title: Adverse Outcomes and Mortality in Users of Non-Steroidal Anti-Inflammatory Drugs tested positive for SARS-CoV-2: A Danish Nationwide Cohort Study

text: Background Concerns over the safety of non-steroidal anti-inflammatory drug (NSAID) use during SARS-CoV-2 infection have been raised. Objectives To study whether use of NSAIDs is associated with adverse outcomes and mortality during SARS-CoV-2 infection. Design Population based cohort study Setting Danish administrative and health registries. Participants Individuals tested positive for SARS-CoV-2 during Feb 27, 2020 to Apr 29, 2020. Treated individuals (defined as a filled NSAID prescription up to 30 days before the SARS-CoV-2 test) were matched to up to 4 non-treated individuals on propensity scores based on age, sex, relevant comorbidities and prescription fills. Outcome measures The main outcome was 30-day mortality and treated individuals were compared to untreated individuals using risk ratios (RR) and risk differences (RD). Secondary outcomes included hospitalisation, intensive care unit (ICU) admission, mechanical ventilation and acute renal replacement therapy. Results A total of 9236 SARS-CoV-2 PCR positive individuals were eligible for inclusion. Of these, 248 (2.7%) had filled a prescription for NSAIDs and 535 (5.8%) died within 30 days. In the matched analyses, treatment with NSAIDs was not associated with 30-day mortality (RR 1.02, 95% CI 0.57 to 1.82; RD 0.1%, -3.5% to 3.7%), increased risk of hospitalisation (RR 1.16, 0.87 to 1.53; RD 3.3%, -3.4% to 10%), ICU-admission (RR 1.04, 0.54 to 2.02; RD 0.2%, -3.0% to 3.4%), mechanical ventilation (RR 1.14, 0.56 to 2.30; RD 0.5%, -2.5% to 3.6%), or renal replacement therapy (RR 0.86, 0.24 to 3.09; RD -0.2%, -2.0% to 1.6%). Conclusion Use of NSAIDs was not associated with 30-day mortality, hospitalisation, ICU-admission, mechanical ventilation or renal replacement therapy in Danish individuals tested positive for SARS-CoV-2. Registration: The European Union electronic Register of Post-Authorisation Studies, EUPAS-34734 (http://www.encepp.eu/encepp/viewResource.htm?id=34735)


docid: eblxpfds

title: Identifying baseline clinical features of people with COVID-19

text: Objectives: To describe baseline clinical characteristics of adult patients with COVID-19. Methods: We conducted a scoping review of the evidence available at LitCovid, until March 23th, 2020, and selected articles that reported the prevalence of socio-demographic characteristics, symptoms and co-morbidities in adults with COVID-19. Results: In total, 1 572 publications were published on LitCovid. We have included 56 articles in our analysis, with 89% conducted in China, and 75% contained inpatients. Three studies were conducted in North America and one in Europe. Participants age ranged from 28 to 70 years, with balanced gender distribution. Proportion of asymptomatic cases were from 2 to 79%. The most common reported symptoms were fever [4-99%], cough [4-92%], dyspnoea/shortness of breath [1-90%], fatigue 4-89%], myalgia [3-65%], and pharyngalgia [2-61%], while regarding co-morbidities we found cardiovascular disease [1-40%], hypertension [0-40%] and cerebrovascular disease [1-40%]. Such heterogeneity impairs the conduction of meta-analysis. Conclusions: The infection by COVID-19 seems to affect people in a very diverse manner and with different characteristics. With the available data it is not possible to clearly identify those at higher risk of being infected with this condition. Furthermore, the evidence from countries other than China is, at the day, too scarce.


title: A Web-based, Mobile Responsive Application to Screen Healthcare Workers for COVID Symptoms: Descriptive Study

text: Background: The COVID-19 pandemic has impacted over 1 million people across the globe, with over 330,000 cases in the United States. To help limit the spread in Massachusetts, the Department of Public Health required that all healthcare workers must be screened for symptoms daily - individuals with symptoms may not work. We rapidly created a digital COVID-19 symptom screening tool for a large, academic, integrated healthcare delivery system, Partners HealthCare, in Boston, Massachusetts. Objective: We describe the design and development of the COVID-19 symptom screening application and report on aggregate usage data from the first week of use across the organization. Methods: Using agile principles, we designed, tested and implemented a solution over the span of a week using progressively custom development approaches as the requirements and use case become more solidified. We developed the minimum viable product (MVP) of a mobile responsive, web-based self-service application using REDCap (Research Electronic Data Capture). For employees without access to a computer or mobile device to use the self-service application, we established a manual process where in-person, socially distanced screeners asked employees entering the site if they have symptoms and then manually recorded the responses in an Office 365 Form. A custom .NET Framework application was developed solution as COVID Pass was scaled. We collected log data from the .NET application, REDCap and Office 365 from the first week of full enterprise deployment (March 30, 2020 - April 5, 2020). Aggregate descriptive statistics including overall employee attestations by day and site, employee attestations by application method (COVID Pass automatic screening vs. manual screening), employee attestations by time of day, and percentage of employees reporting COVID-19 symptoms Results: We rapidly created the MVP and gradually deployed it across the hospitals in our organization. By the end of the first week of enterprise deployment, the screening application was being used by over 25,000 employees each weekday. Over the first full week of deployment, 154,730 employee attestation logs were processed across the system. Over this 7-day period, 558 (0.36%) employees reported positive symptoms. In most clinical locations, the majority of employees (~80-90%) used the self-service application, with a smaller percentage (~10-20%) using manual attestation. Hospital staff continued to work around the clock, but as expected, staff attestations peaked during shift changes between 7-8am, 2-3pm, 4-6pm, and 11pm-midnight. Conclusions: Using rapid, agile development, we quickly created and deployed a dedicated employee attestation application that gained widespread adoption and use within our health system. Further, we have identified over 500 symptomatic employees that otherwise would have possibly come to work, potentially putting others at risk. We share the story of our implementation, lessons learned, and source code (via GitHub) for other institutions who may want to implement similar solutions.


docid: bawgldfi

title: The origin and underlying driving forces of the SARS-CoV-2 outbreak

text: The spread of SARS-CoV-2 since December 2019 has become a pandemic and impacted many aspects of human society. Here, we analyzed genetic variation of SARS-CoV-2 and its related coronavirus and found the evidence of intergenomic recombination. After correction for mutational bias, analysis of 137 SARS-CoV-2 genomes as of 2/23/2020 revealed the excess of low frequency mutations on both synonymous and nonsynonymous sites which is consistent with recent origin of the virus. In contrast to adaptive evolution previously reported for SARS-CoV in its brief epidemic in 2003, our analysis of SARS-CoV-2 genomes shows signs of relaxation of selection. The sequence similarity of the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression. Therefore, SARS-CoV-2 might have cryptically circulated within humans for years before being recently noticed. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and reveal critical steps required for effective spreading. Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention. The 84S first appeared on 1/5/2020 and reached a plateau around 1/23/2020, the lockdown of Wuhan. 251V emerged on 1/21/2020 and rapidly increased its frequency. Thus, the roles of these mutations on infectivity need to be elucidated. Genetic diversity of SARS-CoV-2 collected from China was two time higher than those derived from the rest of the world. In addition, in network analysis, haplotypes collected from Wuhan city were at interior and have more mutational connections, both of which are consistent with the observation that the outbreak of cov-19 was originated from China. SUMMARY In contrast to adaptive evolution previously reported for SARS-CoV in its brief epidemic, our analysis of SARS-CoV-2 genomes shows signs of relaxation of selection. The sequence similarity of the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression. Therefore, SARS-CoV-2 might have cryptically circulated within humans for years before being recently noticed. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and reveal critical steps required for effective spreading. Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention. The 84S first appeared on 1/5/2020 and reached a plateau around 1/23/2020, the lockdown of Wuhan. 251V emerged on 1/21/2020 and rapidly increased its frequency. Thus, the roles of these mutations on infectivity need to be elucidated.


title: Commodity price volatility and the economic uncertainty of pandemics

text: We empirically investigate the impact of economic uncertainty related to global pandemics on the volatility of the broad commodity price index as well as on the sub-indexes of crude oil and gold. The results show that uncertainty related to pandemics have a strong negative impact on the volatility of commodity markets and especially on crude oil market, while the effect on gold market is positive but less significant.


title: Distribution of droplets and immune responses after aerosol and intra-nasal delivery of influenza virus to the respiratory tract of pigs

text: Recent evidence indicates that local immune responses and tissue resident memory T cells (TRM) are critical for protection against respiratory infections but there is little information on the contributions of upper and lower respiratory tract (URT and LRT) immunity. To provide a rational basis for designing methods for optimal delivery of vaccines to the respiratory tract in a large animal model, we investigated the distribution of droplets generated by a mucosal atomization device (MAD) and two vibrating mesh nebulizers (VMNs) and the immune responses induced by delivery of influenza virus by MAD in pigs. We showed that droplets containing the drug albuterol, a radiolabel (99mTc-DTPA) or a model influenza virus vaccine (S-FLU) have similar aerosol characteristics. 99mTc-DTPA scintigraphy showed that VMNs deliver droplets with uniform distribution throughout the lungs as well as the URT. Surprisingly MAD administration (1ml/nostril) also delivered a high proportion of the dose to the lungs, albeit concentrated in a small area. After MAD administration of influenza virus, antigen specific T cells were found at high frequency in nasal turbinates, trachea, broncho-alveolar lavage, lungs, tracheobronchial nodes and blood. We conclude that the pig is useful for investigating optimal targeting of vaccines to the respiratory tract.


title: Homology-guided identification of a conserved motif linking the antiviral functions of IFITM3 to its oligomeric state

text: The interferon-inducible transmembrane (IFITM) proteins belong to the Dispanin/CD225 family and inhibit diverse virus infections. IFITM3 reduces membrane fusion between cells and virions through a poorly characterized mechanism. We identified a GxxxG motif in many CD225 proteins, including IFITM3 and proline rich transmembrane protein 2 (PRRT2). Mutation of PRRT2, a regulator of neurotransmitter release, at glycine-305 was previously linked to paroxysmal neurological disorders in humans. Here, we show that glycine-305 and the homologous site in IFITM3, glycine-95, drive protein oligomerization from within a GxxxG motif. Mutation of glycine-95 in IFITM3 disrupted its oligomerization and reduced its antiviral activity against Influenza A and HIV-1. The oligomerization-defective variant was used to reveal that IFITM3 promotes membrane rigidity in a glycine-95-dependent manner. Furthermore, a compound which counteracts virus inhibition by IFITM3, amphotericin B, prevented the IFITM3-mediated rigidification of membranes. Overall, these data suggest that IFITM3 oligomers inhibit virus-cell fusion by promoting membrane rigidity.


title: Zu wertvoll für Schnaps

text: AbstractIn Zeiten einer Pandemie wie der jetzigen ist Alkohol ein kostbares Gut Vor allem Krankenhäuser und Arztpraxen können nicht darauf verzichten, da sie ihn als Desinfektionsmittel nutzen Doch die Vorräte sind begrenzt


title: Selection of homemade mask materials for preventing transmission of COVID-19: a laboratory study

text: The Coronavirus Disease 2019 (COVID-19) has swept the whole world with high mortality. Since droplet transmission is the main route of transmission, wearing a mask serves as a crucial preventive measure. However, the virus has spread quite quickly, causing severe mask shortage. Finding alternative materials for homemade masks while ensuring the significant performance indicators will help alleviate the shortage of masks. Referring to the national standard for the "Surgical Mask" of China, 17 materials to be selected for homemade masks were tested in four key indicators: pressure difference, particle filtration efficiency, bacterial filtration efficiency and resistance to surface wetting. Eleven single-layer materials met the standard of pressure difference ([≤]49 Pa), of which 3 met the standard of resistance to surface wetting ([≥]3), 1 met the standard of particle filtration efficiency ([≥]30%), but none met the standard of bacterial filtration efficiency ([≥]95%). Based on the testing results of single-layer materials, fifteen combinations of paired materials were tested. The results showed that three double-layer materials including double-layer medical non-woven fabric, medical non-woven fabric plus non-woven shopping bag, and medical non-woven fabric plus granular tea towel could meet all the standards of pressure difference, particle filtration efficiency, and resistance to surface wetting, and were close to the standard of the bacterial filtration efficiency. In conclusion, if resources are severely lacking and medical masks cannot be obtained, homemade masks using available materials, based on the results of this study, can minimize the chance of infection to the maximum extent.


title: Validation and Performance Comparison of Three SARS-CoV-2 Antibody Assays

text: Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of Coronavirus Disease 2019 (COVID-19). The clinical and epidemiologic utilities of antibody-based SARS-CoV-2 testing are under debate. Characterizing these assays helps to understand the disease and provides scientific basis for deciding how to best use these assays. The study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo Total Antibody Test). Validation included 113 blood samples from 71 PCR-confirmed COVID-19 patients and 1182 samples from negative controls with potential interferences/cross-reactions, including 1063 pre-pandemic samples. IgM antibodies against SARS-CoV-2 were detected as early as post-symptom onset days 3-4. IgG antibodies were first detected post-onset days 5-6 by SQ assays. The detection rates increased gradually, and SQ IgG, Abbott IgG and Wondfo Total detected antibodies from all the PCR-confirmed patients 14 days after symptom onset. Overall agreements between SQ IgM/IgG and Wondfo Total was 88.5% and between SQ IgG and Abbott IgG was 94.6% (Kappa = 0.75, 0.89). No cross-reaction with other endemic coronavirus infections were identified. Viral hepatitis and autoimmune samples were the main cross-reactions observed. However, the interferences/cross-reactions were low. The specificities were 100% for SQ IgG and Wondfo Total and 99.62% for Abbott IgG and 98.87% for SQ IgM. These findings demonstrate high sensitivity and specificity of appropriately validated antibody-based SARS-CoV-2 assays with implications for clinical use and epidemiological seroprevalence studies.


Cronicidad Y Atención Primaria En Tiempos De Pandemia


title: Co-detection of respiratory pathogens in patients hospitalized with Coronavirus viral disease-2019 pneumonia

text: Not applicable: New Data Letter


title: The 2019 novel coronavirus disease (COVID-19) pandemic: A zoonotic prospective

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus (CoV), has recently emerged as a significant pathogen for humans and the cause for the recent outbreak of the 2019 novel coronavirus disease (COVID-19) throughout the globe For developing any preventive measure, an understanding of the zoonotic pattern for this virus is a necessity We should have a clear knowledge of its reservoir host, its distribution pattern and spreading routes Information about zoonotic reservoirs and its transmission among them can help to understand the COVID-19 outbreaks In this article, we discuss about the bats as the zoonotic reservoir of several CoV strains, co-existence of bats and CoV/viruses, the sequence similarity of SARS-CoV-2 with bat SARS-like CoV, the probable source of the origin of SARS-CoV-2 strain and COVID-19 outbreak, intermediate host of CoVs and SARS-CoV-2, human to human transmission and the possibility to maintain the zoonotic barriers Our knowledge about the zoonotic reservoir of SARS-CoV-2 and its transmission ability may help develop the preventive measures and control for the future outbreak of CoV


title: When will the coronavirus outbreak peak?

text: Officials want to know but predictions vary wildly, from now to after hundreds of millions of people are infected Officials want to know but predictions vary wildly, from now to after hundreds of millions of people are infected


title: Associations of Loneliness and Social Isolation with Healthspan and Lifespan in the US Health and Retirement Study

text: Background. Loneliness and social isolation are emerging public health challenges for aging populations. Methods. We followed N=11,305 US Health and Retirement Study (HRS) participants aged 50-95 from 2006-2014 to measure persistence of exposure to loneliness and social isolation. We tested associations of longitudinal loneliness and social-isolation phenotypes with disability, morbidity, mortality, and biological aging through 2018. Results. During follow-up, 18% of older adults met criteria for loneliness and, for 6%, symptoms persisted across two or more follow-up assessments. For social isolation, these fractions were 21% and 8%. HRS participants who experienced loneliness and social isolation were at increased risk for disease, disability, and mortality. Older adults experiencing persistent loneliness were at a 59% increased hazard of mortality compared to those who were never lonely. For social isolation, the increase was 28%. Effect-sizes were somewhat larger for counts of prevalent activity limitations and somewhat smaller for counts of prevalent chronic diseases. Covariate adjustment for socioeconomic and psychological risks attenuated but did not fully explain associations. Older adults who experienced loneliness and social isolation also exhibited physiological indications of advanced biological aging (Cohen's-d for persistent loneliness and social isolation=0.26 and 0.21, respectively). For loneliness, but not social isolation, persistence of symptoms was associated with increased risk. Conclusion. Deficits in social connectedness prevalent in a national sample of older adults in the US were associated with morbidity, disability, and mortality and with more advanced biological aging. Bolstering social connection to interrupt experiences of loneliness may promote healthy aging.


title: Quantitative Estimation of Disruption in Social Contact Structure and its Effect in COVID-19 Spread in India

text: In this paper we use the well-known SIR (Susceptible-Infected-recovered) epidemiology model for quantitatively estimating the impact of this disruption in the social contact structure of India and retrospectively estimate the number of COVID-19 cases in India by neglecting the single source event. Model predicts that around 32% of COVID-19 cases (as on April 14, 2020) are contributed by the single source event. Given this disruption of the social contact structure, the model shows that the country wide lockdown has been effective in bringing down the number of cases in India.


docid: fxdeownw

title: Afrika im Sog des Coronavirus


title: Hacia la inmunidad colectiva como respuesta a la pandemia por SARS-CoV-2/ Towards herd immunity in response to the SARS-CoV-2 pandemic

text: El 31 de diciembre de 2019, la Comisión Municipal de Salud y Sanidad en la pro-vincia de Hubei, China, anunció la aparición de 27 casos de neumonía de causa desconocida, en personas que habían visitado un mercado de mariscos y anima-les vivos en la ciudad de Wuhan. Pocos días después se estaba identificando al agente etiológico como un nuevo virus de la familia de los coronavirus, denomi-nado SARS-CoV-2. El virus causante de COVID-19 es un virus "nuevo" para la humanidad, y por lo tanto, no hay inmunidad hacia el mismo. Mientras se dispone de una vacuna efec-tiva y segura contra el SARS-CoV-2, solo se vislumbra en el futuro inmediato que la población vaya siendo inmunizada de forma natural, idealmente de manera re-gulada. Los aislamientos, las cuarentenas y el cierre de fronteras han sido y siguen siendo utilizadas como primera línea de defensa ante enfermedades infecciosas nuevas. Sin embargo, estas medidas tienen un rol principalmente en la etapa de contención y luego en la fase de mitigación, como estrategia para ralentizar la dispersión del virus en la comunidad. Una vez se alcanza la fase de mitigación, como ocurre actualmente en Colombia, se deben balancear estas soluciones de aislamiento, con estrategias de distanciamiento más regulado que permitan la reactivación de las actividades sociales y comerciales, y así minimizar los efectos contraproducentes por las implicaciones sociales y económicas [3]. La alta transmisibilidad del virus solo podrá combatirse cuando un porcentaje sig-nificativo de la población esté inmune. Lo que se conoce como inmunidad colecti-va o de rebaño se puede lograr de dos formas; la primera con vacunación masiva, y la segunda con la exposición natural al agente infeccioso, en miras a que el sistema inmune desarrolle una respuesta que proteja al individuo, y evite además que sea una fuente de infección para otros. Para que se logre un nivel adecuado de inmunidad colectiva, se requiere que alrededor del 70% de la población sea inmune, dependiendo del agente infeccioso. Algunos ejemplos de inmunidad co-lectiva conseguida a través de la vacunación, son las obtenidas con las campañas contra sarampión, varicela, paperas y polio, las cuales son enfermedades poco frecuentes en la actualidad en los países con esquemas de vacunación masivos.


title: Releasing the lockdown in the UK Covid-19 epidemic: a stochastic model

text: Abstract Background In a classic epidemic, the infected population has an early exponential phase, before slowing and fading to its peak. Mitigating interventions may change the exponent during the rising phase and a plateau can replace a peak. With interventions comes the risk that relaxation causes a second-wave. In the UK Covid-19 epidemic, infections cannot be counted, but their influence is seen in the curve of the mortality data. This work simulated social distancing and the lockdown in the UK Covid-19 epidemic to explore strategies for relaxation. Methods Cumulative mortality data was transposed 20 days earlier to identify three doubling periods separated by the 17th March - social distancing, and 23rd March - lockdown. A set of stochastic processes simulated viral transmission between interacting individuals using Covid-19 incubation and illness durations. Social distancing and restrictions on interactions were imposed and later relaxed. Principal Findings Daily mortality data, consistent with that seen in the UK Covid-19 epidemic to 24th April 2020 was simulated. This output predicts that under a lockdown maintained till early July 2020, UK deaths will exceed 31,000, but leave a large susceptible population and a requirement for vaccination or quarantine. An earlier staged relaxation carries a risk of a second-wave. The model allows exploration of strategies for lifting the lockdown. Interpretation Social distancing and the lockdown have had an impressive impact on the UK Covid-19 epidemic and saved lives, caution is now needed in planning its relaxation.


title: A Modified ACE2 peptide mimic to block SARS-CoV2 entry

text: A 23-residue peptide fragment that forms a part of the α-1 helix of the ACE2 peptidase domain, the recognition domain for SARS-CoV2 on the ACE2 receptor, holds the potential as a drug to block the viral receptor binding domain (RBD) from forming a complex with ACE2. The peptide has recently been shown to bind the viral RBD with good efficiency. Here, we present a detailed analysis of the energetics of binding of the peptide to the SARS-CoV2 RBD. We use equilibrium molecular dynamics simulation to study the dynamics of the complex. We perform end-state binding energy calculations to gain a residue-level insight into the binding process and use the information to incorporate point mutations into the peptide. We demonstrate using binding energy calculations that the peptide with certain point mutations, especially E17L, shows a stronger binding to the RBD as compared to the wild type peptide. We propose that the modified peptide will thus be more efficient in blocking RBD-ACE2 binding.


title: COVID-19 Hospitalization is More Frequent and Severe in Down Syndrome

text: Background. Individuals with rare disorders, like Down syndrome (DS) are historically understudied. Currently, it is not known how COVID-19 pandemic affects individuals with DS. Herein, we report an analysis of individuals with DS who were hospitalized with COVID-19 in the Mount Sinai Health System in New York City, USA. Methods. In this retrospective, single-center study of 4,615 patients hospitalized with COVID-19, we analyzed all patients with DS admitted in the Mount Sinai Health System. Hospitalization rates, clinical and outcomes were assessed. Findings. Contrary to an expected number of one, we identified six patients with DS. We found that patients with DS are at an 8.9-fold higher risk of hospitalization with COVID-19 when compared to non-DS patients. Hospitalized DS individuals are on average 10 years younger than non-DS patients with COVID-19. Moreover, type 2 diabetes mellitus appears to be an important driver of this susceptibility to COVID-19. Finally, patients with DS have more severe outcomes than controls, and are more likely to progress to sepsis in particular. Interpretation. We demonstrate that individuals with DS represent a higher risk population for COVID-19 compared to the general population and conclude that particular care should be taken for both the prevention and treatment of COVID-19 in these patients. Funding. National Institute of Allergy and Infectious Diseases


title: The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline

text: Clinical sepsis is a highly dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single cell RNA sequencing revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. We identified key changes in gene expression that altered cellular functions and can explain features of clinical sepsis. These changes converged towards a remarkable global cell-cell communication failure and organ shutdown at a well-defined point in the sepsis timeline. Importantly, this time point was also a transition towards the emergence of recovery pathways. This rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis.


title: General Model for COVID-19 Spreading with Consideration of Intercity Migration, Insufficient Testing and Active Intervention: Application to Study of Pandemic Progression in Japan and USA

text: A new Susceptible-Exposed-Infected-Confirmed-Removed (SEICR) model with consideration of intercity travel and active intervention is proposed for predicting the spreading progression of the 2019 New Coronavirus Disease (COVID-19). The model takes into account the known or reported number of infected cases being fewer than the actual number of infected individuals due to insufficient testing. The model integrates intercity travel data to track the movement of exposed and infected individuals among cities, and allows different levels of active intervention to be considered so that realistic prediction of the number of infected individuals can be performed. The data of the COVID-19 infection cases and the intercity travel data for Japan (January 15 to March 20, 2020) and the USA (February 20 to March 20, 2020) are used to illustrate the prediction of the pandemic progression in 47 regions of Japan and 50 states (plus a federal district) in the USA. By fitting the model with the data, we reveal that, as of March 19, 2020, the number of infected individuals in Japan and the USA could be twenty-fold and five-fold as many as the number of confirmed cases, respectively. Moreover, the model generates future progression profiles for different levels of intervention by setting the parameters relative to the values found from the data fitting. Results show that without tightening the implementation of active intervention, Japan and the USA will see about 6.55% and 18.2% of the population eventually infected, and with drastic ten-fold elevated active intervention, the number of people eventually infected can be reduced by up to 95% in Japan and 70% in the USA. Finally, an assessment of the relative effectiveness of active intervention and personal protective measures is discussed. With a highly vigilant public maintaining personal hygiene and exercising strict protective measures, the percentage of population infected can be further reduced to 0.23% in Japan and 2.7% in the USA.


title: Thrombotic microvascular injury is not mediated by thrombotic microangiopathy despite systemic complement activation in Covid-19 patients

text: Hypoxemia and coagulopathy are common in severe symptomatic patients of coronavirus disease 2019 (COVID-19). Histological evidence shows implication of complement activation and lung injury. We research sign of complement activation and presence of thrombotic microangiopathy in 8 severe patients. Six of them presented moderate elevation of final pathway of complement / sC5b-9 (median value : 350 ng/mL [IQR : 300,5-514,95 ng/mL]). Two patients have been autopsied and presence of thrombotic microvascular injury have been found. Interestingly, none the 8 patients had signs of mechanical hemolytic anemia (median value of hemoglobin : 10,5 gr/dL[IQR : 8,1-1,9], median value of haptoglobuline 4,49 [IQR 3,55-4,66], none of the patients has schistocyte) and thrombocytopenia (median value: 348000/mL [IQR : 266 000-401 000). Finally, all 8 patients had elevated d-dimer (median value : 2226 microgr/l [IQR : 1493- 2362]) and soluble fibrin monomer complex (median value : 8.5 mg/mL, IQR[ <6-10.6]). In summary, this study show moderate activation of complement and coagulation with presence of thrombotic microvascular injury in patients with severe COVID-19 without evidence of systemic thrombotic microangiopathy.


title: Bidirectional contact tracing is required for reliable COVID-19 control

text: Contact tracing is critical to limiting the spread of pandemics such as COVID-19, but most protocols only "forward-trace" to notify people who were recently exposed. Using a stochastic branching process model, we find that "bidirectional" tracing to identify infector individuals robustly outperforms forward-only approaches across a wide range of scenarios. The addition of rapid smartphone-based exposure notification offers few benefits over conventional manual tracing alone unless uptake of the digital system is near-universal. However, as long as exposure events can be detected by nearly all smartphones, the combination of manual and digital with bidirectional tracing more than doubles the probability of controlling outbreaks across three epidemiological scenarios. Implementing combined bidirectional tracing may be critical to controlling COVID-19 without more costly interventions.


Biopolitics, conspiracy and the immuno-state: an evolving global politico-genetic complex


title: Government Responses Matter: Predicting Covid-19 cases in US under an empirical Bayesian time series framework

text: Since the Covid-19 outbreak, researchers have been predicting how the epidemic will evolve, especially the number in each country, through using parametric extrapolations based on the history. In reality, the epidemic progressing in a particular country depends largely on its policy responses and interventions. Since the outbreaks in some countries are earlier than United States, the prediction of US cases can benefit from incorporating the similarity in their trajectories. We propose an empirical Bayesian time series framework to predict US cases using different countries as prior reference. The resultant forecast is based on observed US data and prior information from the reference country while accounting for different population sizes. When Italy is used as prior in the prediction, which the US data resemble the most, the cases in the US will exceed 300,000 by the beginning of April unless strong measures are adopted.


title: Mechanism of Xinguanzhongqizhenliao formula (XGZQZLF) in treatment of COVID-19 by network pharmacology/ 基于网络药理学的中期诊疗方干预新型冠状病毒肺炎（COVID-19）作用机制研究

text: Objective: To research the mechanism of Xinguanzhongqizhenliao formula (XGZQZLF) for COVID-19 treatment by network pharmacology. Methods: “Drug-active ingredient-target-disease” network was constructed by Cytoscape based on TCMSP and GeneCards databases. Mechanism of XGZQZLF in treatment of COVID-19 was implemented by GO and KEGG analysis. Results: A total of 80 active ingredients of XGZQZLF were screened out. They could regulate 208 targets of COVID-19, including AKT1, IL-6, MAPK3, VEGFA, CASP3 and so on, which exerted therapeutic effect on COVID-19 through regulating multiple signaling pathways such as TNF signaling pathway, IL-17 signaling pathway, Th17 cell differentiation, HIF-1 signaling pathway and so on. Conclusion: XGZQZLF plays an important role in the treatment of COVID-19 through multi-component, multi-target and multi-pathway, which can provide reference for the synergistic theory of TCM compound prescription.


title: Derivation and validation of a prognostic model for predicting in-hospital mortality in patients admitted with COVID-19 in Wuhan, China: the PLANS (Platelet Lymphocyte Age Neutrophil Sex) model

text: OBJECTIVE To develop and validate a prognostic model for in-hospital mortality in COVID-19 patients using routinely collected demographic and clinical characteristics. DESIGN Multicenter, retrospective cohort study. SETTING Jinyintan Hospital, Union Hospital, and Tongji Hosptial in Wuhan, China. PARTICIPANTS A pooled derivation cohort of 1008 COVID-19 patients from Jinyintan Hospital, Union Hospital in Wuhan and an external validation cohort of 1031 patients from Tongji Hospital in Wuhan, China. MAIN OUTCOME MEASURES Outcome of interest was in-hospital mortality, treating discharged alive from hospital as the competing event. Fine-Gray models, using backward elimination for inclusion of predictor variables and allowing non-linear effects of continuous variables, were used to derive a prognostic model for predicting in-hospital mortality among COVID-19 patients. Internal validation was implemented to check model overfitting using bootstrap approach. External validation to a separate hospital was implemented to evaluate the generalizability of the model. RESULTS The derivation cohort was a case-mix of mild-to-severe hospitalized COVID-19 patients (n=1008, 43.6% females, median age 55). The final model (PLANS), including five predictor variables of platelet count, lymphocyte count, age, neutrophil count, and sex, had an excellent predictive performance (optimism-adjusted C-index: 0.85, 95% CI: 0.83 to 0.87; averaged calibration slope: 0.95, 95% CI: 0.82 to 1.08). Internal validation showed little overfitting. External validation using an independent cohort (n=1031, 47.8% female, median age 63) demonstrated excellent predictive performance (C-index: 0.87, 95% CI: 0.85 to 0.89; calibration slope: 1.02, 95% CI: 0.92 to 1.12). The averaged predicted survival curves were close to the observed survival curves across patients with different risk profiles. CONCLUSIONS The PLANS model based on the five routinely collected demographic and clinical characteristics (platelet count, lymphocyte count, age, neutrophil count, and sex) showed excellent discriminative and calibration accuracy in predicting in-hospital mortality in COVID-19 patients. This prognostic model would assist clinicians in better triaging patients and allocating healthcare resources to reduce COVID-19 fatality.


title: Recomendaciones para la comunicación de malas noticias por teléfono durante la pandemia por SARS-CoV-2

text: The current SARS-CoV-2 pandemic presents specific challenges for health professionals in the healthcare setting. In this emergency context, the communication of bad news is especially relevant because of the particular way it must be done: the need to maintain social distance or mobility restrictions imposed on the general population means that this task must often be carried out remotely, mostly by telephone calls. This confronts professionals with a number of particular obstacles: a) most of them have little or no training in this kind of communication skills, b) effective communication of bad news largely depends on body language, which is absent in this type of exchange, and c) since this type of remote dialogue is not recommended — except in particular circumstances such as the current ones — there is little literature available to guide the professionals who must carry out this task. This manuscript offers recommendations for remote communication of bad news by telephone, applicable to situations in which this task cannot be carried out in person. A proposal structured around four “moments” is presented to guide the remote transmission of bad news in order to improve the care of patients, families and caregivers during this exchange and to reduce the negative impact from it on health professionals.


title: Hypertension and renin-angiotensin system blockers are not associated with expression of Angiotensin Converting Enzyme 2 (ACE2) in the kidney

text: Angiotensin converting enzyme 2 (ACE2) is the cellular entry point for severe acute respiratory syndrome coronavirus (SARS-CoV-2) - the cause of COVID-19 disease. It has been hypothesized that use of renin-angiotensin system (RAS) inhibiting medications in patients with hypertension, increases the expression of ACE2 and thereby increases the risk of COVID-19 infection and severe outcomes or death. However, the effect of RAS-inhibition on ACE2 expression in human tissues of key relevance to blood pressure regulation and COVID-19 infection has not previously been reported. We examined how hypertension, its major metabolic co-phenotypes and antihypertensive medications relate to ACE2 renal expression using information from up to 436 patients whose kidney transcriptomes were characterised by RNA-sequencing. We further validated some of the key observations in other human tissues and/or a controlled experimental model. Our data reveal increasing expression of ACE2 with age in both human lungs and the kidney. We show no association between renal expression of ACE2 and either hypertension or common types of RAS inhibiting drugs. We demonstrate that renal abundance of ACE2 is positively associated with a biochemical index of kidney function and show a strong enrichment for genes responsible for kidney health and disease in ACE2 co-expression analysis. Collectively, our data indicate that neither hypertension nor antihypertensive treatment are likely to alter individual risk of SARS-CoV-2 infection or influence clinical outcomes in COVID-19 through changes of ACE2 expression. Our data further suggest that in the absence of SARS-CoV-2 infection, kidney ACE2 is most likely nephro-protective but the age-related increase in its expression within lungs and kidneys may be relevant to the risk of SARS-CoV-2 infection.


title: Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients

text: ARS-CoV-2 outbreak is a world-wide pandemic. The Spike protein plays central role in cell entry of the virus, and triggers significant immuno-response. Our understanding of the immune-response against S protein is still very limited. Herein, we constructed a peptide microarray and analyzed 55 convalescent sera, three areas with rich linear epitopes were identified. Potent neutralizing antibodies enriched from sera by 3 peptides, which do not belong to RBD were revealed.


title: The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2

text: we made the first-ever successful effort from India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of WBE surveillance in India. Sampling was carried out on 8 and 27 May 2020 from Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat with 106 million liters per day (MLD) capacity receiving effluent of Civil Hospital treating COVID-19 patient. All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents with no gene spotted in the effluent collected on 8 and 27 May 2020. Temporal difference between 8 and 27 May 2020 samples was of 10x in gene copy loading with a corresponding change of 2x in the number active COVID-19 patient in the city. Number of gene copies was found comparable to that reported in the untreated wastewaters of Australia, China, and Turkey and lower than that of the USA, France, and Spain. This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have an explicit picture of the phase of the pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and thus can be a great tool for pandemic monitoring.


title: The politics of scale in the coordinated management and emergency response to the COVID-19 pandemic

text: This commentary examines how coordinated management and emergency response (CMER) have been mobilized within the United States and Ireland to tackle the COVID-19 pandemic. Drawing upon a performative conception of scale, I argue that it is crucial to recognize the potency of the scalar politics of CMER organization to understand the differences in public health responses within and between political jurisdictions.


title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR

text: In this study, serial dilutions of SARS-CoV 2 RNA extract were tested using RT-dPCR using three different primer-probe assays aiming SARS-CoV 2 nucleocapsid coding region. Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. High accuracy of this test allowed conclusions regarding the ability of this technique to evaluate precisely the amount of genomic copies present in a sample. We believe that this fast and safe method can assist other researchers in titration of SARS-CoV2 controls used in RT-qPCR without the need of virus isolation.


COVID-19 disrupts research plans: The coronavirus pandemic has interrupted fieldwork and lab experiments - [News]


title: Detection of lung hypoperfusion in Covid-19 patients during recovery by digital imaging quantification

text: Purpose. A large number of patients affected by the SARS-Cov-2 virus worldwide undergo recovery of symptoms in about one month. Among these patients, the healing process is still under observation, with some patients in need of careful clinical monitoring. While the radiological findings have been shown to regress almost completely, little knowledge is available at the moment about other complications in the lung and in other organs. We then investigated the lung perfusion conditions in patients affected by COVID- 19 during recovery. Method. We retrospectively studied 20 patients, from 14 to 60 days after resolution of the COVID-19 symptoms, using chest CT. In a subgroup of 5 patients contrasted CT was used. Beside normal radiological evaluation of lung tissue, perfusion conditions were evaluated by digital image processing in the lung volume automatically segmented. Results. Pulmonary lung evaluation showed that COVID-19 pneumonia almost completely regressed, with mild focal areas affected by fibrous stripes. In patients that reported dyspnea, lung CT showed complete resolution of interstitial changes. Quantification of lung perfusion condition by contrasted CT, showed that dyspnea in 3 patients was associated with areas of hypoperfusion, while in 2 patients not reporting dyspnea perfusion conditions were comparable to normal controls. Conclusions. Although we obtained preliminary data, this is the first report on quantitative evaluation of hypoperfused lung tissue detected in recovering COVID-19 patients. These results suggest the need to further investigate these patients and to redefine the role of CT evaluation for diagnostic purposes as well as for evaluation of potential treatments.


title: Remodeling Point-of-Care Ultrasound Education in the era of COVID-19

text: The COVID-19 pandemic requires a new approach to point-of-care ultrasound (POCUS) education. Although virtual education offers a unique solution to didactic material, education that require hands-on learning is limited. POCUS education is predominantly done at the bedside and as a result could pose risk to health-care providers and patients as well as increase utilization of personal protective equipment (PPE). This paper discusses the challenges and unique solutions to address POCUS education in the era of COVID-19.


title: Meta-analysis of diagnostic performance of serological tests for SARS-CoV-2 antibodies and public health implications

text: Serology-based tests have become a key public health element in the COVID-19 pandemic to assess the degree of herd immunity that has been achieved in the population. These tests differ between one another in several ways. Here, we conducted a systematic review and meta-analysis of the diagnostic accuracy of currently available SARS-CoV-2 serological tests, and assessed their real-world performance under scenarios of varying proportion of infected individuals. We included independent studies that specified the antigen used for antibody detection and used quantitative methods. We identified nine independent studies, of which six were based on commercial ELISA or CMIA/CLIA assays, and three on in-house tests. Test sensitivity ranged from 68% to 93% for IgM, from 65% to 100% for IgG, and from 83% to 98% for total antibodies. Random-effects models yielded a summary sensitivity of 82% (95%CI 75-88%) for IgM, and 85% for both IgG (95%CI 73-93%) and total antibodies (95%CI 74-94%). Specificity was very high for most tests, and its pooled estimate was 98% (95%CI 92-100%) for IgM and 99% (95%CI 98-100%) for both IgG and total antibodies. The heterogeneity of sensitivity and specificity across tests was generally high (I2[≤]50%). In populations with a low prevalence ([≤]5%) of seroconverted individuals, the positive predictive value would be [≤]88% for most assays, except those reporting perfect specificity. Our data suggest that the use of serological tests for large-scale prevalence surveys (or to grant "immunity passports") are currently only justified in hard-hit regions, while they should be used with caution elsewhere.


News from our societies – ICSW: COVID-19 – Five tests we face


title: Stability of SARS-CoV-2 on environmental surfaces and in human excreta

text: At room temperature, SARS-CoV-2 was stable on environmental surfaces and remained viable up to 7 days on smooth surfaces. This virus could survive for several hours in feces and 3-4 days in urine.


docid: xieqswct

title: Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza

text: The outbreak of the coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), has infected more than 100,000 people worldwide with over 3,000 deaths since December 2019. There is no cure for COVID-19 and the vaccine development is estimated to require 12-18 months. Here we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (Prophylactic Antiviral CRISPR in huMAN cells), for viral inhibition that can effectively degrade SARS-CoV-2 sequences and live influenza A virus (IAV) genome in human lung epithelial cells. We designed and screened a group of CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs for cleaving SARS-CoV-2. The approach is effective in reducing respiratory cell viral replication for H1N1 IAV. Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses. The PAC-MAN approach is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic strains.


title: Flattening the mental ill-health curve: the importance of primary prevention in managing the mental health impacts of COVID19

text: The COVID19 pandemic is one the biggest challenges the global community has faced. The threat of the virus coupled with the impacts of the social and economic shut-down measures required to slow its spread, already appear to be impacting on people's mental health and wellbeing. Over the weeks, months and years ahead it is likely that many countries will experience a ‘wave’ of COVID19 related mental disorders as a result of an increase in risk factors linked to the pandemic such as social isolation; child-maltreatment; intimate partner violence; unemployment; housing and income stress; workplace trauma; and grief and loss. The ‘two-pronged’ approach used to deal with COVID19, provides an excellent blueprint for managing its mental health impacts as well. Nations must focus on preventing the occurrence of new cases of mental disorders as well as strengthening their mental healthcare response to support people who become mentally unwell. A focus on primary prevention is particularly important to ‘flatten the curve’ and avoid a surge in incidence of mental disorders stemming from the COVID19 pandemic. Many evidence-based interventions designed to prevent common disorders are already available and should be scaled-up. These interventions include parenting programs, social and emotional learning programs, self-care strategies, and workplace mental wellbeing programs, among others.


title: Diminishing Marginal Benefit of Social Distancing in Balancing COVID-19 Medical Demand-to-Supply

text: Social distancing has been adopted as a non-pharmaceutical intervention to prevent the COVID-19 pandemic from overwhelming the medical resources across the United States (US). The catastrophic socio-economic impacts of this intervention could outweigh its benefits if the timing and duration of implementation are left uncontrolled and ill-strategized. Here we investigate the dynamics of social distancing on age-stratified US population and benchmark its effectiveness in reducing the burden on hospital and ICU beds. Our findings highlight the diminishing marginal benefit of social distancing, characterized by a linear decrease in medical demands against an exponentially increasing social distancing duration. We determine an optimal intermittent social-to-no-distancing ratio of 5:1 corresponding to ~80% reduction in healthcare demands; beyond this ratio, benefit of social distancing diminishes to a negligible level. COVID-19 Medical Forecast: https://eece.wustl.edu/chakrabarty-group/covid/


title: Principles and Practice of SARS-CoV-2 Decontamination of N95 Masks with UV-C

text: A mainstay of personal protective equipment (PPE) during the COVID-19 pandemic is the N95 filtering facepiece respirator. N95 respirators are commonly used to protect healthcare workers from respiratory pathogens, including the novel coronavirus SARS-CoV-2, and are increasingly employed by other frontline workers and the general public. Under routine circumstances, these masks are disposable, single-use items, but extended use and reuse practices have been broadly enacted to alleviate critical supply shortages during the COVID-19 pandemic. While extended-time single use presents a low risk of pathogen transfer, repeated donning and doffing of potentially contaminated masks presents increased risk of pathogen transfer. Therefore, efficient and safe decontamination methods for N95 masks are needed to reduce the risk of reuse and mitigate local supply shortages. Here we review the available literature concerning use of germicidal ultraviolet-C (UV-C) light to decontaminate N95 masks. We propose a practical method for repeated point-of-use decontamination, using commercially-available UV-C crosslinker boxes from molecular biology laboratories or a simple low-cost, custom-designed and fabricated device to expose each side of the mask to 800-1200 mJ/cm2 of UV-C. We measure the dose that penetrated to the interior of the respirators and model the potential germicidal action on SARS-CoV-2. Our experimental results, in combination with modeled data, suggest that a two-minute UV-C treatment cycle should induce a >3-log-order reduction in viral bioburden on the surface of the respirators, and a 2-log order reduction throughout the interior. The resulting exposure is 100-fold less than the dose expected to damage the masks, facilitating repeated decontamination. As such, UV-C germicidal irradiation (UVGI) is a practical strategy for small-scale point-of-use decontamination of N95s.


title: A mathematical model for estimating the age-specific transmissibility of a novel coronavirus

text: Background: A novel coronavirus named as "SARS-CoV-2" has spread widely in many countries since December 2019, especially in China. This study aimed to quantify the age-specific transmissibility by using a mathematical model. Methods: An age-specific susceptible - exposed - symptomatic - asymptomatic - recovered - seafood market (SEIARW) model was developed based on two suspected transmission routes (from market to person and person to person). The susceptible people from Wuhan City were divided into different age groups. We used the subscript i and j to represent age group 1 to 4 (1: <= 14 years; 2: 15-44 years; 3: 45-64 years; 4: >= 65 years) and 1 to 5 (1: <= 5 years; 2: 6-14 years; 3: 15-24 years; 4: 25-59 years; 4: >= 60 years), respectively. Data of reported COVID-19 cases were collected from one published literature from 26 November to 22 December, 2019 in Wuhan City, China. The age-specific transmissibility of the virus was estimated accordingly secondary attack rate (SAR). Results: The age-specific SEIARW model fitted with the reported data well by dividing the population into four age groups (χ2 = 4.99 × 10-6, P > 0.999), and five age groups (χ2 = 4.85 × 10-6, P > 0.999). Based on the four-age-group SEIARW model, the highest transmissibility occurred from age group 2 to 3 (SAR23 = 17.56 per 10 million persons), followed by from age group 3 to 2 (SAR32 = 10.17 per 10 million persons). The lowest transmissibility occurred from age group 1 to 2 (SAR12 = 0.002 per 10 million persons). Based on the five-age-group SEIARW model, the highest transmissibility occurred from age group 4 to 5 (SAR45 = 12.40 per 10 million persons), followed by from age group 5 to 4 (SAR54 = 6.61 per 10 million persons). The lowest transmissibility occurred from age group 3 to 4 (SAR34 = 0.0002 per 10 million persons). Conclusions: SARS-CoV-2 has high transmissibility among adults and elder people but low transmissibility among children and young people.


title: Application of new topsis approach to identify the most significant risk factor and continuous monitoring of death of COVID-19

text: A pandemic is a disease that spreads across a large area like multiple continents or worldwide. More than 211 nations are already affected by Covid-19. The World Health Organization (WHO) on 11 March 2020 declared Covid19 a pandemic. There are more than 1,282,931 cases of the coronavirus illness over 211 countries and territories around the world. Currently coronavirus has no proper treatment in Medical Science, increasing the number of affected people day by day with the number of cases worldwide of novel coronavirus surpassing 1,282,931, with some 72,616 deaths approximately. That is why the main objective of the present investigation is to identify the significant risk factor. Also, in this study we are continuously monitoring the spread of coronavirus. In this study we use a new TOPSIS MCDM approach and GMDH apply to select the significant risk factor and continuous monitoring of death due to Covid-19. Result indicates that “contamination due to contact with the infected person” is the main responsible factor behind the pandemic COVID-19. Also, in this investigation we get an optimal model by which we can monitor the death from Coronavirus within the affected person continuously.


title: Findings and prognostic value of lung ultrasound in COVID-19 pneumonia

text: Objectives: The aim is to systematically describe the findings of lung ultrasound in patients with COVID-19 pneumonia and to analyze its prognostic value. Methods: Lung ultrasound was performed to 63 patients with COVID-19 pneumonia admitted to a University Hospital. Lung involvement was evaluated using a 4-point scale with a 12-area pulmonary division (lung score -LS-). Ultrasound findings, along with clinical characteristics, were recorded. Results: All patients showed ultrasound involvement in at least 1 area (mean 8 {+/-} 3.5). Total LS was 15.3 {+/-} 8.1, without differences between left and right lung. Most affected regions were the lower one (95.2%) and the posterior one (73.8%). Total LS showed a strong correlation (r = -0.765) with PaO2/FiO2; by lung regions, those with a higher correlation were the LS of the anterior one (r = -0.823) and the LS of the upper one (r = -0.731). 22.2% of patients required non-invasive respiratory support (NIRS). Multivariate analysis shows that anterior region LS, adjusted for age and sex, is significant (odds ratio 2.159, 95% confidence interval 1.309 to 3.561) for the risk of requiring NIRS. Anterior region LS [≥] 4 and total LS [≥] 19 have similar characteristics to predict the need for NIRS. Conclusions: Ultrasound involvement in COVID-19 pneumonia is bilateral and heterogeneous. Most affected regions are the posterior and the lower ones. The anterior region has prognostic value, because its involvement strongly correlates with the risk of requiring NIRS, and an anterior region LS [≥] 4 has high sensitivity and specificity for predicting the need for NIRS.


title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases

text: Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes.


title: Impact of relaxing Covid-19 social distancing measures on rural North Wales: a simulation analysis

text: Background: Social distancing policies aimed to limit Covid-19 are gradually being relaxed as nationally reported peaks in incident cases are passed. Population density is an important driver of national incidence rates; however peak incidences in rural regions may lag national figures by several weeks. We aimed to forecast the impact of relaxed social distancing rules on rural North Wales. Methods: Daily data on the deaths of people with a positive test for Covid-19 were obtained from Public Health Wales and the UK Government. Sigmoidal growth functions were fitted by non-linear least squares and model averaging used to extrapolate mortality over time. The dates of peak mortality incidences for North Wales, Wales and the UK; and the percentage predicted maximum mortality (as of 7th May 2020) were estimated. Results: The peak daily death rates in Wales and the UK were estimated to have occurred on the 14/04/2020 and 15/04/2020, respectively. For North Wales, this occurred on the 07/05/2020, corresponding to the date of analysis. The number of deaths reported in North Wales represents 31% of the predicted total cumulative number, compared with 71% and 60% for Wales and the UK, respectively. Conclusion: Policies governing the movement of people in the gradual release from lockdown are likely to impact significantly on areas -principally rural in nature- where cases of Covid-19, deaths and immunity are likely to be much lower than in populated areas. This is particularly difficult to manage across jurisdictions, such as between England and Wales, and in popular holiday destinations.


title: Facing the COVID-19 outbreak in children with cancer

text: Europe is now the epicenter of the COVID-19 outbreak. Many concerns have arisen about the management and treatment of children with cancer while researchers are wondering how to deal with this devastating pandemic. In view of the epidemiological and clinical characteristics of the COVID-19 outbreak, it is fundamental to stress that the behavior and hygiene rules adopted by children with cancer must be respected and implemented in order to continue to safeguard their health for the current pandemic.


title: Climatic-niche evolution of SARS CoV-2

text: Adaptation of species to new environments is governed by natural selection that discriminates among genetic variations and favors survival of the fittest. Here, we propose climate plays an important role in the evolution of SARS CoV-2 and the spread of COVID-19 all over the world which was previously not known. To understand the climatic factors responsible for shaping the molecular determinants of the novel coronavirus, genotyping SARS CoV-2 across different latitudes and Koppen’s climate is imperative. It seems this virus follows inverse latitudinal biodiversity gradient due to its preference towards Koppen’s temperate (C) and cold climate (D). Our molecular phylogenetic analysis revealed division of 176 SARS CoV-2 strains into two variant groups, G1 and G2, well defined by four mutations. Initially, SARS CoV-2 was restricted to a “humid-subtropical” (Cfa) climate of southeast China, which soon spread all over the world having C climate. Genomic information superimposed on global Koppen’s climate map elucidates that the gradation “humid-subtropical” (Cfa) and “marine-temperate” (Cfb) to “humid-continental” (Dfa-Dfb) climate drives the evolution of G1 into G2 variant group. It seems an early infection in Europe and USA is due to the dominance of C climate. Russia and North America were infected through linkage of C to D climate and South America from C to A climate. Our study elucidates viruses are sensitive to climate and combined genomic and climatic studies provide crucial information about the pathogenesis and natural spreading pathways during a pandemic which will enable us to take pre-emptive precautionary measures in such outbreaks. Graphical Abstract In Brief The authors elucidate adaptation of SARS CoV-2 to different climates by studying phylogenetics and the distribution of strains on Koppen’s climate map. Highlights SARS CoV-2 follows inverse latitudinal gradient. Phylogenetic network divides SARS CoV-2 strains into two variant groups, G1 and G2. G1 strains is restricted to Koppen’s “temperate” climate (mainly Cfa-Cfb). G2 strains has evolved from G1 to sustain in “humid-continental” (Dfa-Dfb) and “tropical-savannah” (Aw) climate.


title: Diagnosis of Acute Respiratory Syndrome Coronavirus 2 Infection by Detection of Nucleocapsid Protein

text: BACKGROUND Nucleic acid test and antibody assay have been employed in the diagnosis for SARS-CoV-2 infection, but the use of viral antigen for diagnosis has not been successfully developed. Theoretically, viral antigen is the specific marker of the virus and precedes antibody appearance within the infected population. There is a clear need of detection of viral antigen for rapid and early diagnosis. METHODS We included a cohort of 239 participants with suspected SARS-CoV-2 infection from 7 centers for the study. We measured nucleocapsid protein in nasopharyngeal swab samples in parallel with the nucleic acid test. Nucleic acid test was taken as the reference standard, and statistical evaluation was taken in blind. We detected nucleocapsid protein in 20 urine samples in another center, employing nasopharyngeal swab nucleic acid test as reference standard. RESULTS We developed a fluorescence immunochromatographic assay for detecting nucleocapsid protein of SARS-CoV-2 in nasopharyngeal swab sample and urine within 10 minutes. 100% of nucleocapsid protein positive and negative participants accord with nucleic acid test for same samples. Further, earliest participant after 3 days of fever can be identified by the method. In an additional preliminary study, we detected nucleocapsid protein in urine in 73.6% of diagnosed COVID-19 patients. CONCLUSIONS Those findings indicate that nucleocapsid protein assay is an accurate, rapid, early and simple method for diagnosis of COVID-19. Appearance of nucleocapsid protein in urine coincides our finding of the SARS-CoV-2 invading kidney and might be of diagnostic value.


title: The COVID-19 infection in Italy: a statistical study of an abnormally severe disease

text: We statistically investigate the Coronavirus Disease 19 (hereinafter Covid-19) epidemics, which is particularly invasive in Italy. We show that the high apparent mortality (or Case Fatality Ratio, CFR) observed in Italy, as compared with other countries, is likely biased by a strong underestimation of infected cases. To give a more realistic estimate of the mortality of Covid-19, we use the most recent estimates of the IFR (Infection Fatality Ratio) of epidemic, based on the minimum observed CFR, and furthermore analyse data obtained from the ship Diamond Princess, a good representation of a laboratory case-study from an isolated system in which all the people have been tested. From such analyses we derive more realistic estimates of the real extension of the infection, as well as more accurate indicators of how fast the infection propagates. We then point out from the various explanations proposed, the dominant factors causing such an abnormal seriousness of the disease in Italy. Finally, we use the deceased data, the only ones estimated to be reliable enough, to predict the total number of infected people and the interval of time when the infection in Italy could stop.


title: THE PATHOGENESIS OF THROMBOEMBOLIC DISEASE IN COVID-19 PATIENTS: COULD BE A CATASTROPHIC ANTIPHOSPHOLIPID SYNDROME?

text: Background The most severely COVID-19 patients need intensive care and show increased risk of thromboembolic events. Although some patients meet the diagnostic criteria for the Disseminated Intravascular Coagulation, the pathogenesis of the diffuse thrombotic status remains unclear. The aim of the present study is to evaluate the presence of antiphospholipid antibodies (aPL) in sera of deceased patients with autoptic proven thrombotic microangiopathy to evaluate if some patients may have developed Catastrophic Antiphospholipid Syndrome (CAPS). Methods Thirty-five patients were enrolled. The available medical history, comorbidities, therapies, laboratory and autopsy findings were collected post-mortem from clinical records. IgA, IgG and IgM anti cardiolipin (ACA) and anti {beta}2 glycoprotein 1 ({beta}2GP1) antibodies, IgG and IgM anti phosphatidylserine/prothrombin (PS/PT) antibodies were tested for all the patients. Results 3/35 (8.6%) patients were slightly positive for aPL: one for ACA IgG and two for ACA IgM but values were low (< 3X the cut off). No patients tested positive for ACA IgA neither for {beta}2GP1 isotypes. 3/35 (8.6%) patients were positive for PS/PT, one for IgG and two for IgM, but values were less than 2X the cut off. No patients showed simultaneous positivity for ACA and PS/ PT. Conclusions It is difficult to categorize the vascular events into a conventional disease: we did not find significant association with anti-phospholipid antibodies. It is most likely that several factors contribute to trigger the hypercoagulability status and the thromboembolism but, on the basis our results, CAPS is probably not involved into the pathogenesis of these phenomena.


docid: ekejnszp

title: A projection model of COVID-19 pandemic for Belgium

text: We consider a simple model for the COVID-19 pandemic to analyse the relative effectiveness of several stages of the lockdown in Belgium, as well as of several phases of its relaxation. We also make a future projection of different types of measures relative to different stages of the already experienced lockdown.


title: COVID-19 Pandemic: A Neurological Perspective

text: Even though severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed to principally affect the respiratory system, neurological involvements have already been reported in some published work. We have reviewed original articles, case reports, and existing open-source data-sets to delineate the spectrum of neurological disorders potentially observed in SARS-CoV-2 positive cases. Neurological involvement in coronavirus disease 2019 (COVID-19) corresponds to three situations: (a) neurological manifestations of viral infection, (b) post-infective neurological complications, and (c) infection in patients with neurological co-morbidity. Neurological manifestations can further be subdivided into the central nervous system (headache, dizziness, alteration of the sensorium, ataxia encephalitis, stroke, and seizures) and peripheral nervous system (skeletal muscle injury and peripheral nerve involvement including hyposmia and hypogeusia) symptomatology. Post-infective neurological complications include demyelinating conditions. Reduced mobility and dementia as co-morbidities may predispose a patient to have a viral infection. It is concluded that the pandemic of COVID-19 presents for a neurologist some unique challenges. We observe that SARS-CoV-2 may have various neurological manifestations and in many cases, neurological features may precede typical respiratory symptoms.


title: An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

text: SARS-CoV-2 is the etiologic agent of COVID-19, currently causing a devastating pandemic for which pharmacological interventions are urgently needed. The virus enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. The nanobody binds with high affinity in the low nM range to the RBD, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the ‘up’ and ‘down’ conformations and that Ty1 sterically hinders RBD-ACE2 binding. This 12.8 kDa nanobody does not need an Fc domain to neutralize SARS-CoV-2, and can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.


The Socially Distanced Social Animal – In The New Covid-19 Era


title: Charting COVID-19 futures: Mapping, anticipation, and navigation

text: This commentary argues that visualisations of COVID-19 transmission and mortality map out possible futures. It outlines a navigational approach to such mappings which interrogates their role in guiding anticipatory actions that are shaping COVID-19’s emerging geographies.


IT Risk and Resilience-Cybersecurity Response to COVID-19


title: Corona-Krise: (Wirtschafts-)politische Perspektiven: Die Reflexe aus der Finanzkrise sind nicht genug!

text: The explosion of Covid-19 cases is looming in Germany. The German Society for Epidemiology has warned that the number of cases could soon overshoot the capacity of the healthcare system. This may be true even if Germany follows the ‘flatten-the-curve’- approach to reduce infection rates. A suppression of the virus remains the best solution for the crisis. Supply will suffer as long the virus persists. Until then, demand side measures will not cure the epidemic. Coordinated measures for business that ensure compliance and European debt instruments may be part of a strategy to solve the crisis.


title: Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion

text: The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we identify 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and human proteomes, including 20 novel peptides not observed in any previous human coronavirus (HCoV) strains. Four of these mimicked 8-mers/9-mers map onto HLA-B*40:01, HLA-B*40:02, and HLA-B*35:01 binding peptides from human PAM, ANXA7, PGD, and ALOX5AP proteins. This striking mimicry of multiple human proteins by SARS-CoV-2 is made more salient by the targeted genes being focally expressed in arteries, lungs, esophagus, pancreas, and macrophages. Further, HLA-A*03 restricted 8-mer peptides are shared broadly by human and coronaviridae helicases with primary expression of the mimicked human proteins in the neurons and immune cells. These findings highlight molecular mimicry as a shared strategy adopted by evolutionary titans -- the virus in its quest for escaping herd immune surveillance, and the host immune systems that are constantly learning the patterns of “self” and “non-self”.


title: Single-cell analysis of human lung epithelia reveals concomitant expression of the SARS-CoV-2 receptor ACE2 with multiple virus receptors and scavengers in alveolar type II cells

text: The novel coronavirus SARS-CoV-2 was identified as the causative agent of the ongoing pandemic COVID 19. COVID-19-associated deaths are mainly attributed to severe pneumonia and respiratory failure. Recent work demonstrated that SARS-CoV-2 binds to angiotensin converting enzyme 2 (ACE2) in the lung. To better understand ACE2 abundance and expression patterns in the lung we interrogated our in-house single-cell RNA-sequencing dataset containing 70,085 EPCAM+ lung epithelial cells from paired normal and lung adenocarcinoma tissues. Transcriptomic analysis revealed a diverse repertoire of airway lineages that included alveolar type I and II, bronchioalveolar, club/secretory, quiescent and proliferating basal, ciliated and malignant cells as well as rare populations such as ionocytes. While the fraction of lung epithelial cells expressing ACE2 was low (1.7% overall), alveolar type II (AT2, 2.2% ACE2+) cells exhibited highest levels of ACE2 expression among all cell subsets. Further analysis of the AT2 compartment (n = 27,235 cells) revealed a number of genes co-expressed with ACE2 that are important for lung pathobiology including those associated with chronic obstructive pulmonary disease (COPD; HHIP), pneumonia and infection (FGG and C4BPA) as well as malarial/bacterial (CD36) and viral (DMBT1) scavenging which, for the most part, were increased in smoker versus light or non-smoker cells. Notably, DMBT1 was highly expressed in AT2 cells relative to other lung epithelial subsets and its expression positively correlated with ACE2. We describe a population of ACE2-positive AT2 cells that co-express pathogen (including viral) receptors (e.g. DMBT1) with crucial roles in host defense thus comprising plausible phenotypic targets for treatment of COVID-19.


title: Psychological state and family functioning of University of Ibadan students during the COVID-19 lockdown

text: Background: The curtailment of social gatherings as well as lack of online academic engagement, due to the COVID-19 lockdown, could have potentially damaging effects on the psychological state of university students in Nigeria. This study examined the prevalence of anxiety and depression, including associated factors and coping methods among undergraduate students in a Nigerian university. It also examined the association between psychological state and family functioning. Methods: The study design was cross-sectional and involved 386 undergraduate students across the main faculties. The university's ethical review board approved the study with approval number UI/EC/20/0242. An online questionnaire, using Google form, was circulated among the students through their faculty representatives. The Hospital Anxiety and Depression scale (HADs) was used in assessing anxiety and depression, while family functioning was assessed using the McMaster Family Assessment Device, (FAD). Data was entered into Statistical Package for Social Sciences (SPSS), and analysis carried out using descriptive statistics, chi-square, independent t-test, Analysis of Variance (ANOVA), Post-Hoc analysis and linear logistics regression, at 0.05. Results: The mean age was 21 {+/-} 2.9 years, with a female population of 60.1%. Prevalence of anxiety and depression were 41.5% and 31.9% respectively. Students in health-related faculties were significantly less anxious than those in other faculties. Inability to afford three square meals, negative family functioning, having a chronic illness and living in a State/Region with a high incidence of COVID-19, was significantly associated with depression. These factors jointly accounted for 14% of depression seen in undergraduate students. Most of the students coped by engaging themselves in social media, watching television/movies and participating in other online skill development programmes. Conclusion: There was a high prevalence of anxiety and depression among university students with poor family functioning, inability to afford three meals/day, living in a state with a high incidence of COVID-19 and having a chronic illness, contributing to depression. Measures need to be taken to support undergraduate students and their families to prevent the negative consequences of poor mental health. Keywords: COVID-19; lockdown; undergraduate students; anxiety; depression; psychological state; family-functioning, coping.


title: Design for a mail survey to determine prevalence of sars-cov-2 antibodies in the united states

text: Although counts of the novel Coronavirus (SARS-CoV-2) infections and deaths are reported by several sources online, precise estimation of the exposed proportion of the population is not possible in most areas of the world. Estimates of other disease prevalence in the United States are often obtained through in-person seroprevalence surveys. The availability of testing only for individuals with symptoms, combined with stay-at-home and social distancing mandates to stem the spread of the disease, limit in-person data collection options. A probability-based mail survey with at-home, self-administered testing is a feasible method to safely estimate SARS-CoV-2 antibody prevalence within the United States while also easing burden on the U.S. public and health care system. This mail survey could be a one-time, cross-sectional design, or a repeated cross-sectional or longitudinal survey. We discuss several options for designing and conducting this survey.


docid: tvyiegrm

title: Rattrapage vaccinal en pratique: des documents utiles


Migration and Immigration: Uganda and the COVID-19 Pandemic


title: Mining Twitter Data on COVID-19 for Sentiment analysis and frequent patterns Discovery

text: A study with a societal objective was carried out on people exchanging on social networks and more particularly on Twitter to observe their feelings on the COVID-19. A dataset of more than 600,000 tweets with hashtags like COVID and coronavirus posted between February 27, 2020 and March 25, 2020 was built. An exploratory treatment of the number of tweets posted by country, by language and other parameters revealed an overview of the apprehension of the pandemic around the world. A sentiment analysis was elaborated on the basis of the tweets posted in English because these constitute the great majority. On the other hand, the FP-Growth algorithm was adapted to the tweets in order to discover the most frequent patterns and its derived association rules, in order to highlight the tweeters insights relatively to COVID-19.


The necessity of continuous international cooperation for establishing the coronavirus disease 2019 diagnostic capacity despite the challenges of fighting the outbreak in home countries


title: THE EXPERIENCE OF UK BLADDER CANCER PATIENTS DURING THE COVID-19 PANDEMIC: A SURVEY-BASED SNAPSHOT

text: The Covid-19 pandemic has placed unprecedented strain on healthcare systems worldwide. Within this context, UK cancer services have undergone significant disruption to create capacity for the National Health Service. As a charity that endeavours to support bladder cancer (BC) patients and improve outcomes, Action Bladder Cancer UK (ABCUK) designed and administered a SurveyMonkey survey to investigate the prevalence of such disruption for BC patients. From 22nd April to 18th June 2020, 142 BC patients responded. Across all patient groups, 46.8% of patients described disruption to their treatment or follow-up. For non-muscle-invasive BC (NMIBC) patients, disruptions included postponement of: initial transurethral resection of bladder tumour (TURBT) (33.3%), subsequent TURBT (40.0%), and surveillance cystoscopy (58.1%). For NMIBC patients undergoing intravesical therapy, 68.4% experienced treatment postponements or curtailments. For muscle-invasive BC patients, 57.1% had experienced postponement of cystectomy and 14.3% had been changed from cystectomy to radiotherapy. Half of patients undergoing systemic chemotherapy also experienced disruption. Despite the survey's limitations, we have demonstrated considerable disruption to the care of BC patients during the UK Covid-19 pandemic. To avoid a repeat, the UK BC community should define effective contingent ways of working ready for a possible second wave of Covid-19, or any other such threat.


title: Does Early Childhood Vaccination Protect Against COVID-19?

text: The coronavirus disease 2019 (COVID-19) is an on-going pandemic caused by the SARS-coronavirus-2 (SARS-CoV-2) which targets the respiratory system of humans. The published data show that children, unlike adults, are less susceptible to contracting the disease. This article aims at understanding why children constitute a minor group among hospitalized COVID-19 patients. Here, we hypothesize that the measles, mumps, and rubella (MMR) vaccine could provide a broad neutralizing antibody against numbers of diseases, including COVID-19. Our hypothesis is based on the 30 amino acid sequence homology between the SARS-CoV-2 Spike (S) glycoprotein (PDB: 6VSB) of both the measles virus fusion (F1) glycoprotein (PDB: 5YXW_B) and the rubella virus envelope (E1) glycoprotein (PDB: 4ADG_A). Computational analysis of the homologous region detected the sequence as antigenic epitopes in both measles and rubella. Therefore, we believe that humoral immunity, created through the MMR vaccination, provides children with advantageous protection against COVID-19 as well, however, an experimental analysis is required.


title: Clinical characteristics and outcomes of the patients with COVID-19: A report of 62 cases

text: Objective To investigate the early clinical characteristics and diagnosis of and therapeutic approaches for coronavirus disease 2019 (COVID-19). Methods The clinical manifestations and treatment of 62 patients with COVID-19 admitted to Hainan Province People's Hospital during the period from January 21 to February 10, 2019 were analyzed retrospectively. The COVID-19 patients were classified into 3 groups: general, severe and critical types according to the disease severity and the white blood cell, neutrophil and lymphocyte counts were compared between the 3 groups. The 62 patients were given symptomatic and supportive, antiviral, hormonal and Chinese herbal treatment. Results 79.03% (49/62) of patients had a history of traveling or living in Wuhan. The incubation period was (6.85±4.45) d. The clinical features including fever (80.65%), dry cough (62.9%), fatigue (25.81%), shortness of breath (19.35%), and dyspnea (14.52%), sore throat (9.68%), nasal congestion and runny nose (9.68%), muscle soreness (8.06%), diarrhea, vomiting (3.23%), and nausea (4.84%). 95.16% (59/62) of patients had normal or relatively low white blood cell counts. There were statistically significant differences in the counts of leukocytes, neutrophils, and lymphocytes between the 3 groups of the patients (P<0.05). 77.78% (7/9) of the critically ill patients with lymphocyte counts below 0.8×109/L. 90.32% (56/62) of patients typically presented with single or multiple lung lobes/ segments showing ground glass shadow. The average time for CT and CR showing progress and starting to improve and absorb was (9.05±3.75) d and (14.94±7.32) d, respectively. The total course of disease among the 57 discharged patients was 9-38 d, with an average of (21.05±7.17) d. The length of hospital stay was 8-34 d, with an average hospital stay of (15.32±6.49) d. After treatment, the time of the negative mutation of the novel coronavirus was (11.56±6.56) d. Obvious dyspnea occurred in 9 critically ill patients, among them 7 patients needed invasive ventilator support and 2 non-invasive ventilator support. Conclusions In the early clinical stage of COVID-19, fever is the main manifestation. Individual patients are asymptomatic. CT is characterized by ground glass-like changes. Critical patients have significant dyspnea, which can be accompanied by kidney damage. If lung imaging suggests a rapid progress of inflammatory exudation, CRRT (continuous renal replacement therapy) and respiratory support therapy can be given on an individual basis.


title: COVID-19 outcomes, risk factors and associations by race: a comprehensive analysis using electronic health records data in Michigan Medicine

text: Importance: Blacks/African-Americans are overrepresented in the number of COVID-19 infections, hospitalizations and deaths. Reasons for this disparity have not been well-characterized but may be due to underlying comorbidities or sociodemographic factors. Objective: To systematically determine patient characteristics associated with racial/ethnic disparities in COVID-19 outcomes. Design: A retrospective cohort study with comparative control groups. Setting: Patients tested for COVID-19 at University of Michigan Medicine from March 10, 2020 to April 22, 2020. Participants: 5,698 tested patients and two sets of comparison groups who were not tested for COVID-19: randomly selected unmatched controls (n = 7,211) and frequency-matched controls by race, age, and sex (n = 13,351). Main Outcomes and Measures: We identified factors associated with testing and testing positive for COVID-19, being hospitalized, requiring intensive care unit (ICU) admission, and mortality (in/out-patient during the time frame). Factors included race/ethnicity, age, smoking, alcohol consumption, healthcare utilization, and residential-level socioeconomic characteristics (SES; i.e., education, unemployment, population density, and poverty rate). Medical comorbidities were defined from the International Classification of Diseases (ICD) codes, and were aggregated into a comorbidity score. Results: Of 5,698 patients, (median age, 47 years; 38% male; mean BMI, 30.1), the majority were non-Hispanic Whites (NHW, 59.2%) and non-Hispanic Black/African-Americans (NHAA, 17.2%). Among 1,119 diagnosed, there were 41.2% NHW and 37.4% NHAA; 44.8% hospitalized, 20.6% admitted to ICU, and 3.8% died. Adjusting for age, sex, and SES, NHAA were 1.66 times more likely to be hospitalized (95% CI, 1.09-2.52; P=.02), 1.52 times more likely to enter ICU (95% CI, 0.92-2.52; P=.10). In addition to older age, male sex and obesity, high population density neighborhood (OR, 1.27 associated with one SD change [95% CI, 1.20-1.76]; P=.02) was associated with hospitalization. Pre-existing kidney disease led to 2.55 times higher risk of hospitalization (95% CI, 1.62-4.02; P<.001) in the overall population and 11.9 times higher mortality risk in NHAA (95% CI, 2.2-64.7, P=.004). Conclusions and Relevance: Pre-existing type II diabetes/kidney diseases and living in high population density areas were associated with high risk for COVID-19 susceptibility and poor prognosis. Association of risk factors with COVID-19 outcomes differed by race. NHAA patients were disproportionately affected by obesity and kidney disease.


title: COVID-19, smoking, vaping and quitting: A representative population survey in England

text: Aims: To explore 1) associations between suspected SARS-CoV-2 infection, hand washing, smoking status, e-cigarette use, and nicotine replacement therapy (NRT) use and 2) whether COVID-19 has prompted smoking and vaping quit attempts, and more smoking inside the home. Design: Cross-sectional household surveys of a representative sample of the population in England from April-May 2020. Participants: The sample included 3,285 adults aged [≥]18 years. Measurements: Participants who reported they definitely or think they had coronavirus were classified as having a suspected SARS-CoV-2 infection. Participants were asked how often they wash their hands after returning home, before eating, before preparing foods or before touching their face. They were also asked whether, due to COVID-19, they had i) attempted to quit smoking, ii) attempted to quit vaping, and iii) changed the amount they smoke inside the home. Findings: Odds of suspected SARS-CoV-2 infection were significantly greater among current smokers (20.9%, adjusted odds ratio [ORadj]=1.34, 95% confidence interval [CI]=1.04-1.73) and long-term (>1-year) ex-smokers (16.1%, ORadj=1.33, 95%CI=1.05-1.68) than never smokers (14.5%). Recent (<1-year) ex-smokers had non-significantly greater odds of suspected infection (22.2%, ORadj=1.50, 95%CI=0.85-2.53, Bayes factor=0.55-1.17). Bayes factors indicated there was sufficient evidence to rule out large differences in suspected SARS-CoV-2 infection by NRT use and medium differences by e-cigarette use. With the exception of hand washing before face touching, engagement in hand washing behaviours was high (>85%) regardless of nicotine use. A minority (12.2%) of past-year smokers who made a quit attempt in the past three months were triggered by COVID-19, and approximately one-in-ten current e-cigarette users reported attempting to quit vaping because of COVID-19. Most people reported smoking the same amount inside the home. Conclusions: In a representative sample of the adult population in England, current smokers and long-term ex-smokers had higher odds of suspected SARS-CoV-2 infection than never smokers, but there were no large differences by NRT or e-cigarette use. In general, engagement in hand washing was high regardless of nicotine or tobacco use. A minority of past-year smokers and current e-cigarette users, respectively, attempted to quit smoking/vaping due to COVID-19.


title: A Simple, SIR-like but Individual-Based l-i AIR Model: Application in Comparison of COVID-19 in New York City and Wuhan

text: COVID-19 has spread around the world with nearly 360,000 deaths from the virus as of today (5/28/2020). Mathematical models have played an important role in many key policy discussions about COVID-19. SIR or SIR-derived models are a common modeling technique. However, the application of these models needs to solve complicated differential equations, enabling use of these models only by professional researchers. In this study, a simple, SIR-like but individual-based model, the l-i AIR model, is presented. The parameters l and i represent the length of the latent period and the infectious period, respectively. The variable A stands for the number of the infected people in the active infectious period, I for the number of cumulative infected people, and R for the number of the people in recovery or death. The nth terms of the three variables are derived, which can be easily calculated in Microsoft Excel, making the program easy to be used in most offices. A transmission coefficient k and a transient incidence rate of the infected people are induced in the model to examine the effect of social distancing and the testing capacity of coronavirus on the epidemic curves. The simulated daily new cases from this l-i AIR model can fit very well with the reported daily new cases of COVID-19 in Wuhan, China and in New York City, USA, providing important information about latent period, infectious period and lockdown efficiency, and calculating the number of actual infected people who are positive in antibodies.


title: Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China

text: Background: Previous studies have showed clinical characteristics of patients with the 2019 novel coronavirus disease (COVID-19) and the evidence of person-to-person transmission. Limited data are available for asymptomatic infections. This study aims to present the clinical characteristics of 24 cases with asymptomatic infection screened from close contacts and to show the transmission potential of asymptomatic COVID-19 virus carriers. Methods: Epidemiological investigations were conducted among all close contacts of COVID-19 patients (or suspected patients) in Nanjing, Jiangsu Province, China, from Jan 28 to Feb 9, 2020, both in clinic and in community. Asymptomatic carriers were laboratory-confirmed positive for the COVID-19 virus by testing the nucleic acid of the pharyngeal swab samples. Their clinical records, laboratory assessments, and chest CT scans were reviewed. Findings: None of the 24 asymptomatic cases presented any obvious symptoms before nucleic acid screening. Five cases (20.8%) developed symptoms (fever, cough, fatigue and etc.) during hospitalization. Twelve (50.0%) cases showed typical CT images of ground-glass chest and five (20.8%) presented stripe shadowing in the lungs. The remaining seven (29.2%) cases showed normal CT image and had no symptoms during hospitalization. These seven cases were younger (median age: 14.0 years; P = 0.012) than the rest. None of the 24 cases developed severe COVID-19 pneumonia or died. The median communicable period, defined as the interval from the first day of positive nucleic acid tests to the first day of continuous negative tests, was 9.5 days (up to 21 days among the 24 asymptomatic cases). Through epidemiological investigation, we observed a typical asymptomatic transmission to the cohabiting family members, which even caused severe COVID-19 pneumonia. Interpretation: The asymptomatic carriers identified from close contacts were prone to be mildly ill during hospitalization. However, the communicable period could be up to three weeks and the communicated patients could develop severe illness. These results highlighted the importance of close contact tracing and longitudinally surveillance via virus nucleic acid tests. Further isolation recommendation and continuous nucleic acid tests may also be recommended to the patients discharged.