title: Early Stage Prediction of US County Vulnerability to the COVID-19 Pandemic

text: Key Points: Question: What are key factors that define the vulnerability of counties in the US to cases of the COVID-19 virus? Findings: In this epidemiological study based on publicly available data, we develop a model that predicts vulnerability to COVID-19 for each US county in terms of likelihood of going from no documented cases to at least one case within five days and in terms of number of occurrences of the virus. Meaning: Predicting county vulnerability to COVID-19 can assist health organizations to better plan for resource and workforce needs. Abstract Importance: The rapid spread of COVID-19 means that government and health services providers have little time to plan and design effective response policies. It is therefore important to rapidly provide accurate predictions of how vulnerable geographic regions such as counties are to the spread. Objective: Developing county level prediction around near future disease movement for COVID-19 occurrences using publicly available data. Design: Original Investigation; Decision Analytical Model Study for County Level COVID-19 occurrences using data from March 14-31, 2020. Setting: Disease spread prediction for US counties. Participants: All US county level granularity based on data fused from multiple publicly available sources inclusive of health statistics, demographics, and geographical features. Exposure(s) (for observational studies): Daily county level reported COVID-19 occurrences from March 14-31, 2020. Main Outcome(s) and Measure(s): We developed a 3-stage model to quantify, firstly the probability of COVID-19 occurrence for unaffected counties using XGBoost classifier and secondly, the number of potential occurrences of a county via XGBoost regression. Thirdly, these results are combined to compute the county level risk. This risk is then used as an estimated after-five-day-vulnerability of the county. Results: Using data from March 14-31, 2020, the model shows a sensitivity over 71.5% and specificity over 94%. Conclusions and Relevance: We found that population, population density, percentage of people aged 70 or greater and prevalence of comorbidities play an important role in predicting COVID-19 occurrences. We found a positive association between affected and urban counties as well as less vulnerable and rural counties. The developed model can be used for identification of vulnerable counties and potential data discrepancies. Limited testing facilities and delayed results introduces significant variation in reported cases and produces a bias in the model. Trial Registration: Not Applicable


title: Impact of Chronic Comorbidities on Progression and Prognosis in Patients with COVID-19: A Retrospective Cohort Study in 1031 Hospitalized Cases in Wuhan, China

text: Background The recent outbreak of COVID-19 has rapidly spread worldwide. A large proportion of COVID-19 patients with chronic underlying complications have been reported to be in severe condition and show unpromising clinical outcomes. But whether chronic comorbidities are risk factors affecting the severity of COVID-19 has not been well described. Methods We included COVID-19 patients who had been admitted to Tongji Hospital, Tongji medical college of HUST (Wuhan, China) from January, 27, 2020 to March, 8, 2020 in this retrospective cohort study. The final date of follow-up was March, 30, 2020. All patients were diagnosed with COVID-19 according to Prevention and control Scheme for Novel Coronavirus Pneumonia published by National Health Commission of the People' s Republic of China and WHO interim. Demographic data, medical history, clinical symptoms and signs, laboratory findings, chest computed tomography (CT), treatment and clinical outcomes were extracted from electronic medical records with standardized data collection forms and compared among different groups. Results 1031 COVID-19 inpatients were included in this study, of whom 866 were discharged and 165 were dead in hospital. 73% of 165 dead patients had complicated chronic comorbidities. Of the 1031 patients, 514 (50%) were combined with chronic comorbidities, and showed CFR 2.8 times as that of patients without any underlying disease. The number of patients with hypertension accounted for three fourths of those with concomitant underlying diseases. The univariable regression revealed that patients in the simple hypertension group showed overall risk higher than those in the simple diabetes mellitus group. In the age-grouped research, patients in the hypertension senile group were proved to be at the highest risk, which might be associated with the level of LDH and eGFR. In this retrospective cohort study, 166 (43%) patients with hypertension took CCB during the hospitalization, the odds ratio of CFR in patients with hypertension taking CCB group was 0.68 (P = 0.155), compared to those not. Conclusion Our data shows that the clinical manifestations of most hospitalized patients with COVID-19 are actually systemic syndromes, although COVID-19 is defined as novel coronavirus pneumonia in China. Hypertension is not just a chronic underlying comorbidity, but also a risk factor affecting the severity of COVID-19 and does play a critical role in improving patients' clinical outcomes. Therefore, hypertension management in patients with COVID-19 should be a major challenge in the diagnostic and therapeutic strategies, including optimal management of blood pressure and pathophysiological status.


title: Different Cases of SARS-CoV-2 Infection and Its Impact on Health and Economy with Special Emphasis on Antiviral Drug Targets

text: COVID-19 caused by SARS-CoV-2 has not only issued a pandemic situation but also lead to economic disaster and unprecedented health emergency Being a close relative of Bat corona-virus, SARS and MERS it's structural and sequence similarity has abled scientists for repurposing of popular drugs like hydroxychloroquine, cloroquine and also scavenging for lead molecules by in-silico and in-vivo or in-vitro approach The potent drug targets are ACE2;spike protein binding receptor to host cell surface, Mpro;proteo-lytic polyprotein processing enzymes needed for virion maturation and RdRp;RNA dependent RNA polymerase needed for RNA replication The recent trend focuses on the fact that cocktail of anti-corona virus treatment will be available soon by broad spectrum antiviral compounds It takes time to develop such drug targets till then social distancing and following of hygiene are the only way to thrive well This article incorporates the present World scenario related to COVID infection, focuses on its origin and also future possibilities for a COVID free future


title: Mobility network modeling explains higher SARS-CoV-2 infection rates among disadvantaged groups and informs reopening strategies

text: Fine-grained epidemiological modeling of the spread of SARS-CoV-2 -- capturing who is infected at which locations -- can aid the development of policy responses that account for heterogeneous risks of different locations as well as the disparities in infections among different demographic groups. Here, we develop a metapopulation SEIR disease model that uses dynamic mobility networks, derived from US cell phone data, to capture the hourly movements of millions of people from local neighborhoods (census block groups, or CBGs) to points of interest (POIs) such as restaurants, grocery stores, or religious establishments. We simulate the spread of SARS-CoV-2 from March 1-May 2, 2020 among a population of 105 million people in 10 of the largest US metropolitan statistical areas. We show that by integrating these mobility networks, which connect 60k CBGs to 565k POIs with a total of 5.4 billion hourly edges, even a relatively simple epidemiological model can accurately capture the case trajectory despite dramatic changes in population behavior due to the virus. Furthermore, by modeling detailed information about each POI, like visitor density and visit length, we can estimate the impacts of fine-grained reopening plans: we predict that a small minority of "superspreader" POIs account for a large majority of infections, that reopening some POI categories (like full-service restaurants) poses especially large risks, and that strategies restricting maximum occupancy at each POI are more effective than uniformly reducing mobility. Our models also predict higher infection rates among disadvantaged racial and socioeconomic groups solely from differences in mobility: disadvantaged groups have not been able to reduce mobility as sharply, and the POIs they visit (even within the same category) tend to be smaller, more crowded, and therefore more dangerous. By modeling who is infected at which locations, our model supports fine-grained analyses that can inform more effective and equitable policy responses to SARS-CoV-2.


title: IDentif.AI: Artificial Intelligence Pinpoints Remdesivir in Combination with Ritonavir and Lopinavir as an Optimal Regimen Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

text: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) has led to the rapid initiation of urgently needed clinical trials of repurposed drug combinations and monotherapies. These regimens were primarily relying on mechanism-of-action based selection of drugs, many of which have yielded positive in vitro but largely negative clinical outcomes. To overcome this challenge, we report the use of IDentif.AI, a platform that rapidly optimizes infectious disease (ID) combination therapy design using artificial intelligence (AI). In this study, IDentif.AI was implemented on a 12-drug candidate therapy search set representing over 530,000 possible drug combinations. IDentif.AI demonstrated that the optimal combination therapy against SARS-CoV-2 was comprised of remdesivir, ritonavir, and lopinavir, which mediated a 6.5-fold improvement in efficacy over remdesivir alone. Additionally, IDentif.AI showed hydroxychloroquine and azithromycin to be relatively ineffective. The identification of a clinically actionable optimal drug combination was completed within two weeks, with a 3-order of magnitude reduction in the number of tests typically needed. IDentif.AI analysis was also able to independently confirm clinical trial outcomes to date without requiring any data from these trials. The robustness of the IDentif.AI platform suggests that it may be applicable towards rapid development of optimal drug regimens to address current and future outbreaks.


Canadian Geriatrics Society COVID-19 Recommendations for Older Adults. What Do Older Adults Need To Know?


title: Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene

text: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus and the primary causative agent of coronavirus disease 2019 (COVID-19), first occurred in China and rapidly spread worldwide The government of the Republic of Indonesia confirmed its first two cases of COVID-19 in March 2020 COVID-19 is a serious illness with no efficacious antiviral medication or approved vaccine currently available Therefore, there is a need to investigate the genome of SARS-CoV-2 In this study, we characterized SARS-CoV-2 spike glycoprotein genes from Indonesia to investigate their genetic composition and variability Overall, ten SARS-CoV-2 spike glycoprotein gene sequences retrieved from GenBank (National Center for Biotechnology Information, USA) and the GISAID EpiCoV database (Germany) were compared We analyzed nucleotide variants and amino acid changes using Molecular Evolutionary Genetics Analysis (MEGA) X and analyzed gene similarity using the LALIGN web server Interestingly, we revealed several specific mutation sites, however, there were no significant changes in the genetic composition of SARS-CoV-2 spike glycoprotein genes, when compared to the WuhanHu-1 isolate from China However, this is a preliminary study and we recommend that molecular epidemiology and surveillance programs against COVID-19 in Indonesia be improved


title: Clinical course and potential predicting factors of pneumonia of adult patients with coronavirus disease 2019 (COVID-19): A retrospective observational analysis of 193 confirmed cases in Thailand

text: Background: Clinical spectrum of COVID-19 has been unclear, especially with regard to the presence of pneumonia. We aimed to present clinical course of all laboratory-confirmed adult COVID-19 patients and to identify potential predicting factors of pneumonia. Methods: We conducted a retrospective study among adult patients with confirmed COVID-19 who were hospitalized at Bamrasnaradura Infectious Diseases Institute, Thailand, regardless of their disease severity, between January 8 and April 16, 2020. We described the full picture of COVID-19, defined definite outcomes and evaluated factors associated with pneumonia. Results: One-hundred-and-ninety-three patients were included. The median (IQR) age was 37.0 (29.0-53.0) years, and 58.5% were male. Of whom, 189 (97.9%) recovered and 4 (2.1%) died. More than half (56%) of the patients were mild, 22% were moderate, 14% were severe, and 3% were critically ill. Asymptomatic infection was found in 5%. The overall incidence of pneumonia was 39%. Bilateral was more prevalent than unilateral pneumonia (65% vs. 35%). Increasing age (OR 2.60 for every 10-year increase from 30 years old; 95% CI, 1.68 to 3.97; p<0.001), obesity (OR 9.17; 95% CI, 2.11 to 39.89; p=0.003), and higher temperature at presentation (OR 4.66 per one-degree Celsius increase from 37.2 degree Celsius; 95% CI, 2.32 to 9.34; p<0.001) were potential predicting factors of COVID-19 pneumonia. Severe cases had a longer viral RNA shedding duration than the non-severe cases. The longest observed duration of viral RNA shedding was 45 days. Conclusion: Across different disease severities, most patients with COVID-19 in Thailand had a good prognosis. COVID-19 pneumonia was found in one-third of the hospitalized patients. Potential predicting factors included old age, obesity, fever at presentation.


title: Predicting the end-stage of the COVID-19 epidemic in Brazil

text: We develop a dynamic model of a COVID-19 epidemic as a system of differential equations. The model incorporates an asymptomatic infectious stage and a symptomatic infectious stage. We apply the model to the current COVID-19 epidemic in Brazil. We compare the model output to current epidemic data, and project forward in time possible end-stages of the epidemic in Brazil. The model emphasizes the importance of reducing asymptomatic infections in controlling the epidemic.


title: Detection dogs as a help in the detection of COVID-19 Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples ? Proof-of-concept study

text: The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time. The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone. We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus.


title: A Statistical Analysis Of CoV-19 Positive Test Frequency Data Indicates A Need For Greater Attention To CoV-19 Test Quality And Pre-Wuhan Cov-19 Prevalence

text: Increased attention to analysis of SARS-CoV-2 (CoV-19) positive test frequency data is essential for achievement of better knowledge of the natural history of the virus in human populations, improved accuracy of CoV-19 epidemiological data, and development of public response policies that are better crafted to address the current CoV-19-induced global crisis. A statistical analysis of currently available positive test frequency data reveals a surprisingly uniform relationship between the number of CoV-19 test performed and the number of positive tests obtained. The uniformity is particularly striking for United States CoV-19 test data. Such observations warrant closer evaluation of other factors, besides virus spread, that may also contribute to the nature of the coronavirus pandemic. These include indigenous CoV-19 and the quality of CoV-19 testing.


title: Post COVID-19 ecological and social reset: moving away from capitalist growth models towards tourism as Buen Vivir

text: Tourism has been one of the industries most highly affected by COVID-19. The COVID-19 global pandemic is an ‘unprecedented crisis’ and has exposed the pitfalls of a hyper consumption model of economic growth and development. The scale of immediate economic impacts of the COVID-19 pandemic has shattered the myth of ‘catch up development’ and ‘perpetual growth’. The Crisis has brought unintended degrowth, presenting opportunities for an economic and social ‘reset’. In terms of long-term thinking post COVID-19, it is time to change the parameters of how we imagine a trajectory going forward, to prefigure possibilities for contesting capitalist imperatives that ‘there is no alternative’. In relation to tourism, the pandemic provides an opportunity for reimaging tourism otherwise, away from exploitative models that disregard people, places, and the natural environment, and towards a tourism that has positive impacts. Non-western alternatives to neo-colonial and neoliberal capitalism, such the South American concept of ‘Buen Vivir’, can help us to shift priorities away from economic growth, towards greater social and environmental wellbeing, and meaningful human connections. Taking a Buen Vivir approach to tourism will continue the degrowth momentum, for transformative change in society within the earth’s physical limits. Yet Buen Vivir also redefines the parameters of how we understand ‘limits’. In limiting unsustainable practices in development and tourism, a focus on Buen Vivir actually creates growth in other areas, such as social and environmental wellbeing, and meaningful human connection. Buen Vivir can reorient the tourism industry towards localised tourism, and slow tourism because the principles of Buen Vivir require these alternatives to be small-scale, local and benefiting host communities as well as tourists to increase the wellbeing for all.


title: Subject Index * * Unless otherwise defined, a primary entry always refers to a property or structure of a virus.

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title: A fourteen-day experience with coronavirus disease 2019 (COVID-19) induced acute respiratory distress syndrome (ARDS): An Iranian treatment protocol

text: COVID-19 is currently causing concern in the medical community as the virus is spreading around the world. It has a heavy global burden, particularly in low-income countries. The clinical spectrum of COVID-19 pneumonia ranges from mild to critically ill cases and Acute Respiratory Distress Syndrome. An expert panel was held and an internal protocol was developed to manage the COVID-19 induced ARDS according to WHO recommendations and NIH guidelines. Different therapeutic regimens were employed on this protocol based on the ARDS severity and the patients’ special characteristics. The mortality rate, the rate of survivors, and non-survivors were reported. Of the 231 suspected cases of COVID-19 admitted to the hospital during two weeks, 72 patients were admitted to ICU with diagnosis confirmed by RT-PCR. In total, mortality in the ICU was 25% (n = 18) among ARDS patients over two weeks. COVID-19 induced ARDS is a major concern. The rapid progression of ARDS needs specific protocol based on patients’ characteristics and rapid action.


title: An environmental determinant of viral respiratory disease

text: The evident seasonality of influenza suggests a significant role for weather and climate as one of several determinants of viral respiratory disease (VRD), including social determinants which play a major role in shaping these phenomena. Based on the current mechanistic understanding of how VRDs are transmitted by small droplets, we identify an environmental variable, Air Drying Capacity (ADC), as an atmospheric state-variable with significant and direct relevance to the transmission of VRD. ADC dictates the evolution and fate of droplets under given temperature and humidity conditions. The definition of this variable is rooted in the Maxwell theory of droplet evolution via coupled heat and mass transfer between droplets and the surrounding environment. We present the climatology of ADC, and compare its observed distribution in space and time to the observed prevalence of influenza and COVID-19 from extensive global data sets. Globally, large ADC values appear to significantly constrain the observed transmission and spread of VRD, consistent with the significant coherency of the observed seasonal cycles of ADC and influenza. Our results introduce a new environmental determinant, rooted in the mechanism of VRD transmission, with potential implications for explaining seasonality of influenza, and for describing how environmental conditions may impact to some degree the evolution of similar VRDs, such as COVID-19.


title: A Model Based Analysis for COVID-19 Pandemic in India: Implications for Health Systems and Policy for Low- and Middle-Income Countries

text: Background Our analysis aims to model COVID-19 pandemic in India, potential impact of various measures, along with assessment of health system preparedness and cost to manage the epidemic. Methods We developed a susceptible-exposed-infectious-recovered (SEIR) mathematical model to predict the health outcomes under an unmitigated scenario which comprises of air travel restrictions alone, and the current scenario consisting of air travel restrictions along with 8-week lockdown. In addition, we also evaluate the effectiveness of 8-week lockdown along with intensified public health measures at varying level of effectiveness. We assessed the impact of these interventions on COVID-19 related health outcomes in comparison to the unmitigated scenario. Next, we ascertain the need for augmenting infrastructure and the costs of COVID-19 management in India. Findings In the event of a lockdown for 8 weeks, the peak of the epidemic shifts by 34-76 days, and the number of cases at the end of 8-week lockdown reduces by 69% to 97% with varying effectiveness of lockdown. However, the cumulative long-term cases remain the same. Intensification of public health surveillance measures with 60% effectiveness is estimated to reduce the cases at peak and cumulative number of infections by 70% and 26.6% respectively. The requirement of ICU beds and ventilators would reduce by 83% with intensified public health measures. The cost of managing COVID-19 in India is nearly 4.5% of the gross domestic product (GDP) in the absence of any intervention which increases to 6.2% with intensified public health measures for COVID-19 response. Conclusion Lockdown measures delay the onset of peak, and give much needed time to health system to prepare. Strengthening the public health system response in terms of testing, isolation treatment of cases, and contact tracing needs would lead to significant gains in terms of case load, and meeting health system needs.


Ten Facts about UV Radiation and COVID-19


title: Going viral – Covid-19 impact assessment: A perspective beyond clinical practice

text: In the realm of infectious diseases, a global outbreak is a worst-case scenario In the past, outbreaks such as plague, Spanish flu, severe acute respiratory syndrome, and H1N1 (swine flu) have caused great human suffering The novel coronavirus, christened as Covid-19, is a zoonotic disease which originated from the Wuhan province in China and spread like wildfire killing people and devastating the global economy Mammoth efforts are still on to control this viral strain from further spread Cities have been blocked, air travel banned, ships have been quarantined, and panic-stricken people have been evacuated from China As Covid-19 continues to ravage countries across the globe, this article is an effort to provide an overview of the impact of Covid-19 and tickle wits of intellectuals to think how easily a nanometer organism can virtually bring down superpowers of the world


title: Undocumented infectives in the Covid-19 pandemic

text: Background. A crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing. Methods. The dynamics of an infection can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic model which can be applied when the population is much larger than the fraction of infected subjects. Results. We proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by 1-1/R0 , where R0 is the basic reproduction number. Its mean value R0=2.10 (2.09-2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives. Conclusions. Our results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers in the transmission and spread of the SARS-CoV-2 infection. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease control until a vaccine becomes available.


title: Considerations and recommendations for obstetric anesthesia care during COVID-19 pandemic - Saudi anesthesia society guidelines

text: Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) emerged in Wuhan, China late 2019 and became a pandemic causing coronavirus disease 2019 (COVID-19). Despite its lower mortality rate compared to the other coronaviruses, it has a higher human-to-human transmission rate. Anesthesiologists may benefit from a review of the current evidence related to the obstetric patient with COVID-19. Methods: We reviewed the literature for relevant articles as well as experts' opinions from related medical societies' websites. Conclusion: There are several anesthetic considerations in the care of pregnant women with COVID-19 due to their unique physiological changes. We provide considerations and recommendations for departmental and institutional leadership as well as the obstetric anesthesia providers. These recommendations may apply and can be edited, for future droplet or airborne based pandemics. The rapidly evolving literature makes it important to get updates directly from the relevant medical societies' websites.


‘Everywhere’s a here, isn’t it?’: necropolitical power and its circular tendencies


title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

text: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.


title: The Vacuum Assisted Negative Pressure Isolation Hood (VANISH) System: Novel Application of the Stryker Neptune™ Suction Machine to Create COVID-19 Negative Pressure Isolation Environments

text: Coronavirus disease 2019 (COVID-19) may remain viable in the air for up to three hours, placing health care workers in close proximity to aerosolizing procedures particularly at high risk for infection. This combined with the drastic shortage of negative pressure rooms hospitals worldwide has led to the rapid innovation of novel biohazard isolation hoods, which can be adapted to create negative pressure isolation environments around the patient's airway using the hospital wall suction, which carries many limitations, including weaker suction capabilities, single patient use, and immobility. Here, we report our Vacuum Assisted Negative Pressure Isolation Hood (VANISH) system that uses a mobile and readily available in most hospital operating rooms Stryker Neptune™ (Stryker Corporation, Kalamazoo, Michigan) high-powered suction system to more effectively create a negative pressure biohazard isolation environment. VANISH has been utilized regularly in an anesthesia practice of 30+ providers and, to date, there have been no documented COVID-19 infections.


title: Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

text: Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented during March 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.


title: SweetOrigins: Extracting Evolutionary Information from Glycans

text: Glycans, the most diverse biopolymer and crucial for many biological processes, are shaped by evolutionary pressures stemming in particular from host-pathogen interactions. While this positions glycans as being essential for understanding and targeting host-pathogen interactions, their considerable diversity and a lack of methods has hitherto stymied progress in leveraging their predictive potential. Here, we utilize a curated dataset of 12,674 glycans from 1,726 species to develop and apply machine learning methods to extract evolutionary information from glycans. Our deep learning-based language model SweetOrigins provides evolution-informed glycan representations that we utilize to discover and investigate motifs used for molecular mimicry-mediated immune evasion by commensals and pathogens. Novel glycan alignment methods enable us to identify and contextualize virulence-determining motifs in the capsular polysaccharide of Staphylococcus aureus and Acinetobacter baumannii. Further, we show that glycan-based phylogenetic trees contain most of the information present in traditional 16S rRNA-based phylogenies and improve on the differentiation of genetically closely related but phenotypically divergent species, such as Bacillus cereus and Bacillus anthracis. Leveraging the evolutionary information inherent in glycans with machine learning methodology is poised to provide further – critically needed – insights into host-pathogen interactions, sequence-to-function relationships, and the major influence of glycans on phenotypic plasticity.


title: COVID-19 in China: the role and activities of Internet-based healthcare platforms

text: In the fight against the COVID-19 epidemic, the Chinese Government has enhanced its use of Internet-based healthcare A large number of online medical platforms designed for COVID-19 have emerged in China These platforms can be categorized according to the entity operating them, mainly the government, hospitals, and companies Online medical platforms run by public hospitals provide follow-up consultations for common ailments and frequent ailments based on the hospital's offline services Online diagnosis and treatment platforms provided by companies cover most of the regions in China In terms of offering pandemic-related services, corporate platforms provide at least 1,636,440 doctors for online care, 1 685 billion consultations, and 109 million remote consultations In terms of regular medical care, those platforms provide at least 940,182 doctors for online care and 13 7 million remote consultations;more than 84,916 specialists have provided online care during this period During the prevention and control of this epidemic, online diagnosis and treatment has filled the gap of family doctors in epidemic prevention and control, it has reduced the chance of cross-infection of patients with a mild infection, and it has overcome the geographical limitations of medical resources However, online diagnosis and treatment still faces challenges in terms of resource allocation and industry supervision


title: Modeling the Corona Virus Outbreak in IRAN

text: Background: As the outbreak of coronavirus disease 2019 (COVID19) is a worldwide pandemic it is rapidly expanding in Iran realtime analyses of epidemiological data are needed to increase situational awareness and inform interventions. In this study we built a predictive model based on the cumulative trend of new cases and deaths for the top five provinces. we will also look at modeling the trends for confirmed cases deaths and recovered for the whole country. Method: In this study we have chosen to apply the exponential smoothing model to iteratively forecast future values of a regular time seires from weighted averages of past daily values of the series. This method is exponential because the value of each level is influenced by every preceeding actual value to an exponentially decreasing degree more recent values are given a greater weight. The available data is too small to identify seasonal patterns and make predictable variation in value, such as annual fluctuation in temperature relative to the season. Trend is a tendency in the data to increase or decrease over time. Results: If no control measures are put in place it is expected that over 40000 would be infected in Tehran around the middle of June. However if control measures were implemented with a high degree of success one would expect the spread of the COV19 virus would peak at the start of April with a downward trend dropping off by the end of May (70 days). In the scenario that no further measures are implemented, one would expect the spread of COVID19 to continue on a gentle incline reaching 21000 by mid-June. The same process has been applied to review the confirmed deaths and recovered dataset. The forecast has been carried out for the next 30 days a shorter timeframe has been selected as there is a high probability that the Iranian New Years celebration Farvardin first month of Spring (30th March in Western calendar) will have an impact on the infection rate following the event. The best predictive model predicts the confirmed cases to be in the range of 35000 70000 with the number of reported COVDI-19 deaths to be between 3000 5000 and 5000 30000 of recovered cases. Conclusions: Modeling outbreak ofCovid19 shows that the number of patients and deaths is still increasing. Contagious diseases follow an exponential model and the same be Haves this one. This is because the virus can spread to others and finally each person turns into a carrier of the virus and transmit it to another person. Disease control depends on disconnection and social distancing. In addition many factors are effective in stopping the disease. These include citizens participation in the prevention process health education the effectiveness of instructive traditions environmental conditions and so on.


Possible Old Drugs for Repositioning in COVID-19 Treatment: Combating Cytokine Storms from Haloperidol to Anti-interleukin Agents


docid: lmjaldcs

title: Meteorological factors correlate with transmission of 2019-nCoV: Proof of incidence of novel coronavirus pneumonia in Hubei Province, China

text: Objective: many potential factors contribute to the outbreak of COVID-19.It aims to explore the effects of various meteorological factors on the incidence of COVID-19. Methods: Taking Hubei province of China as an example, where COVID-19 was first reported and there were the most cases, we collected 53 days of confirmed cases (total 67773 cases) and ten meteorological parameters up to March 10. Correlation analysis and linear regression were used to judge the relationship of meteorological factors and increment of COVID-19 confirmed cases. Results: Under 95% CI, the increment of confirmed cases in Hubei were correlated with four meteorological parameters of average pressure, average temperature, minimum temperature and average water vapor pressure (equivalent to absolute humidity).The average pressure was positively correlated with the increment (r=+0.358).The negative correlations included average temperature (r=-0.306), minimum temperature (r=-0.347), and average water vapor pressure (r=-0.326). The linear regression results show if minimum temperature increases by 1℃, the incremental confirmed cases in Hubei decreases by 72.470 units on average. Conclusion: Statistically, the incidence of COVID-19 was correlated with average pressure, average temperature, minimum temperature and average water vapor pressure. It is positively correlated with the average pressure and negatively correlated with the other three parameters. Compared with relative humidity, 2019-nCov is more sensitive to water vapor pressure. The reason why the epidemic situation in Hubei expanded rapidly is significantly related to the climate characteristics of low temperature and dryness of Hubei in winter.


title: Analysis and Forecast of COVID-19 Pandemic in Pakistan

text: The COVID-19 infections in Pakistan are spreading at an exponential rate and a point may soon be reached where rigorous prevention measures would need to be adopted. Mathematical models can help define the scale of an epidemic and the rate at which an infection can spread in a community. I used ARIMA Model, Diffusion Model, SIRD Model and Prophet Model to forecast the magnitude of the COVID-19 pandemic in Pakistan and compared the numbers with the reported cases on the national database. Results depicts that Pakistan could hit peak number of infectious cases between June 2020 and July, 2020.


docid: kusqyumn

title: Underreporting of death by COVID-19 in Brazil's second most populous state

text: The COVID-19 pandemic brings to light the reality of the Brazilian health system. The underreporting of COVID-19 deaths in the state of Minas Gerais (MG), where is concentrated the second largest population of the country, reveals government unpreparedness, as there is a low capacity of testing in the population, which prevents the real understanding of the general panorama of Sars-Cov-2 dissemination. The goals of this research are to analyze the causes of deaths in the different Brazilian government databases (ARPEN and SINAN) and to assess whether there are sub-records shown by the unexpected increase in the frequency of deaths from causes clinically similar to COVID-19. A descriptive and quantitative analysis of the number of COVID-19 deaths and similar causes was made in different databases. Ours results demonstrate that the different official sources had a discrepancy of 209.23% between these data referring to the same period. There was also a 648.61% increase in SARS deaths in 2020, when compared to the average of previous years. Finally, it was shown that there was an increase in the rate of pneumonia and respiratory insufficiency (RI) by 5.36% and 5.72%, respectively. In conclusion, there is an underreporting of COVID-19 deaths in MG due to the unexplained excess of SARS deaths, Respiratory insufficiency and pneumonia compared to previous years.


title: Serum responses of children with Kawasaki Disease against SARS-CoV-2 proteins.

text: Recently, numerous reports have suggested association of pediatric Coronavirus Disease 2019 (COVID-19) cases and Kawasaki Disease (KD). KD is a major cause of childhood acquired heart disease and vasculitis in the pediatric population. Epidemiological patterns suggest KD is related to an infectious agent; however, the etiology remains unknown1. As past reports have considered other coronaviruses to be related to KD2,3, these reports of pediatric COVID-19 related inflammatory disorder cases leads to the hypothesis of potential cross-coronavirus reactivity that would account for the past controversial proposals of other coronaviruses and these new cases. We sought to address this hypothesis by assessing the antigen targeting of biobanked plasma samples of febrile children, including those with KD, against SARS-CoV-2 proteins.


title: Seroprevalence of Antibodies to SARS-CoV-2 in Healthcare Workers in Non-epidemic Region: A Report from Iwate Prefecture in Japan

text: Background: As of June 8, 2020, Iwate is the only one of 47 prefectures in Japan with no confirmed coronavirus disease 2019 (COVID-19) cases. Serological survey for COVID-19 antibodies is crucial in area with low prevalence as well as epidemic area when addressing health and social issues caused by COVID-19. Rapid, accurate and easy-to-use antibody tests as well laboratory-based antibody tests are necessary for confirming immunity in a given community. Methods:Serum samples from healthcare workers (n = 1,000, mean 40 {+/-} 11 years) of Iwate Prefectural Central Hospital, Iwate, Japan were tested for the prevalence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Two laboratory-based quantitative tests (Abbott Architect SARS-CoV-2 IgG and Roche Elecsys Anti-SARS-CoV-2 assays) and one point-of-care (POC) qualitative test (Alfa Instant-view plus COVID-19 Test) were performed simultaneously. Sensitivity and specificity were 100%, 99.6% in Abbott assay; 100%, 99.8% in Roche assay; 97.8%, 94.6% in Alfa POC test, respectively. Results:The laboratory-based quantitative tests showed positive in 4 of 1,000 samples (0.4%) (95% CI: 0.01 to 0.79): 4/1,000 (0.4%) (95% CI: 0.01 to 0.79) in Abbott; 0/1,000 (0%) in Roche. Positive samples were not detected for both Abbott and Roche assays. The POC qualitative test showed positive in 33 of 1,000 samples (3.3%) (95% CI: 2.19 to 4.41), showing higher rates than those of the laboratory-based quantitative tests. There were no samples with simultaneous positive reaction for two quantitative tests and a POC test. Conclusions: Infected COVID-2 cases were not confirmed by a retrospective serological study in healthcare workers of our hospital. The POC qualitative tests with lower specificity have the potential for higher false positive reactions than the laboratory-based quantitative tests in areas with very low prevalence of COVID-19.


title: Whole Genome Comparison of Pakistani Corona Virus with Chinese and US Strains along with its Predictive Severity of COVID-19

text: Recently submitted 784 SARS-nCoV2 whole genome sequences from NCBI Virus database were taken for constructing phylogenetic tree to look into their similarities. Pakistani strain MT240479 (Gilgit1-Pak) was found in close proximity to MT184913 (CruiseA-USA), while the second Pakistani strain MT262993 (Manga-Pak) was neighboring to MT039887 (WI-USA) strain in the constructed cladogram in this article. Afterward, four whole genome SARS-nCoV2 strain sequences were taken for variant calling analysis, those who appeared nearest relative in the earlier cladogram constructed a week time ago. Among those two Pakistani strains each of 29,836 bases were compared against MT263429 from (WI-USA) of 29,889 bases and MT259229 (Wuhan-China) of 29,864 bases. We identified 31 variants in both Pakistani strains, (Manga-Pak vs USA=2del+7SNPs, Manga-Pak vs Chinese=2del+2SNPs, Gilgit1-Pak vs USA=10SNPs, Gilgit1-Pak vs Chinese=8SNPs), which caused alteration in ORF1ab, ORF1a and N genes with having functions of viral replication and translation, host innate immunity and viral capsid formation respectively. These novel variants are assumed to be liable for low mortality rate in Pakistan with 385 as compared to USA with 63,871 and China with 4,633 deaths by May 01, 2020. However functional effects of these variants need further confirmatory studies. Moreover, mutated N & ORF1a proteins in Pakistani strains were also analyzed by 3D structure modelling, which give another dimension of comparing these alterations at amino acid level. In a nutshell, these novel variants are assumed to be linked with reduced mortality of COVID-19 in Pakistan along with other influencing factors, these novel variants would also be useful to understand the virulence of this virus and to develop indigenous vaccines and therapeutics.


title: Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion

text: Background. In the background of the current COVID-19 pandemic, serological tests are being used to assess past infection and immunity against SARS-CoV-2. This knowledge is paramount to determine the transmission dynamics of SARS-CoV-2 through the post pandemic period. Several individuals belonging to households with an index COVID-19 patient, reported symptoms of COVID-19 but discrepant serology results. Methods. Here we investigated the humoral and cellular immune responses against SARS-CoV-2 in seven families, including nine index patients and eight contacts, who had evidence of serological discordances within the households. Ten unexposed healthy donors were enrolled as controls. Results. All index patients recovered from a mild COVID-19. They all developed anti-SARS-CoV-2 antibodies and a significant T cell response detectable up to 69 days after symptom onset. Six of the eight contacts reported COVID-19 symptoms within 1 to 7 days after the index patients but all were SARS-CoV-2 seronegative. Six out of eight contacts developed a SARS-CoV-2-specific T cell response against structural and/or accessory proteins that lasts up to 80 days post symptom onset suggesting a past SARS-CoV-2 infection. Conclusion. Exposure to SARS-CoV-2 can induce virus-specific T cell responses without seroconversion. T cell responses may be more sensitive indicators of SARS-Co-V-2 exposure than antibodies. Our results indicate that epidemiological data relying only on the detection of SARS-CoV-2 antibodies may lead to a substantial underestimation of prior exposure to the virus


7 tips to maintain hearing health care amid COVID-19


title: Inclusive Costs of NPI Measures for COVID-19 Pandemic: Three Approaches

text: The paper evaluates total inclusive costs of three public health approaches to address the COVID-19 epidemic in the US based on epidemiological projections in Ferguson et al (2020). We calculate and add costs of lost productivity and costs of mortality measured through the value of statistical life. We find that the aggressive approach which involves strict suppression measures and a drastic reduction of economic activity for three months with extensive testing and case tracking afterwards results in the lowest total costs for the society. The approach of doing no non-pharmaceutical measures results in the lowest total costs if the infection fatality rate falls below 0.15%.


docid: bghgfcxo

title: An age-structured epidemiological model of the Belgian COVID-19 epidemic

text: COVID-19 has prompted many countries to implement extensive social distancing to stop the rapid spread of the virus, in order to prevent overloading health care systems. Yet, the main epidemic parameters of this virus are not well understood. In the absence of broad testing or serological surveillance, it is hard to evaluate or predict the impact of different strategies to exit implemented lock-down measures. An age-structured epidemiological model was developed, which distinguishes between the younger versus older population (e.g. < 65 and >= 65). Because the illness severity is markedly different for these two populations, such a separation is necessary then estimating the model based on death and hospitalization incidence data. The model was applied to data of the Belgian epidemic and used to predict how the epidemic would react to a relaxing of social distancing measures.


title: Population heterogeneity is a critical factor of the kinetics of the COVID-19 epidemics

text: The novel coronavirus pandemic generates extensive attention in political and scholarly domains. Its potentially lasting prospects, economic and social consequences call for a better understanding of its nature. The widespread expectations of large portions of the population to be infected or vaccinated before containing the COVID-19 epidemics rely on assuming a homogeneous population. In reality, people differ in the propensity to catch the infection and spread it further. Here, we incorporate population heterogeneity into the Kermack-McKendrick SIR compartmental model and show the cost of the pandemic may be much lower than usually assumed. We also indicate the crucial role of correctly planning lockdown interventions. We found that an efficient lockdown strategy may reduce the cost of the epidemic to as low as several percents in a heterogeneous population. That level is comparable to prevalences found in serological surveys. We expect that our study will be followed by more extensive data-driven research on epidemiological dynamics in heterogeneous populations.


title: SARS-CoV-2 detection in nasopharyngeal throat swabs by metagenomics

text: Metagenomics could detect SARS-CoV-2 in all eight nasopharyngeal/throat swabs with high/low viral loads, and rhinovirus in a co-infected patient. The sequenced viruses belonged to lineage B1. Because metagenomics could detect novel pathogen and co-infection, and generate sequence data for epidemiological investigation, it is an attractive approach for infectious-disease diagnosis.


title: How will this continue? Modelling interactions between the COVID-19 pandemic and policy responses

text: Much of the uncertainty about the progression of the COVID-19 pandemic stems from questions about when and how non-pharmaceutical interventions (NPI) by governments, in particular social distancing measures, are implemented, to what extent the population complies with these measures, and how compliance changes through time. Further uncertainty comes from a lack of knowledge of the potential effects of removing interventions once the epidemic is declining. By combining an epidemiological model of COVID-19 for the United Kingdom with simple sub-models for these societal processes, this study aims to shed light on the conceivable trajectories that the pandemic might follow over the next 1.5 years. We show strong improvements in outcomes if governments review NPI more frequently whereas, in comparison, the stability of compliance has surprisingly small effects on cumulative mortality. Assuming that mortality does considerably increase once a country's hospital capacity is breached, we show that the inherent randomness of societal processes can lead to a wide range of possible outcomes, both in terms of disease dynamics and mortality, even when the principles according to which policy and population operate are identical.. Our model is easily modified to take other aspects of the socio-pandemic interaction into account.


docid: lwaweuym

title: How a SARS antibody binds to SARS-CoV-2

text: esearchers at Scripps Research and the University of Hong Kong have shown how a human antibody for the virus that causes severe acute respiratory syndrome (SARS) can also bind the new COVID-19-causing coronavirus (Science 2020, DOI: 10 1126/science abb7269) The structural insights from might help in COVID-19 vaccine and drug design, the researchers say During a SARS epidemic in 2006, researchers isolated antibodies for the virus, SARS-CoV, from infected patients Earlier this year, researchers in China showed that one of those antibodies, CR3022, also binds to the spike protein of the virus that causes COVID-19, SARS-CoV-2 (Emerging Microbes Infect 2020, DOI: 10 1080/22221751 2020 1729069) To see how exactly the antibody binds to the spike protein, a group led by Ian A Wilson ordered a sample of CR3022 and produced sections of SARS-CoV-2’s spike protein called the receptor-binding domain (RBD) The group used X-ray crystallography to find that, as predicted by the Chinese researchers, the View: PDF ;Full Text HTML


title: Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations

text: Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV-2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10-30 °C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40 °C and attains a completely closed conformation at 50 °C. The closed conformation disables its ability to bind to ACE2, due to the burying of its receptor binding residues. Our results clearly show that there are active and inactive states of the protein at different temperatures. This would not only prove beneficial for understanding the fundamental nature of the virus, but would be also useful in the development of vaccines and therapeutics. Graphical Abstract Highlights Statistical and epidemiological evidence show that external climatic conditions influence the SARS-CoV infectivity, but we still lack a molecular level understanding of the same. Here, we study the influence of temperature on the structure of the Spike glycoprotein, the outermost structural protein, of the virus which binds to the human receptor ACE2. Results show that the Spike’s S1 domain is very sensitive to external atmospheric conditions compared to the S2 transmembrane domain. The N-terminal domain comprises of several solvent exposed charged residues that are capable of binding to human proteins. The region is specifically stable at temperatures ranging around 10-30° C. The Receptor Binding Motif adopts a closed conformation at 40°C and completely closes at higher temperatures making it unsuitable of binding to human receptors


title: COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection

text: Background Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are therefore a key source of information. Methods We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV-host interactome was carried out in order to provide a theoretic host-pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein-protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. Results Although the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines. Conclusions In this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided pharmaceutical and diagnostic research with the prospect to identify potential new biological targets.


Breaking News: 16 Common-Sense Tips and Facts for Dealing with COVID-19


title: TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes

text: Both gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA have been frequently observed in COVID-19 patients. However, whether SARS-CoV-2 replicate in the human intestine and its clinical relevance to potential fecal-oral transmission remain unclear. Here, we demonstrate productive infection of SARS-CoV-2 in ACE2+ mature enterocytes in human small intestinal enteroids. In addition to TMPRSS2, another mucosa-specific serine protease, TMPRSS4, also enhanced SARS-CoV-2 spike fusogenic activity and mediated viral entry into host cells. However, newly synthesized viruses released into the intestinal lumen were rapidly inactivated by human colonic fluids and no infectious virus was recovered from the stool specimens of COVID-19 patients. Our results highlight the intestine as a potential site of SARS-CoV-2 replication, which may contribute to local and systemic illness and overall disease progression.


Can adenoviral vectors overcome a checkered past to win the COVID-19 vaccine race?


title: A Pilot Comparative Study of Dental Students' Ability to Detect Enamel-only Proximal Caries in Bitewing Radiographs With and Without the use of AssistDent (R) Deep Learning Software

text: Enamel-only proximal caries, if detected, can be reversed by non-invasive treatments. Dental bitewing radiograph analysis is central to diagnosis and treatment planning and when used to detect enamel-only proximal caries it is an important tool in minimum intervention and preventive dentistry. However, the subtle patterns of enamel-only proximal caries visible in a bitewing radiographs are difficult to detect and often missed by dental practitioners. This pilot study measures the ability of a cohort of third-year dental students to detect enamel-only proximal caries in bitewing radiographs with and without the use of a deep learning assistive software AssistDent(R). We demonstrate an increased ability in the detection of enamel-only proximal caries by the students using AssistDent, showing a mean sensitivity level of 0.80 (95%CI {+/-} 0.04), increased from 0.50 (95%CI {+/-} 0.13) p<0.01 shown by students not using AssistDent. This improvement in ability was achieved without an increase in false positives. Mean false positives per bitewing radiograph recorded by students when using AssistDent was 2.64 (95%CI {+/-} 0.57), and by students without using AssistDent was 2.46 (95%CI {+/-} 1.51). Based on these results we conclude that the AI-based software AssistDent significantly improves third-year dental students' ability to detect enamel-only proximal caries and could be considered as a tool to support minimum intervention and preventive dentistry in teaching hospitals and general practice. We also discuss how the experience of conducting this pilot study can be used to inform the design and methodology of a follow-on study of AssistDent in dental practice use.


title: Mortality rates from COVID-19 in Spain and Italy, Lessons for the UK!

text: The Covid-19 pandemic brings major new challenges to health services resulting from the lack of a vaccine and from the enormous resources it can consume over a prolonged period. The available control measures are currently limited to quarantining, contact tracking-and-tracing and social distancing. Disease transmission to health care workers is common and deaths among clinical and nursing staff have been reported in the UK (where serious concerns about the availability of personal protective equipment - PPE - have been raised) and elsewhere; particularly in Lombardy, where General Practitioners (Medici di Base) have died in disproportionate numbers.


title: Clinical Performance of SARS-CoV-2 Molecular Testing

text: Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the test clinical performance is poorly understood. From 3/10/2020-5/1/2020 NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed in 3,432 patients, of which 2,413 had negative and 1,019 had positive first day results. Repeat-tested patients were more likely to be older, male, African-American or Hispanic, and to have severe disease. Among the patients with initially negative results, 18.6% became positive upon repeat-testing. Only 58.1% of any-time positive patients had a result of "detected" on the first test. The clinical sensitivity of COVID-19 molecular assays is estimated between 66.2% and 95.6%, depending on the unknown number of false negative results in single-tested patients. Conversion to a negative result is unlikely to occur before 15 to 20 days after initial testing or 20-30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Forty-nine initially-positive patients converted to negative and then back to positive in subsequent days. Conversion from first day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19.


title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014

text: Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this viral family as a zoonotic public health threat. To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013-2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151). Coronaviruses were detected in the majority of wildlife farms (60.7%, 17/28) and in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are farmed. We identified six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including the Alpha-, Beta-, and Gammacoronaviruses. Our analysis also suggested either mixing of animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and avian coronaviruses were detected in rodent feces in the trade. The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spillover to people.


title: Pandemic of the new coronavirus SARSCoV-2 in Venezuela/ Venezuela y su índice de seguridad sanitaria global para afrontar la pandemia del nuevo coronavirus SARSCoV-2

text: Respiratory viruses have starred in the history of humanity's pandemics. At the end of the year 2019 the appearance of a new respiratory disease COVID-19 begins, the novel coronavirus is designated SARSCoV-2. The clinical manifestations are mild in approximately 80% of cases, fever and dry cough are its predominant signs, in severe cases it is difficult to breathe, more severely in elderly patients, hypertension and diabetes. Emerging viruses represent a challenge for effective clinical treatment, rendesivir, lopinavir, chloroquine, and nitasoxanide, among others, are being tested. Clinical trials with drugs that are known and approved for use in humans are suggested. It would be interesting to test the use of tetracyclines or their semi-synthetic derivatives. Venezuela is among the least prepared countries to react to major infectious disease outbreaks, managing this new epidemic represents a significant challenge, especially considering that health centers and research institutes are greatly affected by the abandonment and the diaspora.


title: Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes

text: Over half of the world’s population lives in urban areas with, according to the United Nations (UN), nearly 70% expected to live in cities by 2050 (United Nations, 2019). Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city’s microbiome. Our design decisions for the built environment shape these invisible populations, and we interact with them on a constant basis. A growing body of evidence shows us that our health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms—bacteria or fungi—with which they live in continual exchange and symbiosis. While the processing and sequencing of samples can be high-throughput, gathering samples is still very expensive, labor intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city, such as City Sampling Day (metasub.org). Here we postulate that honeybees may be effective collaborators in the sampling process, as they daily forage within a 2-mile radius of their hive. We describe the results of a pilot study conducted with 3 rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (beeswax, honey, debris, pollen, propolis) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities in this manner: Sydney, Melbourne, Venice and Tokyo. While the molecular and computational methods used here were based on DNA analysis, it is possible they could be used to monitor RNA-based viruses such as Sars-Cov-2. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.


title: Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa

text: Background: The SARS-CoV-2 virus may affect both adults and children. Although the disease, named COVID-19, has a lower prevalence in infancy and has been described as mild, the clinical characteristics may vary and there is a possibility of complications. Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children admitted with COVID-19 to a secondary hospital. Methods: This case series includes all patients with SARS-CoV-2 infection confirmed by PCR testing, identified in the state epidemiological surveillance system between March 1 and May 31, 2020. Confirmed patients admitted to the Sinaloa Pediatric Hospital (HPS) during the same dates are also described. Results: Fifty one children with SARS-CoV-2 were included, 10 of the admitted to HPS. The median age was 10 years. The more frequent symptoms were fever (78%), cough (67%) and headache (57%). Most cases were mild or asymptomatic. Three patients with comorbidities died. Only 4 of 10 patients identified in HPS had been admitted with the diagnosis of possible COVID-19. Conclusions: SARS-CoV-2 infection in children was mostly mild or asymptomatic, but with a wide range of clinical presentations.


docid: mykkncgo

title: Methodological problems and solutions for sampling in epidemiological SARS-CoV-2 research

text: Existing reporting systems and surveys give biased estimates of the true prevalence of SARS-CoV-2 infections and the development of these rates over time. Little is known on progression of the disease in persons who are already identified as infected. Finally, the number of deaths due to the infection (not during the infection) is also unknown. We describe data requirements for epidemiological and social research and give details of the sampling and fieldwork procedures required for different types of studies.


title: Injury-Prone: Peripheral nerve injuries associated with prone positioning for COVID-19-related acute respiratory distress syndrome

text: Patients with Coronavirus disease 2019 (COVID-19) who require invasive mechanical ventilation frequently meet the acute respiratory distress syndrome (ARDS) diagnostic criteria. Hospitals based in the United States have been incorporating prone positioning (PP) into the COVID-19-related ARDS treatment plan at a higher rate than normal. Here, we describe 11 patients admitted to a single inpatient rehabilitation hospital who were subsequently diagnosed with acquired focal/multifocal peripheral nerve injury (PNI) in association with the use of PP for COVID-19-related ARDS. The reason for the high rate of PNI associated with PP in COVID-19 ARDS is likely multifactorial, but may include an underlying state of hyperinflammation and hypercoagulability already linked to other the neurological sequelae of COVID-19. Physicians must be aware of this elevated susceptibility to PNI in severe COVID-19 and refined standard PP protocols in order to reduce the risk.


docid: dgyvbarm

title: A Nationwide Survey of UK cardiac surgeons view on clinical decision making during the COVID-19 pandemic

text: Background: No firm recommendations are currently available to guide decision making for patients requiring cardiac surgery during the COVID-19 pandemic. Systematic appraisal of national expert consensus can be used to generate interim recommendations until data from clinical observations will become available. Hence, we aimed to collect and quantitatively appraise nationwide UK senior surgeons opinion on clinical decision making for patients requiring cardiac surgery during the COVID-19 pandemic. Methods: We mailed a web-based questionnaire to all consultant cardiac surgeons through the Society for Cardiothoracic Surgery in Great Britain and Ireland (SCTS) mailing list on the 17th April 2020 and we pre-determined to close the survey on the 21st April 2020. This survey was primarily designed to gather information on UK surgeons opinion using 12 items. Strong consensus was predefined as an opinion shared by at least 60% of responding consultants. Results: A total of 86 consultant surgeons undertook the survey. All UK cardiac units were represented by at least one consultant. Strong consensus was achieved for the following key questions:1) before hospital admission every patient should receive nasopharyngeal swab, PCR and chest CT; 2) the use of full PPE should to be adopted in every case by the theatre team regardless patients COVID-19 status; 3) the risk of COVID-19 exposure for patients undergoing heart surgery should be considered moderate to high and likely to increase mortality if it occurs; 4) cardiac procedure should be decided based on ad-hoc multidisciplinary team discussion for every patient. The majority believed that both aortic and mitral surgery should be considered in selected cases. The role of CABG surgery during the pandemic was more controversial. Conclusions: In the current unprecedented scenario, the present survey provides information for generating interim recommendations until data from clinical observations will become available.


title: Better Safe than Sorry: Interventional Radiology Should Be Prepared for the Coronavirus Disease 2019 Pandemic

text: Coronavirus disease 2019 (COVID-19) is a viral pneumonia that has plagued the world for much of the first quarter of 2020 and was recently declared a global pandemic. The caregivers must be aware of the disease and take steps to curb its transmission within the premises of our care settings (hospitals/clinics). In this article, we suggest a few proactive steps that can be taken at the institutional and departmental levels to break the transmission chain.


Commentary: “Leave No One Behind” and Access to Protection in the Greek Islands in the COVID‐19 Era


title: Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline

text: In order to explore nonsynonymous mutations and deletions in the spike (S) protein of SARS-CoV-2, we comprehensively analyzed 35,750 complete S protein gene sequences from across six continents and five climate zones around the world, as documented in the GISAID database as of June 24th, 2020. Through a custom Python-based pipeline for analyzing mutations, we identified 27,801 (77.77 % of spike sequences) mutated strains compared to Wuhan-Hu-1 strain. 84.40% of these strains had only single amino-acid (aa) substitution mutations, but an outlier strain from Bosnia and Herzegovina (EPI_ISL_463893) was found to possess six aa substitutions. The D614G variant of the major G clade was found to be predominant across circulating strains in all climates. We also identified 988 unique aa substitution mutations distributed across 660 positions within the spike protein, with eleven sites showing high variability – these sites had four types of aa variations at each position. Besides, 17 in-frame deletions at four major regions (three in N-terminal domain and one just downstream of the RBD) may have possible impact on attenuation. Moreover, the mutational frequency differed significantly (p= 0.003, Kruskal–Wallis test) among the SARS-CoV-2 strains worldwide. This study presents a fast and accurate pipeline for identifying nonsynonymous mutations and deletions from large dataset for any particular protein coding sequence and presents this S protein data as representative analysis. By using separate multi-sequence alignment with MAFFT, removing ambiguous sequences and in-frame stop codons, and utilizing pairwise alignment, this method can derive nonsynonymus mutations (Reference:Position:Strain). We believe this will aid in the surveillance of any proteins encoded by SARS-CoV-2, and will prove to be crucial in tracking the ever-increasing variation of many other divergent RNA viruses in the future.


title: Why do People Share Misinformation during the COVID-19 Pandemic?

text: The World Health Organization have emphasised that misinformation - spreading rapidly through social media - poses a serious threat to the COVID-19 response. Drawing from theories of health perception and cognitive load, we develop and test a research model hypothesizing why people share unverified COVID-19 information through social media. Our findings suggest a person's trust in online information and perceived information overload are strong predictors of unverified information sharing. Furthermore, these factors, along with a person's perceived COVID-19 severity and vulnerability influence cyberchondria. Females were significantly more likely to suffer from cyberchondria, however, males were more likely to share news without fact checking their source. Our findings suggest that to mitigate the spread of COVID-19 misinformation and cyberchondria, measures should be taken to enhance a healthy skepticism of health news while simultaneously guarding against information overload.


Corona I - Home alone


title: Determinants of COVID-19 incidence and mortality: A cross-country analysis

text: Objective: We undertook this study to explore the role of important determinants affecting global COVID-19 incidence and mortality taking multifactorial disease dynamics into consideration. Design: Secondary data as on March 28, 2020 were obtained for 97 countries. Association of COVID-19 cumulative incidence and mortality measures were assessed with ten indictors representing health system characteristics, climate, demography, promptness of international travel restriction and population movement using Generalized Linear Modelling. Main outcome measures: Country-specific COVID-19 cumulative incidence, cumulative cause-specific mortality and case fatality rate. Results: Significant inter-country variation in incidence and mortality rates were observed. Five variables were found to be associated with cumulative incidence: testing rate per 1000 population ({beta} = 0.119, p < 0.01), UHC index ({beta} = 0.043, p = 0.04), percentage elderly population ({beta} = 0.122, p < 0.01), percentage below-poverty line population ({beta} = -0.048, p < 0.01) and disability adjusted life years due to NCDs ({beta} = -0.013, p < 0.01). Case fatality rate was observed to be associated with testing rate per 1000 population ({beta} = -0.058, p = 0.03) and population density ({beta} = 0.002, p = 0.02), while the cumulative cause-specific mortality was associated with only percentage elderly population ({beta} = 0.096, p = 0.04) in the country. Conclusions: Health system response, population susceptibility and demography were the most important factors determining the progression. Policy response should focus towards increasing testing, primarily targeting high population density areas. Health system strengthening and reduction in population risk factors should be long term goals for a better response to such epidemics.


title: SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped and remodels intracellular membranes for genome replication and assembly. Here, we report critical insights into the budding mechanism of the virus and provide structural details of virions and virus induced double-membrane vesicles by in situ cryo-electron tomography. We directly visualized double-stranded RNA within double-membrane vesicles, forming a loosely organized network with frequent RNA branching consistent with template-directed RNA synthesis intermediates. Our data indicate that membrane bending is orchestrated by the spike trimer and viral ribonucleoprotein complex recruitment into virion budding sites, suggesting the synergistic interplay of both viral components as a possible drug target for intervention.


title: Tensions between research and public health: modelling the risks and benefits of SARS-CoV-2 vaccine field trials versus human infection challenge studies.

text: Background: Human infection challenge studies (HICS) with SARS-CoV-2 are under consideration as a way of accelerating vaccine development. We evaluate potential vaccine research strategies under a range of epidemic conditions determined, in part, by the intensity of public health interventions. Methods: We constructed a compartmental epidemiological model incorporating public health interventions, vaccine efficacy trials and a post-trial population vaccination campaign. The model was used to estimate the duration and benefits of large-scale field trials in comparison with HICS accompanied by an expanded safety trial, and to assess the marginal risk faced by HICS participants. Results: Field trials may demonstrate vaccine efficacy more rapidly than a HICS strategy under epidemic conditions consistent with moderate mitigation policies. A HICS strategy is the only feasible option for testing vaccine efficacy under epidemic suppression, and maximises the benefits of post-trial vaccination. Less successful or absent mitigation results in minimal or no benefit from post-trial vaccination, irrespective of trial design. Conclusions: SARS-CoV-2 HICS are the optimal method of vaccine testing for populations maintained under epidemic suppression, where vaccination offers the greatest benefits to the local population.


The use of Guedel Airway for Naso-Orogastric tube insertion in patients with COVID-19. A way to minimize aerosol generation


Hackers paradise: Hackers across Latin America are taking advantage of the current crisis to access people’s personal data. If not protected it could spell disaster


title: Social Distancing Has Merely Stabilized COVID-19 in the US

text: Social distancing measures, with varying degrees of restriction, have been imposed around the world in order to stem the spread of COVID-19. In this work we analyze the effect of current social distancing measures in the United States. We quantify the reduction in doubling rate, by state, that is associated with social distancing. We find that social distancing is associated with a statistically-significant reduction in the doubling rate for all but three states. At the same time, we do not find significant evidence that social distancing has resulted in a reduction in the number of daily confirmed cases. Instead, social distancing has merely stabilized the spread of the disease. We provide an illustration of our findings for each state, including point estimates of the effective reproduction number, R, both with and without social distancing. We also discuss the policy implications of our findings.


title: Effects of latency on estimates of the COVID-19 replication number

text: It is not currently known how long it takes a person infected by the COVID-19 virus to become infectious. Models of the spread of COVID-19 use very different lengths for this latency period, leading to very different estimates of the replication number R, even when models work from the same underlying data sets. In this paper we quantify how much varying the length of the latency period affects estimates of R, and thus the fraction of the population that is predicted to be infected in the first wave of the pandemic. This variation underscores the uncertainty in our understanding of R and raises the possibility that R may be considerably greater than has been assumed by those shaping public policy.


title: Development and validation of the Elecsys Anti-SARS-CoV-2 immunoassay as a highly specific tool for determining past exposure to SARS-CoV-2

text: Background: The Elecsys(R) Anti-SARS-CoV-2 immunoassay (Roche Diagnostics) was developed to provide an accurate and reliable method for the detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated the sensitivity, specificity, and cross-reactivity of the Elecsys Anti-SARS-CoV-2 immunoassay. Methods: The performance of the Elecsys Anti-SARS-CoV-2 immunoassay was assessed at Roche Diagnostics (Penzberg, Germany). Sensitivity was evaluated using anonymised residual frozen samples from patients who had previously tested positive for SARS-CoV-2 infection by polymerase chain reaction (PCR); one or more consecutive samples were collected from patients at various timepoints after PCR confirmation. Specificity was evaluated using anonymised unselected residual frozen samples from routine diagnostic testing or from blood donors; all samples were collected before December 2019 and thus deemed negative for SARS-CoV-2-specific antibodies. Cross-reactivity was evaluated using anonymised frozen samples containing a wide range of potentially cross-reacting analytes, which were purchased from commercial vendors. For sensitivity and specificity, point estimates and 95% confidence intervals (CIs) were calculated. Results: Sensitivity of the Elecsys Anti-SARS-CoV-2 immunoassay in 496 samples from 102 patients with prior PCR-confirmed SARS-CoV-2 infection was 99.5% (95% CI 97.0-100.0) at [≥]14 days after PCR confirmation. Overall specificity in 10,453 samples from routine diagnostic testing (n = 6305) and blood donors (n = 4148) was 99.80% (95% CI 99.69-99.88). Only 4/752 samples containing potential cross-reacting analytes were reactive with the Elecsys Anti-SARS-CoV-2 immunoassay, resulting in an overall specificity in this cohort of 99.5% (95% CI 98.6-99.9). Conclusion: The Elecsys Anti-SARS-CoV-2 immunoassay demonstrated a sensitivity of 99.5% at [≥]14 days after PCR confirmation and a very high specificity of 99.80%. Our findings support the use of the Elecsys Anti-SARS-CoV-2 immunoassay as a tool for the identification of past SARS-CoV-2 infection, including in populations with a low disease prevalence.


title: Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In silico analysis

text: The novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we, therefore, designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of nucleocapsid protein that aid in viral replication. Promising antigenic B-cells and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and non-allergenic property. Two CD8+ and Three CD4+ T-cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and II alleles. With these selected epitopes, a non-allergenic chimeric peptide vaccine incapable of inducing a Type II hypersensitivity reaction was constructed. The molecular interaction between the toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.


News from our societies – IFSW: COVID-19: The struggle, success and expansion of social work – Reflections on the profession’s global response, 5 months on


title: A structured open dataset of government interventions in response to COVID-19

text: In response to the COVID-19 pandemic, governments have implemented a wide range of nonpharmaceutical interventions (NPIs). Monitoring and documenting government strategies during the COVID-19 crisis is crucial to understand the progression of the epidemic. Following a content analysis strategy of existing public information sources, we developed a specific hierarchical coding scheme for NPIs. We generated a comprehensive structured dataset of government interventions and their respective timelines of implementation. To improve transparency and motivate collaborative validation process, information sources are shared via an open library. We also provide codes that enable users to visualise the dataset. Standardization and structure of the dataset facilitate inter-country comparison and the assessment of the impacts of different NPI categories on the epidemic parameters, population health indicators, the economy, and human rights, among others. This dataset provides an in-depth insight of the government strategies and can be a valuable tool for developing relevant preparedness plans for pandemic. We intend to further develop and update this dataset on a weekly basis until the end of December 2020.


title: COVID-19 Pandemic: Marked Global Disparities in Fatalities According to Geographic Location and Universal Health Care

text: Since its outbreak, COVID-19 pandemic has been the biggest global concern with exponentially increasing number of cases and associated deaths across all habitable continents. Various countries around the world with their diverse health care systems, have responded to the pandemic in very distinctive ways. In this paper, we: compared COVID-19 mortality rates across global geographic regions; and assessed differences in COVID-19-related case fatality rate (CFR) based on presence or absence of Universal Health Coverage (UHC). We found that as of May 6, 2020, Europe had experienced the highest CFR globally of 9.6%, followed by 5.9% in North America. Although the pandemic originated in Asia, the continent ranked second to the last in terms of CFR (3.5%). Countries with UHC had lower number of cases of 37.6%, but the CFR of countries with UHC was twice that of countries without UHC (10.5% versus 4.9%). In conclusion, UHC does not appear to protect against mortality in a pandemic environment such as with COVID-19.


title: Pitfalls in SARS-CoV-2 PCR diagnostics

text: To combat the COVID-19 pandemic, millions of PCR tests are performed worldwide. Any deviation of the diagnostic sensitivity and specificity will reduce the predictive values of the test. Here, we report the occurrence of contaminations of commercial primers/probe sets with the SARS-CoV-2 target sequence of the RT-qPCR as an example for pitfalls during PCR diagnostics affecting diagnostic specificity. In several purchased in-house primers/probe sets, quantification cycle values as low as 17 were measured for negative control samples. However, there were also primers/probe sets that displayed very low-level contaminations, which were detected only during thorough internal validation. Hence, it appears imperative to pre-test each batch of reagents extensively before use in routine diagnosis, to avoid false-positive results and low positive predictive value in low-prevalence situations. As such, contaminations may have happened more widely, COVID-19 diagnostic results should be re-assessed retrospectively to validate the epidemiological basis for control measures.


Czech Republic and low COVID-19 mortality in the heart of Europe: possible explanations


title: Impact Of Temperature and Sunshine Duration on Daily New Cases and Death due to COVID-19

text: Background: The coronavirus pandemic (COVID-19) control has now become a critical issue for public health. Many ecological factors are proven to influence the transmission and survival of the virus. In this study, we aim to determine the association of different climate factors with the spread and mortality due to COVID-19. Methods: The climate indicators included in the study were duration of sunshine, average minimum temperature and average maximum temperature, with cumulative confirmed cases, deceased and recovered cases. The data was performed for 138 different countries of the world, between January 2020 to May 2020. Both univariate and multivariate was performed for cumulative and month-wise analysis using SPSS software. Results: The average maximum temperature, and sunshine duration was significantly associated with COVID-19 confirmed cases, deceased and recovered. For every one degree increase in mean average temperature, the confirmed, deceased and recovered cases decreased by 2047(p=0.03), 157(p=0.016), 743 (p=0.005) individuals. The association remained significant even after adjusting for environmental such as sunshine duration as well as non-environmental variables. Average sunshine duration was inversely correlated with increase in daily new cases ({rho}= -2261) and deaths ({rho}= -0.2985). Conclusion: Higher average temperature and longer sunshine duration was strongly associated with COVID-19 cases and deaths in 138 countries. Hence the temperature is an important factor in SARS CoV-2 survival and this study will help in formulating better preventive measures to combat COVID-19 based on their climatic conditions.


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title: Healthcare-resource-adjusted vulnerabilities towards the 2019-nCoV epidemic across China

text: We integrate the human movement and healthcare resource data to identify cities with high vulnerability towards the 2019-nCoV epidemic with respect to available health resources. The results inform public health responses in multiple ways.


title: A new estimation method for COVID-19 time-varying reproduction number using active cases

text: We propose a new method to estimate the time-varying effective (or instantaneous) reproduction number of the novel coronavirus disease (COVID-19). The method is based on a discrete-time stochastic augmented compartmental model that describes the virus transmission. A two-stage estimation method, which combines the Extended Kalman Filter (EKF) to estimate reported state variables (active and removed cases) and a low pass filter based on a rational transfer function to remove short term fluctuations of the reported cases, is used with case uncertainties that are assumed to follow a Gaussian distribution. Our method does not require information regarding serial intervals, which makes the estimation procedure simpler without reducing the quality of the estimate. We show that the proposed method is comparable to common approaches, e.g., age-structured and new cases based sequential Bayesian models. We also apply it to COVID-19 cases in the Scandinavian countries: Denmark, Sweden, and Norway, where we see a delay of about four days in predicting the epidemic peak.


title: Stabilizing the Closed SARS-CoV-2 Spike Trimer

text: The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers, with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify two regions in the S-protein critical for the protein’s stability: the heptad repeat region 1 of the S2 subunit and subunit domain 1 at the interface with S2. We combined a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics.