participants. Patients with confirmed SARS CoV 2 infection requiring admission to UHB between 10th March 2020 and 17th April 2020 Exposure. Ethnicity Main outcome measures. Standardised Admission Ratio (SAR) and Standardised Mortality Ratio (SMR) for each ethnicity was calculated using observed sex specific age distributions of COVID19 admissions/deaths and 2011 census data for Birmingham/Solihull. Hazard Ratio (aHR) for mortality was estimated for each ethnic group with white population as reference group, using Cox proportional hazards model adjusting for age, sex, social deprivation and co-morbidities, and propensity score matching. Results. 2217 patients admitted to UHB with a proven diagnosis of COVID19 were included. 58.2% were male, 69.5% White and the majority (80.2%) had co morbidities. 18.5% were of South Asian ethnicity, and these patients were more likely to be younger (median age 61 years vs.77 years), have no co morbidities (27.8% vs. 16.6%) but a higher prevalence of diabetes mellitus (48.0% vs 28.2%) than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted. South Asian patients were also more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.66 (95%CI 1.32 to 2.10)) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, (Hazard ratio 1.68 (1.33 to 2.13), using the same factors but categorising ethnicity into South Asian or not. Conclusions. Current evidence suggests those of South Asian ethnicity may be at risk of worse COVID19 outcomes, further studies need to establish the underlying mechanistic pathways.


title: Analysis and annotation of genome-wide DNA methylation patterns in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips

text: The Infinium Human Methylation450 and Methylation EPIC BeadChips are useful tools for the study of the methylation state of hundreds of thousands of CpG across the human genome at affordable cost. However, in a wide range of experimental settings in particular for studies in infectious or brain-related diseases, human samples cannot be easily obtained. Hence, due to their close developmental, immunological and neurological proximity with humans, non-human primates are used in many research fields of human diseases and for preclinical research. Few studies have used DNA methylation microarrays in simian models. Microarrays designed for the analysis of DNA methylation patterns in the human genome could be useful given the genomic proximity between human and nonhuman primates. However, there is currently information lacking about the specificity and usability of each probe for many nonhuman primate species, including rhesus macaques (Macaca mulatta), originating from Asia, and African green monkeys originating from West-Africa (Chlorocebus sabaeus). Rhesus macaques and African green monkeys are among the major nonhuman primate models utilized in biomedical research. Here, we provide a precise evaluation and re-annotation of the probes of the two microarrays for the analysis of genome-wide DNA methylation patterns in these two Cercopithecidae species. We demonstrate that up to 162,000 of the 450K and 255,000 probes of the EPIC BeadChip can be reliably used in Macaca mulatta or Chlorocebus sabaeus. The annotation files are provided in a format compatible with a variety of preprocessing, normalization and analytical pipelines designed for data analysis from 450K/EPIC arrays, facilitating high-throughput DNA methylation analyses in Macaca mulatta and Chlorocebus sabaeus. They provide the opportunity to the research community to focus their analysis only on those probes identified as reliable. The described analytical workflow leaves the choice to the user to balance coverage versus specificity and can also be applied to other Cercopithecidae species.


title: The contact activation system as a potential therapeutic target in patients with COVID‐19

text: Coronavirus disease 2019 (COVID‐19) is predicted to overwhelm health care capacity in the United States and worldwide, and, as such, interventions that could prevent clinical decompensation and respiratory compromise in infected patients are desperately needed. Excessive cytokine release and activation of coagulation appear to be key drivers of COVID‐19 pneumonia and associated mortality. Contact activation has been linked to pathologic upregulation of both inflammatory mediators and coagulation, and accumulating preclinical and clinical data suggest it to be a rational therapeutic target in patients with COVID‐19. Pharmacologic inhibition of the interaction between coagulation factors XI and XII has been shown to prevent consumptive coagulopathy, pathologic systemic inflammatory response, and mortality in at least 2 types of experimental sepsis. Importantly, inhibition of contact activation also prevented death from Staphylococcus aureus–induced lethal systemic inflammatory response syndrome in nonhuman primates. The contact system is likely dispensable for hemostasis and may not be needed for host immunity, suggesting it to be a reasonably safe target that will not result in immunosuppression or bleeding. As a few drugs targeting contact activation are already in clinical development, immediate clinical trials for their use in patients with COVID‐19 are potentially feasible for the prevention or treatment of respiratory distress.


title: Evidence for a Past Martian Ring from the Orbital Inclination of Deimos

text: We numerically explore the possibility that the large orbital inclination of the martian satellite Deimos originated in an orbital resonance with an ancient inner satellite of Mars more massive than Phobos. We find that Deimos's inclination can be reliably generated by outward evolution of a martian satellite that is about 20 times more massive than Phobos through the 3:1 mean-motion resonance with Deimos at 3.3 Mars radii. This outward migration, in the opposite direction from tidal evolution within the synchronous radius, requires interaction with a past massive ring of Mars. Our results therefore strongly support the cyclic martian ring-satellite hypothesis of Hesselbrock and Minton (2017). Our findings, combined with the model of Hesselbrock and Minton (2017), suggest that the age of the surface of Deimos is about 3.5-4 Gyr, and require Phobos to be significantly younger.


title: The Red Queen’s Crown: an evolutionary arms race between coronaviruses and mammalian species reflected in positive selection of the ACE2 receptor among many species

text: The world is going through a global viral pandemic with devastating effects on human life and socioeconomic activities. This pandemic is the result of a zoonotic coronavirus, Severe Acute Respirsatory Syndrom Coronavirus 2 (SARS-CoV-2) which is believed to have originated in bats and transferred to humans possibly through an intermediate host species (Zhou et al. 2020; Coronaviridae Study Group of the International Committee on Taxonomy of Viruses 2020). The virus attacks host cells by attaching to a cell membrane surface protein receptor called ACE2 (Ge et al. 2013; Zhou et al. 2020). Given the critical role of ACE2 as a binding receptor for a number of coronaviruses, we studied the molecular evolution of ACE2 in a diverse range of mammalian species. Using ACE2 as the target protein, we wanted to specifically test the Red Queen hypothesis (Dawkins and Krebs 1979) where the parasite and host engage in an evolutionary arms race which can result in positive selection of their traits associated to their fitness and survival. Our results clearly show a phylogenetically broad evolutionary response, in the form of positive selection detected at the codon-level in ACE2. We see positive selection occurring at deep branches as well as 13 incidents at the species level. We found the strongest level of positive selection in Tasmanian devil (Sarcophilus harrisii), donkey (Equus asinus), large flying fox (Pteropus vampyrus), Weddell seal (Leptonychotes weddellii), and dog (Canis lupus familiaris). At the codon-level, we found up to 10% of ACE2 codons are impacted by positive selection in the mammalian lineages studied. This phylogenetically broad evolutionary arms race can contribute to the emergence of new strains of coronaviruses in different mammalian lineages with a potential to transfer between species given the common binding receptor ACE2. Our study provides a molecular evolutionary perspective to the current pandemic and sheds light on its evolutionary mechanisms. “Nothing in biology makes sense except in the light of evolution” (Theodosius Dobzhansky)


title: Evaluating the effectiveness of social distancing interventions against COVID-19

text: SARS-CoV-2 has infected over 140,000 people as of March 14, 2020. We use a mathematical model to investigate the effectiveness of social distancing interventions lasting six weeks in a middle-sized city in the US. We explore four social distancing strategies by reducing the contacts of adults over 60 years old, adults over 60 years old and children, all adults (25, 75 or 95% compliance), and everyone in the population. Our results suggest that social distancing interventions can avert cases by 20% and hospitalizations and deaths by 90% even with modest compliance within adults as long as the intervention is kept in place, but the epidemic is set to rebound once the intervention is lifted. Our models suggest that social distancing interventions will buy crucial time but need to occur in conjunction with testing and contact tracing of all suspected cases to mitigate transmission of SARS-CoV-2.


title: Hospitals find ways to disinfect N95 face masks

text: In March, health-care facilities in the US began preparing for a predicted avalanche of cases of COVID-19, the respiratory disease caused by the novel coronavirus Hospital officials scrutinized their supplies of items like gloves and face masks and predicted a shortage Many pieces of personal protective equipment (PPE), like N95 masks, the tightly fitted respirators designed to filter at least 95% of small infectious particles, are cheap and readily available from distributors Under normal circumstances, hospitals have little need to keep large supplies of PPE on hand But 2 months ago, in the midst of a global pandemic, formerly reliable distribution channels had dried up Leaders at OhioHealth, which operates 12 hospitals in central Ohio, estimated that their existing supplies of the masks could be expended in a matter of weeks if they could not secure new shipments, according to Chris Clinton, who oversees the network’s supply chain operations


title: Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses

text: Within four months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in the ORF1 of the virus isolated from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of nonsynonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerated sites towards uracil residues is seen in ORF1 of all the studied coronaviruses. A more substantial mutational U pressure is observed in ORF1a than in ORF1b owing to the translation of ORF1ab via programmed ribosomal frameshifting. Unlike other nucleotide mutations, mutational U pressure caused by cytosine deamination, mostly occurring in the RNA-plus strand, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the direction of mutational pressure during translation of viral RNA-plus strands has implications for vaccine and nucleoside analogue development for treating covid-19 and other coronavirus infections.


title: Manufacturing Process Design of a Microchannel Solar Receiver using Electrically-Assisted Embossing

text: Abstract Manufacturing process design (MPD) represents a design-oriented approach to manufacturing engineering. In this paper, Haynes 230 (H230), a solid solution strengthened Ni-based superalloy, was chosen to meet the material requirements of a microchannel solar receiver (MSR) needed to increase the efficiency and reduce the cost of solar thermal power generation. A MPD was developed to enable the cost-effective production of the MSR. This MPD revealed the need to increase the height-to-diameter aspect ratio of posts using electrically-assisted (EA) forming to reduce the mass and cost of MSR fluidic interconnects. Preliminary efforts to validate the MPD through fabrication of sub-scale MSR test articles resulted in several process failures. Among them, die and platen failure, accelerated creep during bonding due to grain refinement as a result of forming. This resulted in poorly formed channels in the final bonded devices. Suggestions for EA forming die material and adjusted forming setup geometry to reduce feature variability are discussed. Results suggest the need to perform solutionizing heat treatments of H230 after EA forming, prior to diffusion bonding, in order to meet the requirements of the MSR. Suggestions for EA forming die material and adjusted forming setup geometry to reduce feature variability are discussed


title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation

text: There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. We evaluated specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison SARS-CoV-2 S1/S2 IgG (research use only), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] in comparison with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel included sera from PCR confirmed COVID-19 patients, and the negative panel included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies with median of 11 days (range 3-51) after onset of symptoms. The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS-CoV-2 serodiagnostics.


title: A Mathematical prediction of the time evolution of the Covid-19 pandemic in some countries of the European Union using Monte Carlo simulations

text: In this paper we study the statistical evolution in time of the Covid-19 pandemic in Spain, Italy, Germany, Belgium, The Netherlands, Austria and Portugal, i.e., the countries of the European Union (EU) that have a number of positive cases higher than 12 thousand at April 7, 2020. France is the third country of the EU for number of cases but a jump in the data on April 3, 2020 does not allow, at least for the moment, to have a reliable prediction curve. The analysis is based on the use of a function of the type of a Gauss Error Function, with four parameters, as a Cumulative Distribution Function (CDF). A Monte Carlo analysis is used to estimate the uncertainty. The approach used in this paper is mathematical and statistical and thus does not explicitly consider a number of relevant issues, including number of nasopharyngeal swabs, mitigation measures, social distancing, virologic, epidemiological and models of contamination diffusion.


title: Occupation and risk of COVID-19: prospective cohort study of 120,621 UK Biobank participants

text: Objectives: To investigate COVID-19 risk by occupational group. Design: Prospective study of linked population-based and administrative data. Setting: UK Biobank data linked to SARS-CoV-2 test results from Public Health England from 16 March to 3 May 2020. Participants: 120,621 UK Biobank participants who were employed or self-employed at baseline (2006-2010) and were 65 years or younger in March 2020. Overall, 29% (n=37,890) were employed in essential occupational groups, which included healthcare workers, social and education workers, and other essential workers comprising of police and protective service, food, and transport workers. Poisson regression models, adjusted for baseline sociodemographic, work-related, health, and lifestyle-related risk factors were used to assess risk ratios (RRs) of testing positive in hospital by occupational group as reported at baseline relative to non-essential workers. Main outcome measures: Positive SARS-CoV-2 test within a hospital setting (i.e. as an inpatient or in an Emergency Department). Results: 817 participants were tested for SARS-CoV-2 and of these, 206 (0.2%) individuals had a positive test in a hospital setting. Relative to non-essential workers, healthcare workers (RR 7.59, 95% CI: 5.43 to 10.62) and social and education workers (RR 2.17, 95% CI: 1.37 to 3.46) had a higher risk of testing positive for SARS-CoV-2 in hospital. Using more detailed groupings, medical support staff (RR 8.57, 95% CI: 4.35 to 16.87) and social care workers (RR 2.99, 95% CI: 1.71 to 5.24) had highest risk within the healthcare worker and social and education worker categories, respectively. In general, adjustment for covariates did not substantially change the pattern of occupational differences in risk. Conclusions: Essential workers in health and social care have a higher risk of severe SARS-CoV-2 infection. These findings underscore the need for national and organisational policies and practices that protect and support workers with elevated risk of SARS-CoV-2 infection.


title: First 12 patients with coronavirus disease 2019 (COVID-19) in the United States

text: Introduction: More than 93,000 cases of coronavirus disease (COVID-19) have been reported worldwide. We describe the epidemiology, clinical course, and virologic characteristics of the first 12 U.S. patients with COVID-19. Methods: We collected demographic, exposure, and clinical information from 12 patients confirmed by CDC during January 20-February 5, 2020 to have COVID-19. Respiratory, stool, serum, and urine specimens were submitted for SARS-CoV-2 rRT-PCR testing, virus culture, and whole genome sequencing. Results: Among the 12 patients, median age was 53 years (range: 21-68); 8 were male, 10 had traveled to China, and two were contacts of patients in this series. Commonly reported signs and symptoms at illness onset were fever (n=7) and cough (n=8). Seven patients were hospitalized with radiographic evidence of pneumonia and demonstrated clinical or laboratory signs of worsening during the second week of illness. Three were treated with the investigational antiviral remdesivir. All patients had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset, with lowest rRT-PCR Ct values often detected in the first week. SARS-CoV-2 RNA was detected after reported symptom resolution in seven patients. SARS-CoV-2 was cultured from respiratory specimens, and SARS-CoV-2 RNA was detected in stool from 7/10 patients. Conclusions: In 12 patients with mild to moderately severe illness, SARS-CoV-2 RNA and viable virus were detected early, and prolonged RNA detection suggests the window for diagnosis is long. Hospitalized patients showed signs of worsening in the second week after illness onset.


title: Evidence Supports a Causal Model for Vitamin D in COVID-19 Outcomes

text: We analyse global data for COVID-19 deaths and recoveries and show that outbreak severity displays a striking latitude relationship with a northern hemisphere bias. Transmission rates can be explained by seasonal weather conditions, but this does not account for observed variations in fatality rates. Many factors point to Vitamin D as a candidate explanation but historical controversy surrounding Vitamin D studies and the lack of a coherent framework for causal inference has hampered acceptance of this explanation despite a wealth of evidence in its favour. We analyse global COVID-19 data using Causal Inference, constructing two contrasting directed acyclic graph (DAG) models, one causal and one acausal, and set out clearly multiple predictions made by each model. We show that observed data strongly match predictions made by the causal model but largely contradict those of the acausal model. We explore historic evidence further supporting the causal model. We review biochemical mechanisms that may explain the various ways in which vitamin D acts. We detail the mechanisms by which the SARS-Cov-2 virus causes the disease and known pathways that involve Vitamin D and show how these both protect against viral infection, as well as ameliorating disease symptoms in COVID-19 and other respiratory diseases. We examine the factors that govern confidence in causal inference models and conclude that a high level of confidence in a causal beneficial role for Vitamin D is justified.


title: Survey of WU and KI polyomaviruses, coronaviruses, respiratory syncytial virus and parechovirus in children under 5 years of age in Tehran, Iran

text: Background and Objectives: Severe acute respiratory infections (SARI) remain an important cause for childhood morbidity worldwide. We designed a research with the objective of finding the frequency of respiratory viruses, particularly WU and KI polyomaviruses (WUPyV & KIPyV), human coronaviruses (HCoVs), human respiratory syncytial virus (HRSV) and human parechovirus (HPeV) in hospitalized children who were influenza negative. Materials and Methods: Throat swabs were collected from children younger than 5 years who have been hospitalized for SARI and screened for WUPyV, KIPyV, HCoVs, HRSV and HPeV using Real time PCR. Results: A viral pathogen was identified in 23 (11.16%) of 206 hospitalized children with SARI. The rate of virus detection was considerably greater in infants <12 months (78.2%) than in older children (21.8%). The most frequently detected viruses were HCoVs with 7.76% of positive cases followed by KIPyV (2%) and WUPyV (1.5%). No HPeV and HRSV were detected in this study. Conclusion: This research shown respiratory viruses as causes of childhood acute respiratory infections, while as most of mentioned viruses usually causes mild respiratory diseases, their frequency might be higher in outpatient children. Mean-while as HRSV is really sensitive to inactivation due to environmental situations and its genome maybe degraded, then for future studies, we need to use fresh samples for HRSV detection. These findings addressed a need for more studies on viral respiratory tract infections to help public health.


title: Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?

text: The pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected over 3.8 million people, including pregnant women. To date, no consistent evidence of vertical transmission for SARS-CoV-2 exists. This new coronavirus canonically utilizes the angiotensin-converting enzyme 2 (ACE2) receptor and the serine protease TMPRSS2 for cell entry. Herein, building upon our previous single cell study of the placenta (Pique-Regi, 2019), another study, and new single-cell/nuclei RNA-sequencing data, we investigated the expression of ACE2 and TMPRSS2 throughout pregnancy as well as in third-trimester chorioamniotic membranes. We report that co-transcription of ACE2 and TMPRSS2 is negligible, thus not a likely path of vertical transmission for SARS-CoV-2 at any stage of pregnancy. In contrast, receptors for Zika virus and cytomegalovirus which cause congenital infections are highly expressed by placental cell types. These data suggest that SARS-CoV-2 is unlikely to infect the human placenta through the canonical cell entry mediators; yet, other interacting proteins could still play a role in the viral infection.


title: Infoveillance based on Social Sensors to Analyze the impact of Covid19 in South American Population

text: Infoveillance is an application from Infodemiology field with the aim to monitor public health and create public policies. Social sensor is the people providing thought, ideas through electronic communication channels(i.e. Internet). The actual scenario is related to tackle the covid19 impact over the world, many countries have the infrastructure, scientists to help the growth and countries took actions to decrease the impact. South American countries have a different context about Economy, Health and Research, so Infoveillance can be a useful tool to monitor and improve the decisions and be more strategical. The motivation of this work is analyze the capital of Spanish Speakers Countries in South America using a Text Mining Approach with Twitter as data source. The preliminary results helps to understand what happens two weeks ago and opens the analysis from different perspectives i.e. Economics, Social.


title: COVID‐19 transmission through asymptomatic carriers is a challenge to containment

text: 3 He had radiological ground‐glass lung opacities, and he was RT‐PCR positive for genes encoding the internal RNA‐dependent RNA polymerase and surface spike protein of this novel coronavirus, which were confirmed by Sanger sequencing [ ]vigilant control measures are warranted at this stage of the COVID‐19 epidemic to avoid a resurgence in cases Author Contribution Xingxia Yu: Conceptualization (equal);Data curation (equal);Formal analysis (equal);Investigation (equal);Methodology (equal);Project administration (equal);Resources (equal);Software (equal);Supervision (equal);Validation (equal);Visualization (equal);Writing‐original draft (equal);Writing‐review & editing (equal)


title: No way out? Intention zur Einhaltung von Corona-Ausgangsbeschränkungen im Kontext einer „extended theory of reasoned action“

text: BACKGROUND: In March 2020, it was necessary to impose so-called curfews for several weeks across Germany due to the COVID-19 pandemic. This meant massive restraints for the population. OBJECTIVES: It was to be investigated whether the theory of reasoned action (TORA) is an adequate method for explaining the intention to follow the curfews and to explain whether anticipation of sanctions influences the intention. There are two key questions: (1) is the TORA suitable for explaining the intention to comply with the imposed curfews? and (2) does an extension of TORA by the variable sanction-anticipation influence the intention to obey the imposed curfews? METHODS: Using an online survey, it was investigated the individual’s intention, attitudes and subjective norm to follow the restrictions, and also the anticipation of sanctions for noncompliance using a rating scale (1–7). Multiple linear regression and hierarchical regression analysis were used to clarify key questions. RESULTS: In all, 1269 evaluable records demonstrated that the intention to follow the curfews is high (mean 6.24, standard deviation 1.2) and that this can be elucidated through the attitudes and subjective norm to 67% (p < 0.001). There is no impact of impending sanctions for noncompliance (∆R(2) = 0.002). DISCUSSION: The TORA is suitable for explaining the intention to comply with the curfews. Key political decision-makers should avoid threatening sanctions during speeches to increase compliance but instead emphasize the meaning and benefit of the measures for society and also for the individual’s own social environment in order to positively influence the intended goals.


title: Chaos, Percolation and the Coronavirus Spread: a two-step model.

text: We discuss a two-step model for the rise and decay of the COVID-19. The first stage is well described by the same equation for turbulent flows and chaotic maps: a small number of infected d0 grows exponentially to a saturation value d{infty}. The typical growth time is given by {tau}=1/{lambda}, where {lambda} is the Lyapunov exponent. After a time tcrit determined by social distancing and/or other measures, the spread decreases exponentially as for nuclear decays and non-chaotic maps. A few countries, like China, S. Korea, Italy are in this second stage while other including the USA is near the end of the growth stage. The model predicts 15,000 ({+/-}1,500) casualties for the Lombardy region (Italy) at the end of the spreading around May 10,2020. Without the quarantine, the casualties would have been more than 50,000, hundred days after the start of the epidemics. The data from the 50 US states are of very poor quality because of an extremely late response to the epidemics, resulting unfortunately in a large number of casualties, more than 70,000 on May 6,2020. S. Korea, notwithstanding the high population density (511/km{superscript 2}) and the closeness to China, responded best to the epidemics with 255 deceased as of May 6,2020.


title: Should contact bans be lifted in Germany? A quantitative prediction of its effects

text: Many countries consider the lifting of restrictions of social contacts (RSC). We quantify the effects of RSC for Germany. We initially employ a purely statistical approach to predicting prevalence of COVID19 if RSC were upheld after April 20. We employ these findings and feed them into our theoretical model. We find that the peak of the number of sick individuals would be reached already by mid-April. The number of sick individuals would fall below 1,000 at the beginning of July. When restrictions are lifted completely on April 20, the number of sick should rise quickly again from around April 27. A balance between economic and individual costs of RSC and public health objectives consists in lifting RSC for activities that have high economic benefits but low health costs. In the absence of large-scale representative testing of CoV-2 infections, these activities can most easily be identified if federal states of Germany adopted exit strategies that differ across states.


title: A minimal model for household effects in epidemics

text: Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. We introduce a minimal model that incorporates these household effects in the framework of mean-field theory and numerical simulations. We show that the reproduction number R0 depends on the household size in a surprising way: linearly for relatively small households, and as a square root of size for larger households. We discuss the implications of the findings for the lockdown, test, tracing, and isolation policies.


title: RETRACTED: Synthesis and antimicrobial activity of some new quinazolin-4(3H)-one derivatives

text: This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief because the author has plagiarized in its entirety an article that has already been published in 2008 by Ahmed M. Alafeefy [Pharmaceutical Biology, 2008 Vol. 46 Issue 10–11, pp. 751–756, http://dx.doi.org/10.1080/13880200802315907]. The author was contacted through the Scientific Council of the King Saud University and Saudi Chemical Society and it was decided by the council to withdraw the article due to duplication of content. This article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.


The health of refugees – public health perspectives from crisis to settlement


docid: aadgxxol

title: Clinical Features of Hemodialysis (HD) patients confirmed with Coronavirus Disease 2019 (COVID-19): a Retrospective Case-Control Study

text: Background: Since December 2019, Coronavirus Disease 2019(COVID-19) occurred in wuhan, China, and outbreaked rapidly into a global pandemic. This current poses great challenges to hemodialysis (HD) patients. Objective: To make a comprehensive evaluation and comparison between HD patients confirmed with COVID-19 and the general HD patients. Methods: HD patients confirmed with COVID-19 in Wuhan No.5 Hospital were admitted as confirmed group from Jan 10 to Mar 15, 2020. And HD patients not infected in our dialysis center were chosen as control group. General characteristics, laboratory indicators were retrospectively collected, analyzed and compared. Results: A total of 142 cases were admitted, including 43 cases in confirmed group and 99 in control group. Body mass index (BMI) was slightly lower in confirmed group than that in control group (P=0.011). The proportion of one or less underlying disease in confirmed group(51.16%) was higher than that in control group(14.14%)(P< 0.001), and the proportion of three or more underlying diseases in confirmed group(11.63%) was lower than that in control group(52.53%)(P< 0.001). Patients in confirmed group exhibited significantly lower hemoglobin, lymphocyte count, and lymphocyte percentage, but higher neutrophil percentage, neutrophil-to-lymphocyte ratio (NLR), C-reactive protein, aspartate transaminase, and alkaline phosphatase. There was no significant difference in age, gender, dialysis age, primary disease, the using of ACEI/ARB, platelet-to-lymphocyte ratio (PLR) , and other indicators between the two groups. Conclusions: Faced with Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2), HD patients with lower BMI and hemoglobin were more susceptible to be infected, which might be related to malnutrition. Once confirmed with COVID-19, HD patients expressed obviously disregulated in inflammation and immune.


title: COVID-19 Generation: A Conceptual Framework of the Consumer Behavioral Shifts to Be Caused by the COVID-19 Pandemic

text: This paper reviews the potential impact of the COVID-19 pandemic of 2020 on global consumer traits, buying patterns, global interconnectedness and psychographic behavior, and other marketing activities. Eschewing the branding of generational cohorts by their birth segments (Baby Boomers, Millennials, Centennials, etc.), this paper focuses upon major historical milestones (JFK assassination, Vietnam War, Iran Hostage Crisis, Terrorism, 2008 worldwide economic contraction) and how those milestones had more effects upon future behavior than simply being born during a certain segment of years and labeling entire cohorts in that manner. The implications of this paper are to suggest to marketers the long-term behavioral shifts we could see from the COVID-19 pandemic of 2020, and the resulting shifts in consumer behavior.


title: Vaporized H2O2 decontamination against surrogate viruses for the reuse of N95 respirators in the COVID-19 emergency

text: Decontamination of N95 respirators has become critical to alleviate PPE shortages for healthcare workers in the current COVID-19 emergency. The factors that are considered for the effective reuse of these masks are the fit, filter efficiency and decontamination/disinfection level both for SARS-CoV-2, which is the causative virus for COVID-19, and for other organisms of concern in the hospital environment such as Staphylococcus aureus or Clostridium difficile. In its guidance entitled 'Recommendations for Sponsors Requesting EUAs for Decontamination and Bioburden Reduction Systems for Surgical Masks and Respirators During the Coronavirus Disease 2019 (COVID19) Public Health Emergency' (May 2020)[1], the FDA recommends a 6-log10 reduction in either the most resistant bacterial spores for the system or in a mycobacterium species to authorize the use of a decontamination method of N95 respirators for single or multiple users. While the goal is primarily inactivation against SARS-CoV-2, testing of decontamination methods against the virus may not always be available. For decontamination methods considered for only single users, the recommendation is a 6-log10 reduction in the infective virus concentration of 3 non-enveloped viruses or in the concentration of two Gram (+) and two Gram (-) bacteria. Based on these recommendations, we explored the efficacy of vaporized H2O2 (VHP) treatment of N95 respirators against surrogate viruses covering a wide range of disinfection resistance for emergency decontamination and reuse to alleviate PPE shortages for healthcare workers in the COVID-19 emergency.


title: Virtual health care for community management of patients with COVID-19.

text: Objectives: To describe the implementation and early experience of virtual health care for community management of patients with COVID-19. Design: observational cohort study. Setting: large Australian metropolitan health service with established virtual health care program and remote patient monitoring capability. Participants: patients with COVID-19 living within the health service who can self-isolate safely, do not require immediate admission to an inpatient setting, have no major active comorbid illness and can be managed at home or other suitable accommodation. Main outcome measures: care escalation rates, including hospital admission. Results: between 11-29 March 2020, 162/173 (93.6%) locally diagnosed patients with COVID-19 were accepted to the virtual health care program, median age 38y (range 11-79). For the 62 patients discharged during this period the median length of stay was 8 days (range 1-17). The peak of 100 prevalent patients equated to approximately 25 patients per Registered Nurse per shift. Patients were contacted a median of 16 times (range 1-30) during this period, with video consultations used 66.3% of the time; 132/162 (81.5%) patients were monitored remotely. Care escalation rates were low: ambulance attendance, 5 (3%); ED attendance, 4 (2.5%); hospital admission, 3 (1.9%). There were no deaths. Conclusions: community-based virtual health care is feasible for managing most patients with COVID-19 and can be rapidly implemented in an urban Australian context for pandemic management. Health services implementing virtual health care should anticipate challenges with rapid technology deployments and provide adequate support to resolve them including strategies supporting consumer use of health information technologies.


title: COVID-19 severe pneumonia in Mexico City - First experience in a Mexican hospital

text: Background: Coronavirus Disease 2019 (Covid-19) pandemic since its first confirmed case, has changed the world. The need for accurate and truthful information is vital. Mexico and Latin America have been widely affected, so having local epidemiological data, will be of great clinical utility. Methods: A total of 33 hospitalized patients with Covid-19 pneumonia (either severe or critical) were identified from electronic health record in a third level care private hospital in Mexico City from March 13rd to April 13rd, 2020. We conducted a descriptive study of patients for characterization of the clinical, laboratory and radiologic findings, as well as complications. Results: The mean age was 60.6 (12.68) years and 23 (69.7%) were males. Twenty-three patients (69.6%) were overweight or obese. The median duration of symptoms before admission was 7 days. All the patients required mechanical invasive ventilation. The median duration of the mechanical ventilation was 12(2.6) days and all patients were extubated except one. All patients were started on antiviral treatment in the first 24 hours after admission once the diagnosis of Covid19 pneumonia was made. There was no difference between the treatment option and the length of stay. The extubation rate was higher (91.6%) than in other series, with no fatalities even though they were treated with different regimens. Conclusions: This one-centre experience describes the epidemiology, treatment and outcome of 33 patients with severe or critical COVID pneumonia admitted to the ICU. Most patients in our series were overweight or obese male, which we observed were of higher risk to present critical pneumonia, as well as high levels of Interleukin-6. The foregoing is relevant, due to the high incidence of these comorbidities in our country.


title: Rapid increase of Care Homes reporting outbreaks a sign of eventual substantial disease burden

text: Enclosed societies (i.e. locations that are connected to wider community only by subgroups of their population and that are dominated by within society transmission) have the potential, upon establishment of a respiratory disease, to suffer a large proportion of the population within becoming infected. Care homes are particularly susceptible to COVID19 outbreaks and suffer high mortality due to vulnerable population within. Recent data on the number of new outbreak reports in care homes to Public Health England shows an initial increase then plateau perhaps associated with an SIS model dynamic. Without change in policy moving forward a high prevalence in such setting is predicted of around 75%. Action is needed to support staff in such settings.


title: Enhanced COVID-19 data for improved prediction of survival

text: The current COVID-19 pandemic, caused by the rapid world-wide spread of the SARS-CoV-2 virus, is having severe consequences for human health and the world economy. The virus effects individuals quite differently, with many infected patients showing only mild symptoms, and others showing critical illness. To lessen the impact of the pandemic, one important question is which factors predict the death of a patient? Here, we construct an enhanced COVID-19 dataset by processing two existing databases (from Kaggle and WHO) and using natural language processing methods to enhance the data by adding local weather conditions and research sentiment. Author summary In this study, we contribute an enhanced COVID-19 dataset, which contains 183 samples and 43 features. Application of Extreme Gradient Boosting (XGBoost) on the enhanced dataset achieves 95% accuracy in predicting patients survival, with country-wise research sentiment, and then age and local weather, showing the most importance. All data and source code are available at http://ab.inf.uni-tuebingen.de/publications/papers/COVID-19.


title: Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

text: The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be confirmed. Therefore, we herein used a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed plasma membrane fusion capacity superior to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. We then generated a series of lipopeptides and found that the EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than that of EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, potently inhibiting replication of 4 live human coronaviruses, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by currently circulating SARS-CoV-2 and emerging SARSr-CoVs.


title: The Challenge of Using Epidemiological Case Count Data: The Example of Confirmed COVID-19 Cases and the Weather

text: The publicly available data on COVID-19 cases provides an opportunity to better understand this new disease. However, strong attention needs to be paid to the limitations of the data to avoid making inaccurate conclusions. This article, which focuses on the relationship between the weather and COVID-19, raises the concern that the same factors influencing the spread of the disease might also affect the number of tests performed and who gets tested. For example, weather conditions impact the prevalence of respiratory diseases with symptoms similar to COVID-19, and this will likely influence the number of tests performed. This general limitation could severely undermine any similar analysis using existing COVID-19 data or similar epidemiological data, which could, therefore, mislead decision-makers on questions of great policy relevance.


title: Modelling the evolution of COVID-19 in high-incidence European countries and regions: estimated number of infections and impact of past and future intervention measures

text: A previously developed mechanistic model of COVID-19 transmission has been adapted and applied here to study the evolution of the disease and the effect of intervention measures in some European countries and territories where the disease had major impact. A clear impact of the major intervention measures on the reproduction number (Rt) has been found in all studied countries and territories, as already suggested by the drop in the number of deaths over time. Interestingly, the impact of such major intervention measures seems to be the same in most of these countries. The model has also provided realistic estimates of the total number of infections, active cases and future outcome. While the predictive capabilities of the model are much more uncertain before the peak of the outbreak, we could still reliably predict the evolution of the disease after a major intervention by assuming the afterwards reproduction number from current study. More challenging is to foresee the long-term impact of softer intervention measures, but this model can estimate the outcome of different scenarios and help planning changes in the implementation of control measures in a given country or region.


title: Women in power: Female leadership and public health outcomes during the COVID-19 pandemic

text: Some countries have been more successful than others at dealing with the COVID-19 pandemic. When we explore the different policy approaches adopted as well as the underlying socio-economic factors, we note an interesting set of correlations: countries led by women leaders have fared significantly better than those led by men on a wide range of dimensions concerning the global health crisis. In this paper, we analyze available data for 35 countries, focusing on the following variables: number of deaths per capita due to COVID-19, number of days with reported deaths, peaks in daily deaths, deaths occurred on the first day of lockdown, and excess mortality. Results show that countries governed by female leaders experienced much fewer COVID-19 deaths per capita and were more effective and rapid at flattening the epidemic's curve, with lower peaks in daily deaths. We argue that there are both contingent and structural reasons that may explain these stark differences. First of all, most women-led governments were more prompt at introducing restrictive measures in the initial phase of the epidemic, prioritizing public health over economic concerns, and more successful at eliciting collaboration from the population. Secondly, most countries led by women are also those with a stronger focus on social equality, human needs and generosity. These societies are more receptive to political agendas that place social and environmental wellbeing at the core of national policymaking.


title: An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

text: Background The COVID-19 pandemic is causing a major global health and socio-economic burden, instigating the mobilisation of resources into the development of control tools, such as diagnostics and vaccines. The poor performance of some diagnostic serological tools has emphasised the need for up to date immune-informatic analyses to inform the selection of viable targets for further study. This requires the integration and analysis of genetic and immunological data for SARS-CoV-2 and its homology with other human coronavirus species to understand cross-reactivity. Methods We have developed an online tool for SARS-CoV-2 research, which combines an extensive epitope mapping and prediction meta-analysis, with an updated variant database (55,944 non-synonymous mutations) based on 16,087 whole genome sequences, and an analysis of human coronavirus homology. To demonstrate its utility, we present an integrated analysis of the SARS-CoV-2 spike and nucleocapsid proteins, which are candidate vaccine and serological diagnostic targets. Results Our analysis reveals that the nucleocapsid protein in its native form appears to be a sub-optimal target for use in serological diagnostic platforms. Whilst, a further analysis suggests that orf3a proteins may be a suitable alternative target for diagnostic assays. Conclusions The tool can be accessed online (http://genomics.lshtm.ac.uk/immuno) and will serve as a useful tool for biological discovery in the fight against SARS-CoV-2. Further, it may be adapted to inform on biological targets in future outbreaks, including new human coronaviruses that spill over from animal hosts.


title: Investiagation of possible mechanism of eye transmission of SARS-CoV-2 based on SARS-CoV/ 从SARS冠状病毒探讨新型冠状病毒眼途径传播的可能机制

text: SARS-CoV-2 has been spreading rapidly since its outbreak in December 2019.Understanding its epidemiological characteristics, especially cutting off transmission routes, is crucial to controlling the spread of the disease. In the study of transmission pathway, the issue of whether SARS-CoV-2 is transmitted through ocular surface tissue has also aroused concerns, but there are still no clinically confirmed cases and laboratory evidence of its infection through ocular surface tissue. New research suggests that the SARS-CoV-2 belongs to the same genus as SARS coronavirus (SARS-CoV), and that it enters cells in the same way as SARS-CoV. This paper reviews the research on SARS-CoV to investigate the possible mechanism of eye transmission of SARS-CoV-2.


title: Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation

text: The potential for transmission of SARS-CoV-2 shed in stool via fecal microbiota transplantation is not yet known, and the effectiveness of various testing strategies to prevent FMT-based transmission has also not yet been quantified. Here we use a mathematical model to simulate the utility of different testing strategies.


title: COVID-19 and Environmental factors. A PRISMA-compliant systematic review

text: The emergence of a novel human coronavirus, SARS-CoV-2, has become a global health concern causing severe respiratory tract infections in humans. Human-to-human transmissions have been described with incubation times between 2-10 days, facilitating its airborne spread via droplets. The impact of environmental factors on the coronavirus disease 2019 (COVID-19) outbreak is under consideration. We therefore reviewed the literature on all available information about the impact of environmental factors on human coronaviruses. Temperature, humidity and other environmental factors have been recorded as environmental drivers of the COVID-19 outbreak in China and in other countries. Higher temperatures might be positive to decrease the COVID-19 incidence. In our review, the analysis of 23 studies show evidence that high temperature and high humidity reduce the COVID-19 transmission. However, further studies concerning other environmental (namely meteorological) factors role should be conducted in order to further prove this correlation. As no specific therapies are available for SARS-CoV-2, early containment and prevention of further spread will be crucial to stop the ongoing outbreak and to control this novel infectious thread.


title: Modeling layered non-pharmaceutical interventions against SARS-CoV-2 in the United States with Corvid

text: Background: The novel coronavirus SARS-CoV-2 has rapidly spread across the globe and is poised to cause millions of deaths worldwide. There are currently no proven pharmaceutical treatments, and vaccines are likely over a year away. At present, non-pharmaceutical interventions (NPIs) are the only effective option to reduce transmission of the virus, but it is not clear how to deploy these potentially expensive and disruptive measures. Modeling can be used to understand the potential effectiveness of NPIs for both suppression and mitigation efforts. Methods and Findings: We developed Corvid, an adaptation of the agent-based influenza model called FluTE to SARS-CoV-2 transmission. To demonstrate features of the model relevant for studying the effects of NPIs, we simulated transmission of SARS-CoV-2 in a synthetic population representing a metropolitan area in the United States. Transmission in the model occurs in several settings, including at home, at work, and in schools. We simulated several combinations of NPIs that targeted transmission in these settings, such as school closures and work-from-home policies. We also simulated three strategies for testing and isolating symptomatic cases. For our demonstration parameters, we show that testing followed by home isolation of ascertained cases reduced transmission by a modest amount. We also show how further reductions may follow by isolating cases in safe facilities away from susceptible family members or by quarantining all family members to prevent transmission from likely infections that have yet to manifest. Conclusions: Models that explicitly include settings where individuals interact such as the home, work, and school are useful for studying the effectiveness of NPIs, as these are more dependent on community structure than pharmaceutical interventions such as vaccination. Corvid can be used to help evaluate complex combinations of interventions, although there is no substitute for real-world observations. Our results on NPI effectiveness summarize the behavior of the model for an assumed set of parameters for demonstration purposes. Model results can be sensitive to the assumptions made about disease transmission and the natural history of the disease, both of which are not yet sufficiently characterized for SARS-CoV-2 for quantitative modeling. Models of SARS-CoV-2 transmission will need to be updated as the pathogen becomes better-understood.


title: Growth rate and acceleration analysis of the COVID-19 pandemic reveals the effect of public health measures in real time

text: Background: Ending the COVID-19 pandemic is arguably one of the most prominent challenges in recent human history. Following closely the growth dynamics of the disease is one of the pillars towards achieving that goal. Objective: We aimed at developing a simple framework to facilitate the analysis of the growth rate (cases/day) and growth acceleration (cases/day^2) of COVID-19 cases in real-time. Methods: The framework was built using the Moving Regression (MR) technique and a Hidden Markov Model (HMM). The dynamics of the pandemic was initially modeled via combinations of four different growth stages: lagging (beginning of the outbreak), exponential (rapid growth), deceleration (growth decay) and stationary (near zero growth). A fifth growth behavior, namely linear growth (constant growth above zero), was further introduced to add more flexibility to the framework. An R Shiny application was developed, which can be accessed at http://www.theguarani.com.br/covid-19 or downloaded from https://github.com/adamtaiti/SARS-CoV-2. The framework was applied to data from the European Center for Disease Prevention and Control (ECDC), which comprised 853,200 cases reported worldwide as of April 2nd 2020. Results: We found that the impact of public health measures on the prevalence of COVID-19 could be perceived in seemingly real-time by monitoring growth acceleration curves. Restriction to human mobility produced detectable decline in growth acceleration within few days, deceleration within ~2 weeks and near-stationary growth within ~6 weeks. Countries exhibiting different permutations of the five growth stages indicated that the evolution of COVID-19 prevalence is more complex and dynamic than previously appreciated. Conclusions: These results corroborate that mass social isolation is a highly effective measure against the dissemination of SARS-CoV-2, as previously suggested. Apart from the analysis of prevalence partitioned by country, the proposed framework is easily applicable to city, state, region and arbitrary territory data, serving as an asset to monitor the local behavior of COVID-19 cases.


COVID-19 in Brazil: Epidemiological update and perspectives


title: Initial stage of the COVID-19 infection process in human population

text: The simplest approximation for the first stages of the infection spread is considered. The specific feature of the COVID-19 characterized by its long latent period is taken into account. Exponential increase of numbers of infected people is determined by the half period of the maximal latent time for the COVID-19. The averaging over latent period leads to additional increase of the infected numbers.


title: A New, Simple Projection Model for COVID-19 Pandemic

text: With the worldwide outbreak of COVID-19, an accurate model to predict how the coronavirus pandemic will evolve becomes important and urgent to help policy makers in different countries address the epidemic outbreak and determine policies to control spread more efficiently and effectively. Unlike the classic public health and virus propagation models, this new projection model takes government intervention and public response into account to make reliable projections of the outbreak 10 days to 2 weeks in advance.


COVID-19 leads to a new context for the “right to tourism”: a reset of tourists’ perspectives on space appropriation is needed


title: Forecast analysis of the epidemics trend of COVID-19 in the United States by a generalized fractional-order SEIR model

text: Abstract In this paper, a generalized fractional-order SEIR model is proposed, denoted by SEIQRP model, which has a basic guiding significance for the prediction of the possible outbreak of infectious diseases like COVID-19 and other insect diseases in the future. Firstly, some qualitative properties of the model are analyzed. The basic reproduction number R0 is derived. When R0 < 1, the disease-free equilibrium point is unique and locally asymptotically stable. When R0 > 1, the endemic equilibrium point is also unique. Furthermore, some conditions are established to ensure the local asymptotic stability of disease-free and endemic equilibrium points. The trend of COVID-19 spread in the United States is predicted. Considering the influence of the individual behavior and government mitigation measurement, a modified SEIQRP model is proposed, defined as SEIQRPD model. According to the real data of the United States, it is found that our improved model has a better prediction ability for the epidemic trend in the next two weeks. Hence, the epidemic trend of the United States in the next two weeks is investigated, and the peak of isolated cases are predicted. The modified SEIQRP model successfully capture the development process of COVID-19, which provides an important reference for understanding the trend of the outbreak.


title: Organization of Primary Health Care in pandemics: a rapid systematic review of the literature in times of COVID-19

text: The world is experiencing one of the greatest public health emergencies in history with the global spread of COVID-19. Health systems, including Primary Health Care (PHC) services, are pillars of pandemic coping strategies, and there are important gaps in the literature on the best ways to organize PHC in health crisis scenarios such as the one currently experienced. Given the urgency of responses, we performed a rapid systematic literature review on MEDLINE (via PubMed), EMBASE and LILACS (via VHL), in order to analyze empirical studies on the effectiveness of PHC organization strategies in the context of epidemics to improve access and reduce morbidity and mortality. We selected seven articles, which studied the responses to different epidemics in different parts of the world. In terms of access, the studies suggest positive results with the adoption of adjustments of work processes of the teams and the structure of the services, combined with diversification of actions (including call center), adequate provision of inputs and personal protective equipment, adequate action plans and communication strategies, and effective integration with public health services and other levels of care. No study analyzed population morbidity and mortality. The included studies suggest also that community-oriented PHC is more effective in crisis scenarios, indicating the necessity of strengthening of the Family Health Strategy in the Brazilian context.


title: Control dynamics of the COVID-19 pandemic in China and South Korea

text: Social isolation measures reduce the population's infection rate with the COVID-19 virus, but its effectiveness is difficult to quantify. The successful control of the pandemic carried out by China and South Korea is studied using a scheme based on the net relative rate of infection which is very sensitive to sudden changes in the epidemic evolution. The net relative rate of infection for China and South Korea without containment measures, that is, with free proliferation of the virus, lies between 10 and 40 %/day or doubling times of infected persons between 3.5 and 2 days. After measures of containment it dropped and stabilized. South Korea stabilized it around 1 %/day and China around 0.05 %/day with doubling times of 70 days and 1400 days, respectively. A discussion is provided about their processes of control and stabilization of the epidemic process and about the scheme used to study them.


title: Broad-Range Virus Detection and Discovery Using Microfluidic PCR Coupled with High-throughput Sequencing

text: There is a need for a comprehensive and sensitive method to test for a broad range of viral pathogens in samples without any identifiable pathogen detected. Real-time PCR assays are sensitive and rapid, but their specificity limits their utility in detecting divergent agents. Shotgun high-throughput sequencing methods provide unbiased sequence identification, however, they have limited sensitivity and require complex analyses. In order to meet the need for a sensitive, high-throughput virus detection and discovery platform with good sensitivity, we combine two existing technologies, broadly-reactive consensus-degenerate pan-viral group PCR and the MiSeq sequencer (Illumina), using the Access Array (Fluidigm), a commercially-available microfluidic PCR system. Pan-viral group primers target conserved regions of virus taxonomic groups and can amplify known and potentially novel species. The Access Array employs dozens of these assays in parallel, which are then sequenced all at once on the MiSeq. In this study, we run a respiratory panel of pan-viral group PCR assays using AA-PCR-Seq. We validate the panel on a collection of representative human and animal samples, comparing it to qPCR and shotgun next-generation sequencing (NGS). AA-PCR-Seq provides a robust, straightforward method for screening large numbers of samples for virus detection and discovery.


title: Tocilizumab for patients with COVID-19 pneumonia. The TOCIVID-19 phase 2 trial

text: Background: Tocilizumab blocks pro-inflammatory activity of interleukin-6 (IL-6) which might be important in the pathogenesis of interstitial pneumonia. Objective: to evaluate efficacy of tocilizumab in COVID-19 pneumonia patients. Design: multicenter single-arm phase 2 trial, powered to detect 10% absolute lethality rate reduction at 14 and 30-days, with 20% and 35% expected rates. A consecutive prospective validation cohort was also evaluated. Setting: 185 Italian public hospitals, during coronavirus breakout. Patients: 1221 patients hospitalized with pneumonia, from March 19th to 24th, 2020. Intervention: tocilizumab 8 mg/kg, intravenously, one or two administrations with 12 hours interval. Measurements: lethality rates at 14 and 30-days; safety according to CTCAE. Results: 301 and 920 cases were available for intention-to-treat (ITT) analysis in phase 2 and validation cohorts. Due to delayed drug availability, 60% of patients received tocilizumab, and with some delays. In phase 2, 67 patients died; lethality rates were 18.4% (97.5%CI: 13.6-24.0, P=0.52) and 22.4% (97.5%CI: 17.2-28.3, P<0.001) at 14 and 30-days. Lower rates (15.6% and 20.0%) were reported in the modified ITT including only treated patients (mITT). Lethality rates in the validation cohort were smaller than in phase 2, at 14 and 30 days and in ITT and mITT populations. Multivariable logistic regression model suggests tocilizumab be more effective in patients not requiring mechanical respiratory support at baseline. No relevant signal of specific drug toxicity was reported, many severe adverse events being disease-related. Limitations: single-arm design. In addition, delayed availability of the drug induced indication bias and immortal time bias. Conclusion: Tocilizumab reduced lethality rate at 30 but not at 14-days, compared with the expectations, without significant toxicity. Efficacy was more evident among patients not requiring mechanical respiratory support.


title: Modeling Covid-19 dynamics for real-time estimates and projections: an application to Albanian data

text: The SARS-CoV-2 epidemic is one of the biggest challenges healthcare systems worldwide have ever had to face. To curb transmission many countries have adopted social distancing measures and travel restrictions. Estimating the effect of these measures in each context is challenging and requires mathematical models of the transmission dynamics. Projections for the future course of the epidemic strongly rely on model predictions and accurate representation of real-time data as they accumulate. Here I develop an SEIR modeling framework for Covid-19, to evaluate reported cases and fatalities, and to enable forecasting using evidence-based Bayesian parameter estimation. This Bayesian framework offers a tool to parametrize real-time dynamics of Covid-19 cases, and explore the effect of control as it unfolds in any setting. I apply the model to Covid-19 data from Albania, where drastic control measures were put in place already on the day of the first confirmed case. Evaluating the dynamics of reported cases 9-31 March 2020, I estimate parameters and make preliminary projections. Three weeks into the measures, Albanian data already indicate a strong signature of more than 40% transmission reduction, and lend support to a progressively increasing effect of control measures rather than a static one. In the Albanian setting, the model and data match well, projecting the peak of the outbreak may be around 5-15 April, and be contained within 300 active confirmed cases if control continues with the same trend. This framework can be used to understand the quantitative effects of different control measures in real-time, and inform adaptive intervention for success in other settings.


title: Detection of SARS-CoV-2 RNA on public surfaces in a densely populated urban area of Brazil

text: Importance: The COVID-19 pandemic has resulted in more than 3.5 million cases and 245 thousand deaths worldwide as of May 6, 2020. Determining the extent of the presence of the virus on public surfaces is critical for understanding the potential risk of infection in these areas. Objective: To evaluate the presence of SARS-CoV-2 RNA on public surfaces in a densely populated urban area in Brazil. Design and Setting: A total of 101 samples were collected from different surfaces in public places in the region of Belo Horizonte with the highest number of COVID-19 cases. Samples were collected near the hospital and public transportation areas using sterile swabs, and then submitted to nucleic acid extraction and genomic detection and quantification by one-step qPCR. Results: Seventeen of the 101 samples tested positive (16.8%) for SARS-CoV-2 RNA, including samples from bus stations/terminals, public squares, and sidewalks, including those near hospitals. Conclusions and Relevance: Our data indicated the contamination of public surfaces by SARS-CoV-2, especially near hospital areas, highlighting the risk of infection for the population. Constant monitoring of the virus in urban areas is required as a strategy to fight the pandemic and prevent further infections.


title: First Data-Set on SARS-CoV-2 Detection for Istanbul Wastewaters in Turkey

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in Wuhan, China, in December 2019 and became a global pandemic [1]. By 26 April 2020, more than 2.9 million people were infected by SARS-CoV-2 and over 203 thousand people lost their life globally. By 26 April 2020, 107773 confirmed cases were reported in Turkey with 2706 deaths. Majority of the cases in Turkey has been observed in Istanbul. In the world, the duration of availability of SARS-CoV-2 was found to be significantly longer in stool samples than in respiratory and serum samples [2]. SARS-CoV-2 was detected in wastewaters in Australia [3], Netherlands [4], USA [5], France [6], Spain [7] and USA [8] by using different virus concentration techniques. In this work, Istanbul metropole with 65 % of Covid-19 cases was chosen as the pilot city. On the 21st of April 2020, 24-hr composite samples were collected from the Ambarli, Pasakoy and Kadikoy wastewater treatment plants (WWTP). On the 25th of April 2020, more wastewater samples were taken from Terkos, Buyukcekmece, Baltalimani and Tuzla WWTPs. These wastewater treatment plants were selected among 81 plants in Istanbul in order to take representative samples from 4 different districts of Istanbul according to the severity of Covid-19 cases, like very serious, serious, moderate and mild. Grab samples were also collected from Bagcilar and Kartal manholes located nearby the pandemic hospitals on April 21st, 2020. Polyethylene glycol 8000 (PEG 8000) adsorption [5] SARS-Cov-2 concentration method was used for SARS-CoV-2 concentration after optimization. Real time RT-PCR diagnostic panel validated by US was used to quantify SARS-CoV-2 RNA in raw sewage taken from the inlets of treatment plants and manholes. Five samples out of seven from wastewater and all samples from manholes were tested positive. SARS-CoV-2 in raw sewage from Ambarli, Pasakoy, Kadikoy, Terkos, Buyukcekmece, Baltalimani and Tuzla WWTPs were found as 8.26x103, 1.80x104, ND, ND, 3.73x103, 4.95x103, 2.89x103, respectively. The Bagcilar and Kartal manholes nearby pandemic hospitals exhibited 4.49x104 and 9.33x104, respectively. SARS-CoV-2 virus titers of manhole were higher than those of inlet of WWTPs. The observed copy numbers were presented against the number of Covid-19 cases coming to the WWTP per treatment plant capacity. Quantitative measurements of SARS-CoV-2 in wastewater can be used as a tool in wastewater-based epidemiology (WBE) and it can provide information about SARS-CoV-2 distribution in wastewater of various districts of Istanbul which exhibit different scores of Covid-19 cases. The distribution of epidemy was followed not only with blood test but with wastewater monitoring. This may allow us to identify the districts not exhibiting many Covid-19 cases, but under high risk. Continuous monitoring of wastewater for SARS-Cov-2 may provide an early warning signs before an epidemy starts in case of infection resurge.


title: Covid-19: accelerating recovery

text: Covid-19 infections and related illness and death are rightly at the forefront of our minds. It is critical that we consider how to reduce infections, treat those who are ill and protect health systems. We must, however, also consider how the pandemic is affecting the families of those infected, and how interventions to prevent the spread of the virus come with large negative economic and social consequences. We must begin to identify the ways in which we can soften these blows and recover from the negative consequences over the medium and long-term. We highlight here the importance of moving away the tendency to search for interventions to improve one outcome at a time. It will be essential, particularly in highly resource constrained settings, to look for accelerators, interventions which improve multiple outcomes simultaneously. We discuss how this will be especially important for groups who are at particular risk at this time, including of long-term negative outcomes. These include very young children, adolescents and those who have limited capacity to benefit from narrow interventions given critical needs in multiple domains. Searching for accelerators requires that we take a step back and look to identify common causes of negative outcomes and consider how we might address them. For many countries, recovery from this epidemic will be highly constrained by the limited availability of financial resources. Wise investments will be especially important at this time.


title: Communicating About COVID-19: Practices for Today, Planning for Tomorrow

text: In times of public health crises, effective information on how to perform daily activities can be central to the stability of local communities. Technical communicators can make important contributions to these situations by developing materials that meet local informational needs. This entry reviews strategies technical communicators can use to address public health challenges on the local level both today and in the future.


title: Mechanistic modeling of the SARS-CoV-2 and immune system interplay unravels design principles for diverse clinicopathological outcomes

text: The disease caused by SARS-CoV-2 is a global pandemic that threatens to bring long-term changes worldwide. Approximately 80% of infected patients are asymptomatic or have mild symptoms such as fever or cough, while rest of the patients have varying degrees of severity of symptoms, with 3-4% mortality rate. Severe symptoms such as pneumonia and Acute Respiratory Distress Syndrome can be caused by tissue damage mostly due to aggravated and unresolved innate and adaptive immune response, often resulting from a cytokine storm. However, the mechanistic underpinnings of such responses remain elusive, with an incomplete understanding of how an intricate interplay among infected cells and cells of innate and adaptive immune system can lead to such diverse clinicopathological outcomes. Here, we use a dynamical systems approach to dissect the emergent nonlinear intra-host dynamics among virally infected cells, the immune response to it and the consequent immunopathology. By mechanistic analysis of cell-cell interactions, we have identified key parameters affecting the diverse clinical phenotypes associated with COVID-19. This minimalistic yet rigorous model can explain the various phenotypes observed across the clinical spectrum of COVID-19, various co-morbidity risk factors such as age and obesity, and the effect of antiviral drugs on different phenotypes. It also reveals how a fine-tuned balance of infected cell killing and resolution of inflammation can lead to infection clearance, while disruptions can drive different severe phenotypes. These results will help further the case of rational selection of drug combinations that can effectively balance viral clearance and minimize tissue damage simultaneously. Significance Statement The SARS-CoV-2 pandemic has already infected millions of people, and thousands of lives have been lost to it. The pandemic has already tested the limits of our public healthcare systems with a wide spectrum of clinicopathological symptoms and outcomes. The mechanistic underpinnings of the resultant immunopathology caused by the viral infection still remains to be elucidated. Here we propose a minimalistic but rigorous description of the interactions of the virus infected cells and the core components of the immune system that can potentially explain such diversity in the observed clinical outcomes. Our proposed framework could enable a platform to determine the efficacy of various treatment combinations and can contributes a conceptual understanding of dynamics of disease pathogenesis in SARS-CoV-2 infections.


title: Vertical Stratification in Urban Green Space Aerobiomes

text: Exposure to a diverse environmental microbiome is thought to play an important role in ‘educating’ the immune system and facilitating competitive exclusion of pathogens to maintain human health. Vegetation and soil are known to be key sources of airborne microbiota––the aerobiome. Only a limited number of studies have attempted to characterise the dynamics of the aerobiome, and no studies to date have investigated these dynamics from a vertical perspective simulating human exposure. Studies of pollution and allergenic pollen show vertical stratification at various scales, and present an expectation that such vertical stratification may also be present in the aerobiome. Such stratification could have important implications for public health and for the design, engineering and management of urban green spaces. For example, do children receive the same exposure to airborne microbiota as taller adults, and what are the downstream implications for health? In this study, we combine an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0 m together with high-throughput sequencing of the bacterial 16S rRNA gene to assess whether significant vertical stratification of the aerobiome occurred in a parkland habitat in Adelaide, South Australia. Our results provide evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with diversity increasing roughly with height. We also found significant vertical stratification in known pathogenic and beneficial bacterial taxa, suggesting potentially different exposure attributes between adults and children. These results could have important implications for public health and urban planning, potentially informing ways to optimise the design and management of health-promoting urban green spaces.


title: Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis

text: Background: As COVID-19 has become a global pandemic, early prevention and control of the epidemic is extremely important. Telemedicine, which includes medical advice given over telephone, Internet, mobile phone applications or other similar ways, may be an efficient way to reduce transmission and pressure on medical institutions. Methods: We searched MEDLINE, Web of science, Embase, Cochrane, CBM, CNKI and Wanfang databases for literature on the use of telemedicine for COVID-19, SARS and MERS. from their inception to March 31st, 2020. We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. We conducted meta-analyses on the main outcomes of the studies. Results: A total of 2041 articles were identified after removing duplicates. After reading the full texts, we finally included nine studies. People were most concerned about symptoms (64.2%), epidemic situation and public problems (14.5%), and psychological problems (10.3%) during COVID-19 epidemic. During the SARS epidemic, the proportions of people asking for consultation for symptoms, prevention and therapy, and psychological problems were 35.0%, 22.0%, and 23.0%, respectively. Two studies demonstrated that telemedicine can be used to screen the suspected patients and give advice. One study emphasized the limited possibilities to follow up people calling hotlines and difficulties in identifying all suspect cases. Conclusions: Telemedicine services should focus on the issues that the public is most concerned about, such as then symptoms, prevention and treatment of the disease, and provide reasonable advice to patients with symptoms or people with epidemic history. Keywords：COVID-19; SARS; MERS; telemedicine; rapid review


A model society: maths, models and expertise in viral outbreaks


title: A Validation Study for the Successful Isolation Policy in China: a Meta-Analysis in COVID-19

text: COVID-19 is quickly spreading around the world and carries along with it a significant threat to public health. This study sought to apply meta-analysis to more precisely and accurately estimate the basic reproduction number (R0) of COVID-19 in order to evaluate the effectiveness of the isolation policy across countries, and the corresponding public health capability to care for patients. Prior estimates of R0 have varied widely and range from 1.95 to 6.49. Utilizing meta-analysis techniques we determined a more robust estimation of 3.05 for R0, which is substantially larger than that provided by the WHO. We also present the infectious rate standardized to per million population, which has proved to be a good index to determine whether the isolation measures in specific countries are effective. Also, this standardized infection rate can be used to determine whether the current infectious severity status is out of range of the national health capacity. Finally, we utilize our robust estimate of R0 and the standardized infectious rate to illustrate that the early and aggressive isolation measures enforced by the Chinese government were substantially more effective in controlling the negative impact COVID-19 than the more permissive measures enacted early in Italy and the United States.


title: A mathematical model to investigate the transmission of COVID-19 in the Kingdom of Saudi Arabia

text: Since the first confirmed case of SARS-CoV-2 coronavirus (COVID-19) in the 2nd day of March, Saudi Arabia has not report a quite rapid COVD-19 spread compared to America and many European countries. Possible causes include the spread of asymptomatic cases. To characterize the transmission of COVID-19 in Saudi Arabia, this paper applies a susceptible, exposed, symptomatic, asymptomatic, hospitalized, and recovered dynamical model, along with the official COVID-19 reported data by the Ministry of Health in Saudi Arabia. The basic reproduction number R0 is estimated to range from 2.87 to 4.9.


title: A SIMPLE COLORIMETRIC MOLECULAR DETECTION OF NOVEL CORONAVIRUS (COVID-19), AN ESSENTIAL DIAGNOSTIC TOOL FOR PANDEMIC SCREENING

text: The recent outbreak of the newly emerged novel coronavirus (SARS-CoV-2) presents a big challenge for public health laboratories as virus isolates are not available while there is an increasing evidence that the epidemic is more widespread than initially thought, as well as spreading internationally across borders through travellers does already happen warranting a methodology for the rapid detection of the infection to control SARS-CoV-2. Aim: We intended to develop and deploy a robust and rapid diagnostic methodology using LAMP assay for use in point of care settings to detect SARS-COV-2 infection. Methodology: In the present study, we have developed a validated rapid diagnostic procedure to detect SARS-CoV-2 using LAMP assay, its design relying on isothermal amplification of the nucleic acids of the SARS-CoV-2. Results: The LAMP assay developed detects SARS-CoV-2 infection rapidly with high sensitivity and reliability. The data generated by LAMP assay were comparable and at par with the data generated by real-time PCR method. Conclusion: The present study demonstrates that the LAMP assay developed was a rapid, reliable, sensitive and cost effective method to detect SARS-CoV-2 infection in a point of care as well as in laboratory settings.


docid: wcwyzfgl

title: Corona virus


title: Becoming Reading Group: reflections on assembling a collegiate, caring collective

text: In neoliberalising universities, collegial and collective practices such as reading groups are often positioned by students, staff and managers as less important than meeting individual KPIs (such as producing research publications, seeking research grants, or meeting the increasing demands of producing quality teaching outcomes.) However, reading groups can be vital for cultivating caring collectives and spaces of collegiality. In this paper we use assemblage thinking to explore 25 years of a Geography reading group at the University of Newcastle. The paper addresses two questions: what does reading together do and make possible; and how might we think about the labours of reading together as a way of building caring collectives. The paper draws on reflections from 24 past and present members of reading group to explore how these kinds of academic practices nourish our working lives.


title: ICU admissions and in-hospital deaths linked to covid-19 in the Paris region are correlated with previously observed ambient temperature

text: OBJECTIVE To study the effect of weather on severity indicators of coronavirus disease 2019 (covid-19). DESIGN Ecological study. SETTING Paris region. POPULATION Severely ill patients with covid-19. MAIN OUTCOME MEASURES Daily covid-19-related intensive care unit (ICU) admission and in-hospital deaths in the Paris region, and the daily weather characteristics of Paris midtown. RESULTS Daily ICU admissions and in-hospital deaths were strongly and negatively correlated to ambient temperatures, with a time lag. The highest Pearson correlation coefficients and statistically significant P values were found 8 days before occurrence of ICU admissions and 15 days before deaths. CONCLUSIONS The study findings show a strong effect of previously observed ambient temperature that has an effect on severity indicators of covid-19.


title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests

text: In 2019, a novel coronavirus (SARS-CoV-2) was first discovered in Wuhan, Hubei, China, causing severe respiratory disease in humans, and has been identified as a public health emergency of international concern. With the spread of the virus, there are more and more false negative cases of RT-PCR nucleic acid detection in the early stage of potential infection. In this paper, we collected the epidemiological history, clinical manifestations, outcomes, laboratory results and images of a SARS-CoV-2 carrier with no significant past medical history. The patient was quarantined because of her colleague had been diagnosed. After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. In addition to coughing up phlegm during her stay in the hospital, she did not develop chills, fever, abdominal pain, diarrhea and other clinical symptoms. Since initial antiviral treatment, the lung lesions were absorbed. But the sputum nucleic acid test was still positive. In combination with antiviral and immune therapy, the patient tested negative for the virus. Notably, SARS-CoV-2 was detected only in the lower respiratory tract samples (sputum) throughout the diagnosis and treatment period. This is a confirmed case of SARS-CoV-2 infection with common symptoms, and her diagnosis has undergone multiple false negatives ,suggesting that it is difficult to identify certain carriers of the virus and that such patients may also increase the spread of the SARS-CoV-2.


title: Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

text: The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription and is essential for viral replication. Here we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.