title: A Novel Approach for Estimating the Final Outcome of Global Diseases Like COVID-19

text: The existence of a universal law which maps the bell curve of daily cases to a sigmoid curve for cumulative ones is used for making robust estimations about the final outcome of a disease. Computations of real time effective reproduction rate are presented and its limited usefulness is derived. After using methods ESE and EDE we are able to find the inflection point of the cumulative curve under consideration and study its time evolution. Since mortality processes tend to follow a Gompertz distribution, we apply the properties of it and introduce novel estimations for both the time remaining after inflection time and the capacity of the curve. Special properties of sigmoid curves are used for assessing the quality of estimation and as indices for the cycle completion. Application is presented for COVID-19 evolution for most affected countries and the World.


title: Investigation of Compatibility of SARS-CoV-2 RT-PCR Kits Containing Different Gene Targets During COVID-19 Pandemic

text: Aim:In the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse transcriptase-polymerase chain reaction (RT-PCR) technique is often used. We evaluated the compatibility of SARS-CoV-2 RT-PCR kits containing different gene targets during the pandemic. Materials and methods: Samples were tested by Bio-Speddy (RdRp gene) and Diagnovital (RdRp+E genes). The correlation between two assays were determined by Deming regression and chi-square heatmap analyses. Results: Diagnovital PCR kit showed in a constricted range and conveniently exponential amplification curves than Bio-Speedy PCR kit. While the correlation increased when a secondary biomarker was added to the kit. Conclusion: In an unknown sample, using together different PCR kits that target different genes during the pandemic situation may provide a more accurate diagnosis of SARS-CoV-2.


title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins

text: Background There is a crucial need for effective therapies that are immediately available to counteract COVID-19 disease. Recently, ELISA binding cross-reactivity against components of human epidemic coronaviruses with currently available intravenous immunoglobulins (IVIG) Gamunex-C and Flebogamma DIF (5% and 10%) have been reported. In this study, the same products were tested for neutralization activity against SARS-CoV-2, SARS-CoV and MERS-CoV and their potential as an antiviral therapy. Methods The neutralization capacity of six selected lots of IVIG was assessed against SARS-CoV-2 (two different isolates), SARS-CoV and MERS-CoV in cell cultures. Infectivity neutralization was measured by determining the percent reduction in plaque-forming units (PFU) and by cytopathic effects for two IVIG lots in one of the SARS-CoV-2 isolates. Neutralization was quantified using the plaque reduction neutralization test 50 (PRNT50) in the PFU assay and the half maximal inhibitory concentration (IC50) in the cytopathic/cytotoxic method (calculated as the minus log10 dilution which reduced the viral titer by 50%). Results All IVIG preparations showed neutralization of both SARS-CoV-2 isolates, ranging from 79 to 89.5% with PRNT50 titers from 4.5 to >5 for the PFU method and ranging from 47.0%-64.7% with an IC50 ~1 for the cytopathic method. All IVIG lots produced neutralization of SARS-CoV ranging from 39.5 to 55.1 % and PRNT50 values ranging from 2.0 to 3.3. No IVIG preparation showed significant neutralizing activity against MERS-CoV. Conclusion In cell culture neutralization assays, the tested IVIG products contain antibodies with significant cross-neutralization capacity against SARS-CoV-2 and SARS-CoV. However, no neutralization capacity was demonstrated against MERS-CoV. These preparations are currently available and may be immediately useful for COVID-19 management.


title: Early postmortem brain MRI findings in COVID-19 non-survivors

text: Importance: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to have potential neuro-invasiveness that might lead to acute brain disorders or contribute to respiratory distress in patients with coronavirus disease 2019 (COVID-19). Brain magnetic resonance imaging (MRI) data in COVID-19 patients are scarce due to difficulties to obtain such examination in infected unstable patients during the COVID-19 outbreak. Objective: To investigate the occurrence of structural brain abnormalities in non-survivors of COVID-19 in a virtopsy framework. Design: Prospective, case series study with postmortem brain MRI obtained early (<24h) after death. Setting: Monocentric study. Participants: From 31/03/2020 to 24/04/2020, consecutive decedents who fulfilled the following inclusion criteria were included: death <24 hours, SARS-CoV-2 detection on nasopharyngeal swab specimen, chest computerized tomographic (CT) scan suggestive of COVID-19, absence of known focal brain lesion, and MRI compatibility. Main Outcome(s) and Measure(s): Signs of acute brain injury and MRI signal abnormalities along the olfactory tract and brainstem were searched independently by 3 neuroradiologists, then reviewed with neurologists and clinicians. Results: Among the 62 patients who died from COVID-19 during the inclusion period, 19 decedents fulfilled inclusion criteria. Subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent) were observed. Asymmetric olfactory bulbs were found in 4 other decedents without downstream olfactory tract abnormalities. No brainstem MRI signal abnormality. Conclusions and Relevance: Postmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by the virus-induced endothelial disturbances. SARS-CoV-2-related olfactory impairment seems to be limited to olfactory bulbs. The absence of brainstem MRI abnormalities does not support a brain-related contribution to respiratory distress in COVID-19.


title: Best we be prepared

text: Fast action will help the world contain the new coronavirus


title: Pharmacologicaltreatment of COVID-19: lights and shadows

text: At the end of December 2019, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2, caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China and then the entire world, forcing the World Health Organization to make the assessment that the coronavirus disease (COVID-19) can be characterized as a pandemic, the first ever caused by a coronavirus. To date, clinical evidence and guidelines based on reliable data and randomized clinical trials for the treatment of COVID-19 are lacking. In the absence of definitive management protocols, many treatments for COVID-19 are currently being evaluated and tested worldwide. Some of these options were soon abandoned due to ineffectiveness, while others showed promising results. The basic treatments are mainly represented by antiviral drugs, even if the evidence is not satisfactory. Among the antivirals, the most promising appears to be remdesivir. Corticosteroids and tocilizumab seem to guarantee positive results in selected patients so far, although the timing of starting therapy and the most appropriate therapeutic schemes remain to be clarified. Efficacy of the other drugs is still uncertain, and they are currently used as a cocktail of treatments in the absence of definitive guidelines. What will represent the real solution to the enormous problem taking place worldwide is the identification of a safe and effective vaccine, for which enormous efforts and investments are underway.


title: Societal heterogeneity contributes to complex dynamic patterns of the COVID-19 pandemics: insights from a novel Stochastic Heterogeneous Epidemic Model (SHEM)

text: After months of COVID-19 quarantine, businesses are reopening their doors and people are reentering society. Within the current COVID-19 data, after a slow-down of infection, a new peak in active cases is already forming. Here we developed a new Stochastic Heterogeneous Epidemic Model (SHEM) to investigate genesis of complex pandemic patterns with the focus on the role of heterogenous societal structure. Using this model with R0 of COVID-19, we simulated viral infection in different scenarios where isolated, communities surround the main cluster of the population. Depending on the parameters of heterogeneity and isolation period, our simulations generated a multimodal growth periods with multiple peaks, an extended plateau, a prolonged tail, or a delayed second wave of infection. We show that timing and magnitude of infection for previously unaffected isolated clusters of people, such as suburban neighborhoods, are critical aspects of these patterns. Our model can be applied to communities at any given scale of population described as a fractal-like structure, i.e. from the entire human population, to a country, down to a province or city levels with relevant societal heterogeneity structure. The current COVID-19 pandemic development worldwide and in the US follows a bimodal rise pattern, qualitatively similar to that in our simulations. We interpret our data to indicate that the secondary peak in the pattern is contributed by the states and counties in the US with late infection surges that are analogous to isolated suburbs in our model. Furthermore, the on-going early reopening, i.e. premature partial reopening in our model, is further accelerating the peak rise. This peak now reaches new heights, forcing many states in the US to reverse their policies and reestablish their quarantine measures. Our results support these timely and effective measures: we show that longer quarantine periods can reduce the number of deaths and transform the current trend into a substantially delayed (>1 year) second wave. If this scenario becomes a reality, it is important (i) to develop the vaccine and/or effective treatment before the second wave; (ii) to warn people living in suburbs that it is these isolated areas that may hold a false sense of security, but they should continue to take extra care for their public health.


title: Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

text: An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital system following the emergency use authority (EUA) guidance issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=124) using newly designed dual-target rRT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting of SARS-CoV-2 in upper respiratory and lower respiratory tract specimens, including bronchoalveolar lavage and tracheal aspirates. Accuracy testing demonstrated excellent assay agreement between expected and observed values. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 tests from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Our findings demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarizes clinical data from early in the epidemic in New York City.


COVID-19 infection in Italy: An occupational injury


title: Impact of psychological health on dry eye and management during the coronavirus disease-19 epidemic/ 新型冠状病毒肺炎疫情期间心理健康对干眼的影响及防控

text: At the end of 2019, the coronavirus disease-19 (COVID-19) broke out in Wuhan and has spread throughout the world, bringing great challengees to the public health, prevention, and control work in our country and globally. Although the national medical staff and Public Health Epidemic Prevention personnel are fighting the epidemic, the large numbers of patients and the long-term isolation measures greatly impacted people's lifestyles. The epidemic's development has currently been eased, but the blockades and quarantines in many cities have not been completely lifted. While controlling the coronavirus, lifestyle changes caused by long-term isolation, as well as fear of the disease and economic recession have brought people various negative emotions. These mental health issues may cause or aggravate the occurrence and development of dry eye. Therefore, the authors explore the impact of mental health on dry eye during the COVID-19 epidemic, alongside possible mechanisms, and put forward relevant suggestions for managing eye-related diseases during and after the epidemic.


title: Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: In-field learnings from a clinical microbiology laboratory

text: The unprecedented scale of testing required to effectively control the coronavirus disease (COVID-19) pandemic has necessitated urgent implementation of rapid testing in clinical microbiology laboratories. To date, there are limited data available on the analytical performance of emerging commercially available assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and integration of these assays into laboratory workflows. Here, we performed a prospective validation study of a commercially available assay, the AusDiagnostics Coronavirus Typing (8-well) assay. Respiratory tract samples for SARS-CoV-2 testing were collected between 1st March and 25th March 2020. All positive samples and a random subset of negative samples were sent to a reference laboratory for confirmation. In total, 2,673 samples were analyzed using the Coronavirus Typing assay. The predominant sample type was a combined nasopharyngeal/throat swab (2,640/2,673; 98.8%). Fifty-four patients were positive for SARS-CoV-2 (0.02%) using the Coronavirus Typing assay; 53/54 (98.1%) positive results and 621/621 (100%) negative results were concordant with the reference laboratory. Compared to the reference standard, sensitivity of the Coronavirus Typing assay for SARS-CoV-2 was 100% [95% CI 93.2%-100%], specificity 99.8% [95% CI 99.1%-100%], positive predictive value 98.1% (95% CI 90.2%-99.7%] and negative predictive value 100% [95% CI 99.4%-100%]. In many countries, standard regulatory requirements for the introduction of new assays have been replaced by emergency authorizations and it is critical that laboratories share their post-market validation experiences, as the consequences of widespread introduction of a sub-optimal assay for SARS-CoV-2 are profound. Here, we share our in-field experience, and encourage other laboratories to follow suit.


title: Remdesivir Efficacy in Coronavirus Disease 2019 (COVID-19): A Systematic Review

text: Background: Researchers are working hard to find an effective treatment for the new coronavirus 2019. We performed a comprehensive systematic review to investigate the latest clinical evidence on the treatment efficacy and safety of Remdesivir in hospitalized patients with COVID-19. Methods: We performed a systematic search of the Pubmed, Embase, Web of Science, Google scholar, and MedRxiv for relevant observational and interventional studies. Measured outcomes were mortality rates, improvement rates, time to clinical improvement, all adverse event rates and severe adverse event rates. Results: 3 RCTs and 2 cohorts were included in our study. In 2 cohort studies, patients received Remdesivir for 10 days. 2 RCTs evaluated 10-day treatment of Remdesivir efficacy versus placebo group and the other RCT compared its 5-day regimen versus 10-day regimen. Visual inspection of the forest plots revealed that Remdesivir efficacy was not much different in reducing 28-day mortality versus 14-day mortality rates. Besides, 10-day treatment regimen overpowers 5-day treatment and placebo in decreasing time to clinical improvement. All adverse event rates did not have significant difference; however, severe adverse event rate was lower in 5-day Remdesivir group compared to 10-day and placebo groups. Conclusion: 5-day course of Remdesivir therapy in COVID-19 patients is probably efficacious and safe and patients without invasive mechanical ventilation benefit the most. Treatment can be extended to 10 days if satisfactory improvement is not seen by day 5. Most benefits from Remdesivir therapy take place in the first 14 days of the start of the treatment.


title: Stochastic Compartmental Modelling of SARS-CoV-2 with Approximate Bayesian Computation

text: In this proof-of-concept study, we model the spread of SARS-CoV-2 in various environments with a stochastic susceptible-infectious-recovered (SIR) compartmental model. We fit this model to the latest epidemic data with an approximate Bayesian computation (ABC) technique. Within this SIR-ABC framework, we extrapolate long-term infection curves for several regions and evaluate their steepness. We propose several applications and extensions of the SIR-ABC technique.


Avian Influenza: Virchow’s Reminder


title: Knowledge and attitude towards COVID-19 in Bangladesh: Population-level estimation and a comparison of data obtained by phone and online survey methods

text: Adherence of people to the guidelines and measures suggested in fighting the ongoing COVID-19 pandemic is partly determined by the Knowledge, Attitude, and Practices (KAP) of the population. In this cross-sectional study, we primarily addressed two key issues. First, we tried to determine whether there is a significant difference in the estimated COVID-19 knowledge level from the online and phone survey methods. Second, we tried to quantify the knowledge and attitude of COVID-19 in Bangladeshi adult population. Data were collected through phone calls (April 14-23, 2020) and online survey (April 18-19, 2020) in Bangladesh. The questionnaire had 20 knowledge questions with each correct response getting one point and incorrect/do not know response getting no point (maximum total knowledge score 20). Participants scoring >17 were categorized as having good knowledge. The percentages of good knowledge holders were 57.6%, 75.1%, and 95.8% in the phone (n=1426), online non-medical (n=1097), and online medical participants (n=382), respectively. Comparison between phone and online survey showed that, overall, online survey might overestimate knowledge level than that of phone survey, although there was no difference for elderly, poor, and rural people. Male gender, higher education, living in town/urban areas, good financial condition, and use of internet were positively associated with good knowledge. However, higher knowledge was associated with having less confidence in the final control of COVID-19. Our adult population-level estimates showed that only 32.6% (95% CI 30.1-35.2%) had good knowledge. This study provides crucial information that could be useful for the researchers and policymakers to develop effective strategies.


title: Comparison of SARS-CoV-2 spike protein binding to human, pet, farm animals, and putative intermediate hosts ACE2 and ACE2 receptors

text: The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used recently released X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptor allows to define residues important for binding. From the 20 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S-binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites located near the S-interface. Of note, pigs and dogs which are not or not effectively infected, respectively, have only a few changes in the binding site have relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with viruses from bat and pangolin revealed that the latter contains only one substitution, whereas the bat virus exhibits five. However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-COV-2. IMPORTANCE SARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. However, the lower expression of ACE2 in the upper respiratory tract of some pets and livestock means more research and monitoring should be done to explore the animal source of infection and the risk of potential cross-species transmission. Finally, the analysis also showed that SARS-CoV-2 may not specifically adapted to any of its putative intermediate hosts.


title: The Epidemic Severity Index: Estimating Relative Local Severity of Novel Disease Outbreaks

text: Determining the severity of a novel pathogen in the early stages is difficult in the absence of reliable data. The pattern of outbreaks for COVID-19 across the globe have differed markedly above and below +40N latitudes, suggesting very different levels of severity, but countries worldwide have implemented the same lockdown strategies. Existing methods for estimating severity appear not to have been useful in informing strategic decisions, possibly due to mismatches between the data required and those available, overly sophisticated methods with undesirable biases, or perhaps confusion and uncertainly generated by the wide range of estimates these methods produced early on. The Epidemic Severity Index (ESI) is a simple, robust method for estimating the local severity of novel epidemic outbreaks using early and widely-available data and that does not depend on any estimated values. ESI allows rapid, meaningful comparisons across territories that can be tracked as the outbreaks unfold. The ESI quantifies severity relative to a parameterised baseline rather than attempting to estimate values for infection fatality rates, case fatality rates or transmission rates. The relative nature of the ESI sidesteps any problems of confidence associated with absolute rate estimation methods and offers immediate practical strategic value.


title: Challenges and opportunities brought by COVID-19: Understanding and prevention of COVID-19

text: The ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome (SARS) coronavirus 2 was first reported in Wuhan, Hubei Province at the end of December 2019. The number of confirmed cases is increasing every day, causing more deaths than the SARS outbreak in China from 2002 to 2003. COVID-19 has become a public health emergency of global concern, and all governments and medical institutions are on high alert. Therefore, we summarize the genomics, epidemiology, clinical manifestations, diagnosis, treatment, and other aspects of COVID-19 based on the currently available data.


title: Time courses of COVID-19 infection and local variation in socioeconomic and health disparities in England

text: Objective: To identify factors associated with local variation in the time course of COVID-19 case burden in England. Methods: We analyzed laboratory-confirmed COVID-19 case data for 150 upper tier local authorities, from the period from January 30 to May 6, 2020, as reported by Public Health England. Using methods suitable for time-series data, we identified clusters of local authorities with distinct trajectories of daily cases, after adjusting for population size. We then tested for differences in sociodemographic, economic, and health disparity factors between these clusters. Results: Two clusters of local authorities were identified: a higher case trajectory that rose faster over time to reach higher peak infection levels, and a lower case trajectory cluster that emerged more slowly, and had a lower peak. The higher case trajectory cluster (79 local authorities) had higher population density (p<0.001), higher proportion of Black and Asian residents (p=0.03; p=0.02), higher multiple deprivation scores (p<0.001), a lower proportions of older adults (p=0.005), and higher preventable mortality rates (p=0.03). Local authorities with higher proportions of Black residents were more likely to belong to the high case trajectory cluster, even after adjusting for population density, deprivation, proportion of older adults and preventable mortality (p=0.04). Conclusion: Areas belonging to the trajectory with significantly higher COVID-19 case burden were more deprived, and had higher proportions of ethnic minority residents. A higher proportion of Black residents in regions belonging to the high trajectory cluster was not fully explained by differences in population density, deprivation, and other overall health disparities between the clusters.


title: Causes of Death and Comorbidities in Patients with COVID-19

text: Infection by the new corona virus strain SARS-CoV-2 and its related syndrome COVID-19 has caused several hundreds of thousands of deaths worldwide. Patients of higher age and with preexisting chronic health conditions are at an increased risk of fatal disease outcome. However, detailed information on causes of death and the contribution of comorbidities to death yet is missing. Here, we report autopsy findings on causes of death and comorbidities of 26 decedents that had clinically presented with severe COVID-19. We found that septic shock and multi organ failure was the most common immediate cause of death, often due to suppurative pulmonary infection. Respiratory failure due to diffuse alveolar damage presented as the most immediate cause of death in fewer cases. Several comorbidities, such as hypertension, ischemic heart disease, and obesity were present in the vast majority of patients. Our findings reveal that causes of death were directly related to COVID-19 in the majority of decedents, while they appear not to be an immediate result of preexisting health conditions and comorbidities. We therefore suggest that the majority of patients had died of COVID-19 with only contributory implications of preexisting health conditions to the mechanism of death.


title: Epidemiological characteristics of an outbreak of Coronavirus Disease 2019 in the Philippines

text: The outbreak of Coronavirus disease 2019 (Covid-2019) is a source of great concern in the Philippines. In this paper, we described the epidemiological characteristics of the laboratory-confirmed patients with Covid-2019 in the Philippines as of April 3, 2020 and provided recommendations on how to limit the spread of the disease. Data from the DOH NCOV tracker and University of the Philippines Covid-2019 tracker were extracted, from its initiation (January 30, 2020) until the most recent situation report (April 3, 2020). The total number of cases and deaths were stratified by sex, age, and region of the Philippines. Descriptive statistics were used to analyze the demographic profile of the confirmed cases. Case fatality rate, in percent, was calculated by dividing the total number of deaths to the total number of confirmed cases. Results revealed that a total of 3,018 cases of Covid-2019 spread were confirmed across 17 regions in the Philippines. These cases occurred over the course of 73 days through person-to-person transmission, highlighting an extremely high infectivity rate. The 144 deaths accounted for, equate to 4.51 case fatality rate, seemingly lower compared to its predecessors, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), but higher compared to that of United States of America, Germany, mainland China, and neighboring Southeast Asian countries such as Malaysia, Singapore, Brunei, and Thailand. Of the 3,018 confirmed cases, majority were male, elderly, and diagnosed in Metro Manila region. Case fatality rates were higher in male and highest among elderly and Filipinos in the Ilocos region. With the surge on the number of cases, precautionary measures should remain a responsibility, and protocols for prevention need to be set. Adherence to infection control guidelines such as but not limited to frequently handwashing for at least 20 seconds, observing coughing etiquette, wearing of masks, and social distancing should be maintained in order to contain the disease.


title: The promising barrier: Theoretical investigation

text: Virus has become a global pandemic because of the rapid spread and imaginative numbers of cases and deaths It becomes the most important issue that brings the attention of not only scientists but also the press, international and publishing houses, etc All the countries involved all researches and centres efforts to find a vaccine or treatment to control it to no avail This study not only investigates and explores the interaction between three types of medicine (Hydroxychloroquine, Favipiravir, and Remdesivir), and the angiotensin-converting enzyme (ACE2) receptors but also comparing the results with the interaction between the active part of the virus (Spike protein (S1)) and the cell All interactions and properties of all molecules have been studied theoretically using theoretical calculations and computational methods based on the density functional theory The results indicate that one of the drugs, which is Remdesivir could be an effective barrier inhibits the bind of the S1 with the human cell This result could be interpreted in terms of the binding energy, since the binding energy of the Remdesivir molecule with the ACE2 equals-8 564 eV, while the binding energy of S1 is-5 666 eV This research also founds that the electrons transfer from the drug to the ACE2 is 10 873 e, which is higher than that of S1 (5 155e) In addition, the results exhibit the Hydroxychloroquine does not have enough capability to inhibit the binding process between the virus and the cell since its binding energy (-2 948 eV) and the number of electrons transfer (0 7670) are the lowest Finally, the Fermi energies values of Remdesivir (-3 5 eV) and ACE2 (-3 4 eV) molecules are convergent In the context of the elastic transport, this predication is an important result since it interprets the large number of electrons that have been transferred from Remdesivir to ACE2 molecule, as shown in Figure 3 and Table 2, and this introduces the Remdesivir as a promising drug Copyright © Advanced Scientific Research All rights reserved


How Neurologists Answer Patients' Questions About COVID-19


title: Clinical validation and performance evaluation of the automated Vitros Total Anti-SARS-CoV-2 Antibodies assay for screening of serostatus in COVID-19

text: Objectives: Evaluation of serostatus against SARS-CoV-2 has emerged as an important tool in identification of exposure to COVID-19. We report on the validation of the Vitros Anti-SARS-CoV-2 Total (CoV2T) assay for qualitative serological testing of SARS-CoV-2 antibodies. Methods: We performed validation studies according to COLA guidelines, using samples previously tested for SARS-CoV-2 by RT-PCR. We evaluated precision, analytical interferences, and cross-reactivity with other viral infections. We also evaluated concordance with molecular and other serological testing, and evaluated seroconversion. Results: The Vitros CoV2T assay exhibited acceptable precision, was resistant to analytical interference, and did not exhibit cross-reactivity with samples positive for other respiratory viruses. The CoV2T assay exhibited 100% negative predictive agreement (56/56) and 71% positive predictive agreement (56/79) with RT-PCR across all patient samples, and was concordant with other serological assays. Concordance with RT-PCR was 97% > 7 days after symptom onset. Conclusions: The Vitros CoV2T assay was successfully validated in our laboratory. We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2, however, the use of the CoV2T and other serological assays in clinical management of COVID-19 patients is yet unknown, and must be evaluated in future studies.


title: Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island

text: A stochastic model was created to simulate the impact of various healthcare measures on the COVID-19 epidemic. Travel restrictions and point of entry or exit screening help to delay the onset of the outbreak by a few weeks. Population surveillance is critical to detect the start of community transmission early and to avoid a surge in cases. Contact reduction and contact tracing are key interventions that can help to control the outbreak. To promptly curb the number of new cases, countries should diagnose patients using a highly sensitive test.


title: Prediction of the clinical outcome of COVID-19 patients using T lymphocyte subsets with 340 cases from Wuhan, China: a retrospective cohort study and a web visualization tool

text: Background Wuhan, China was the epicenter of the 2019 coronavirus outbreak. As a designated hospital, Wuhan Pulmonary Hospital has received over 700 COVID-19 patients. With the COVID-19 becoming a pandemic all over the world, we aim to share our epidemiological and clinical findings with the global community. Methods In this retrospective cohort study, we studied 340 confirmed COVID-19 patients from Wuhan Pulmonary Hospital, including 310 discharged cases and 30 death cases. We analyzed their demographic, epidemiological, clinical and laboratory data and implemented our findings into an interactive, free access web application. Findings Baseline T lymphocyte Subsets differed significantly between the discharged cases and the death cases in two-sample t-tests: Total T cells (p < 2.2e-16), Helper T cells (p < 2.2e-16), Suppressor T cells (p = 1.8-14), and TH/TS (Helper/Suppressor ratio, p = 0.0066). Multivariate logistic regression model with death or discharge as the outcome resulted in the following significant predictors: age (OR 1.05, p 0.04), underlying disease status (OR 3.42, p 0.02), Helper T cells on the log scale (OR 0.22, p 0.00), and TH/TS on the log scale (OR 4.80, p 0.00). The McFadden pseudo R-squared for the logistic regression model is 0.35, suggesting the model has a fair predictive power. Interpretation While age and underlying diseases are known risk factors for poor prognosis, patients with a less damaged immune system at the time of hospitalization had higher chance of recovery. Close monitoring of the T lymphocyte subsets might provide valuable information of the patients condition change during the treatment process. Our web visualization application can be used as a supplementary tool for the evaluation.


title: Diarrhea may be underestimated: a missing link in 2019 novel coronavirus

text: The outbreak of pneumonia caused by the 2019 Novel Coronavirus (2019-nCoV) was reported in Wuhan City, China. However, the clinical symptoms varied in different reports. Based on the results of inter-group difference test, we found that the incidence of diarrhea differed in three recent reports. As 2019-nCoV utilizes the same cell entry receptor ACE2 as severe acute respiratory syndrome coronavirus (SARS-CoV) and ACE2 tightly controls intestinal inflammation, to trace the route of infection mediated by 2019-nCoV, we used the single-cell RNA sequencing data for analysis. We found that the ACE2 mRNA was highly expressed in the healthy human small intestine rather than the lung. Besides, single-cell RNA sequencing data showed that ACE2 was significantly elevated in the proximal and distal enterocytes, where the small intestinal epithelium is exposed to the foreign pathogen. Thus, we suspect that ACE2-expressing small intestinal epithelium cells might be vulnerable to 2019-nCoV infection when people eat infected wild animals and diarrhea may serve as an indicator for infection, suggesting that clinicians should pay more attention to patients with diarrhea during the outbreak of pneumonia.


title: Respirators, quarantines, and worst-case scenarios: Lab animal facilities grapple with the pandemic

text: The U S National Institutes of Health announced this week it is “deeply concerned about the impact of [COVID-19] on the ability of … institutions to support the well-being of animals and personnel during this public health emergency ” And indeed, many universities are currently grappling with the best way to care for the millions of mice, monkeys, and other research animals they care for across the country, in addition to protecting the health of their own employees


title: Duration of Viral Clearance in IDF Soldiers with Mild COVID-19

text: Policies determining the duration of quarantine and return to work for confirmed COVID-19 patients still lack evidence. We report our findings regarding viral RNA positivity duration among a cohort of young patients with mild disease. Between March 20th, 2020, and May 10th, 2020, 219 soldiers were admitted to the Israel Defense Forces Medical Corps (IDF-MC) COVID-19 rehabilitation center following a positive RT-PCR test for SARS-CoV-2. 119 of these patients, 84 (70.6%) males, 35 (29.4%) females with a median age of 21 (IQR 19-25) were classified as having mild disease and had two consecutive negative RT-PCR tests by May 10th, 2020. The median time for SARS-CoV-2 positivity in nasopharyngeal or oropharyngeal swabs in the study population was 21 days (IQR 15-27) from symptom onset, with a range of 4 to 45 days. The results of this study suggest that in young and healthy adult patients with COVID-19, the median duration of viral positivity is around three weeks. This duration is higher than previously reported in other populations. Young and healthy adults comprise much of the population workforce, and the results of this study may assist in determining the isolation period for symptomatic adults and confirmed COVID-19 patients with mild symptoms. Further studies on this topic should look to expand and determine the intervals of serial testing for confirmed patients and determine the duration of SARS-CoV-2 positivity in other populations.


title: A systematic review of chest imaging findings in COVID-19

text: Chest computed tomography (CT) is frequently used in diagnosing coronavirus disease 2019 (COVID-19) for detecting abnormal changes in the lungs and monitoring disease progression during the treatment process. Furthermore, CT imaging appearances are correlated with patients presenting with different clinical scenarios, such as early versus advanced stages, asymptomatic versus symptomatic patients, and severe versus nonsevere situations. However, its role as a screening and diagnostic tool in COVID-19 remains to be clarified. This article provides a systematic review and meta-analysis of the current literature on chest CT imaging findings with the aim of highlighting the contribution and judicious use of CT in the diagnosis of COVID-19. A search of PubMed/Medline, Web of Science, ScienceDirect, Google Scholar and Scopus was performed to identify studies reporting chest imaging findings in COVID-19. Chest imaging abnormalities associated with COVID-19 were extracted from the eligible studies and diagnostic value of CT in detecting these abnormal changes was compared between studies consisting of both COVID-19 and non-COVID-19 patients. A random-effects model was used to perform meta-analysis for calculation of pooled mean values and 95% confidence intervals (95% CI) of abnormal imaging findings. Fifty-five studies met the selection criteria and were included in the analysis. Pulmonary lesions more often involved bilateral lungs (78%, 95% CI: 45-100%) and were more likely to have a peripheral (65.35%, 95% CI: 25.93-100%) and peripheral plus central distribution (31.12%, 95% CI: 1.96-74.07%), but less likely to have a central distribution (3.57%, 95% CI: 0.99-9.80%). Ground glass opacities (GGO) (58.05%, 95% CI: 16.67-100%), consolidation (44.18%, 95% CI: 1.61-71.46%) and GGO plus consolidation (52.99%, 95% CI: 19.05-76.79%) were the most common findings reported in 94.5% (52/55) of the studies, followed by air bronchogram (42.50%, 95% CI: 7.78-80.39%), linear opacities (41.29%, 95% CI: 7.44-65.06%), crazy-paving pattern (23.57%, 95% CI: 3.13-91.67%) and interlobular septal thickening (22.91%, 95% CI: 0.90- 80.49%). CT has low specificity in differentiating pneumonia-related lung changes due to significant overlap between COVID-19 and non-COVID-19 patients with no significant differences in most of the imaging findings between these two groups (P>0.05). Furthermore, normal CT (13.31%, 95% CI: 0.74-38.36%) was reported in 26 (47.3%) studies. Despite widespread use of CT in the diagnosis of COVID-19 patients based on the current literature, CT findings are not pathognomonic as it lacks specificity in differentiating imaging appearances caused by different types of pneumonia. Further, there is a relatively high percentage of normal CT scans. Use of CT as a first-line diagnostic or screening tool in COVID-19 is not recommended.


title: Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification

text: Novel Corona virus (COVID-19 or 2019-nCoV) is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for COVID-19 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in under 30 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the COVID-19 nucleic sequence. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected COVID-19 in simulated patient samples. This test was performed in under 30 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.


title: Impact of edge-removal on the centrality betweenness of the best spreaders

text: The control of epidemic spreading is essential to avoid potential fatal consequences and also, to lessen unforeseen socio-economic impact. The need for effective control is exemplified during the severe acute respiratory syndrome (SARS) in 2003, which has inflicted near to a thousand deaths as well as bankruptcies of airlines and related businesses. In this article, we examine the efficacy of control strategies on the propagation of infectious diseases based on removing connections within real world airline network with the associated economic and social costs taken into account through defining appropriate quantitative measures. We uncover the surprising results that removing less busy connections can be far more effective in hindering the spread of the disease than removing the more popular connections. Since disconnecting the less popular routes tend to incur less socio-economic cost, our finding suggests the possibility of trading minimal reduction in connectivity of an important hub with efficiencies in epidemic control. In particular, we demonstrate the performance of various local epidemic control strategies, and show how our approach can predict their cost effectiveness through the spreading control characteristics.


title: A Computer Simulation Study on novel Corona Virus Transmission among the People in a Queue

text: The World Health Organization (WHO) on March 11, 2020, has declared the novel Corona virus (COVID-19) outbreak a global pandemic. It is essential to understand how coronavirus transmits from one person to another and this knowledge will help protect the vulnerable and limit the spread of the Corona virus. The mode of respiratory transmission of Corona virus is not completely understood as of date. Using a computer simulation, this paper analyses the probability of spreading of Corona virus through air among the people who are standing in a queue. The parameters such as the diameter of the virus particle, room temperature, relative humidity, height of the person, distance between the people and the waiting time in the queue are considered in the computer model to determine the distribution of Corona virus and hence identify the risk factor of spreading the Covid-19. This paper describes the possibilities of getting infectious when a Covid-19 infected person present in a queue and the impact on the waiting time and the position in the queue on the transmission of Corona virus.


Social responsibility of medical journal: A concern for covid-19 pandemic


title: Quarantine alone or in combination with other public health measures to control COVID-19: A rapid Cochrane review

text: In March 2020, the South African government implemented various non-pharmacological prevention and control measures (e g isolation, social distancing and quarantine) in response to the COVID-19 pandemic We summarise evidence from a rapid Cochrane review on the effect of quarantine alone v quarantine plus combination measures to prevent transmission of and mortality caused by COVID-19 The findings show that when started earlier, quarantine combined with other prevention and control measures can be more effective than quarantine alone, and cost less


title: Steep increases in fentanyl-related mortality west of the Mississippi River: synthesizing recent evidence from county and state surveillance

text: Background and Aims: Overdose deaths from synthetic opioids (e.g., fentanyl), increased 10-fold in the United States from 2013-2018, despite 88% of deaths occurring east of the Mississippi River. Public health professionals have long feared that further spread of fentanyl could greatly exacerbate the opioid epidemic. We aimed to measure and characterize recent fentanyl deaths in jurisdictions west of the Mississippi River. Design: Systematic search of states and counties in the Western U.S. for publicly available data on fentanyl-related deaths since the most recently published Centers for Disease Control and Prevention (CDC) statistics, which cover through December 2018. Longitudinal study using 2019 and 2020 mortality records to identify changes in fentanyl-involved mortality since most recent CDC statistics. Settings: U.S. states west of the Mississippi River. Measurements: Annual rate of fentanyl-involved deaths per 100,000 population. Proportion of fatal heroin-, stimulant, and prescription pill overdoses also involving fentanyl. Findings: We identified nine jurisdictions with publicly available fentanyl death data through December 2019 or later: State of Arizona, Denver County, CO, Harris County, TX, Humboldt County, CA, King County, WA, Los Angeles County, CA, San Francisco County, CA, Siskiyou County, CA, Dallas-Fort Worth, TX metro area (Denton, Johnson, Parker, Tarrant counties. Fentanyl deaths increased in each jurisdiction. Their collective contribution to national synthetic narcotics mortality tripled from 2017 to 2019. First quarter 2020 data (available from all but San Francisco County) showed a 33% growth in fentanyl-mortality over 2019. Fentanyl-involvement in heroin, stimulant, and prescription pill deaths has grown substantially over time. Conclusions: Fentanyl has spread westward, which could dramatically worsen the already severe opioid epidemic in the United States. Increasing standard-dose of naloxone, expanding Medicaid, improving coverage of addiction treatment, and public health educational campaigns should be prioritized.


title: A Scalable Topical Vectored Vaccine Candidate Against SARS-CoV-2

text: The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) caused an ongoing unprecedented global public health crises of coronavirus disease in 2019 (CoVID-19). The precipitously increased death rates, its impact on livelihood and trembling economies warrant the urgent development of SARS-CoV-2 vaccine which would be safe, efficacious and scalable. Owing to unavailability of the vaccine, we propose a de novo synthesised avian orthoavulavirus 1 (AOaV-1)-based topical respiratory vaccine candidate against CoVID-19. Avirulent strain of Newcastle disease virus, proto-type virus of AOaV-1, was engineered to express full length spike (S) glycoprotein which is highly neutralizing and major protective antigen of the SARS-CoV-2. Broad-scale in vitro characterization of recombinant vaccine candidate demonstrated efficient co-expression of the hemagglutinin-neuraminidase (HN) of AOaV-1 and S protein of SARS-CoV-2, and comparable replication kinetics were observed in cell culture model. The recombinant vaccine candidate virus actively replicated and spread within cells independently of exogenous trypsin. Interestingly, incorporation of S protein of SARS-CoV-2 into the recombinant AOaV-1 particles attributed the sensitivity to anti-SARS-CoV-2 antiserum and more prominently to anti-AOaV-1 antiserum. Finally, our results demonstrated that the recombinant vaccine vector stably expressed S protein after multiple propagation in chicken embryonated eggs, and this expression did not significantly impact the in vitro growth characteristics of the recombinant. Taken together, the presented respiratory vaccine candidate is highly attenuated in primates per se, safe and lacking pre-existing immunity in human, and carries the potential for accelerated vaccine development against CoVID-19 for clinical studies.


title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads

text: The ongoing pandemic of the novel coronavirus, SARS-CoV-2, has led to a global surge in laboratory testing for the virus. The gold standard approach to detecting an active viral infection is the use of RT-qPCR. This approach requires the isolation of viral RNA from respiratory specimens, such as nasopharyngeal swabs. We developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Using a WHO recommended, laboratory-developed RT-qPCR for SARS-CoV-2, we validated this method in a CAP-accredited laboratory, against the IVD-labelled bioMérieux NucliSENS easyMAG automated extraction platform. Our method demonstrates a comparable sensitivity and specificity, making it suitable for large-scale testing and monitoring of suspected COVID-19 cases and healthcare workers. This is especially important as the world faces critical shortages of viral RNA extraction reagents for the existing commercial extraction systems.


title: Spring Weather and COVID-19 Deaths in the U.S.

text: This study used statistically robust regression models to control for a large set of confounders (including county-level time-invariant factors and time trends, regional-level daily variation, state-level social distancing measures, ultraviolet light, and levels of ozone and fine particulate matter, PM2.5) to estimate a reliable rather than simple regression for the impact of weather on the most accurately measured outcome of COVID-19, death. When the average minimum temperature within a five-day window increased by one degree Fahrenheit in spring 2020, daily death rates in northern U.S. counties increased by an estimated 5.1%. When ozone concentration over a five-day window rose by one part per billion, daily death rates in southern U.S. counties declined by approximately 2.0%. Maximum temperature, precipitation, PM2.5, and ultraviolet light did not significantly associate with COVID-19 mortality. The mechanism that may drive the observed association of minimum temperature on COVID-19 deaths in spring months may be increased mobility and contacts. The effect of ozone may be related to its disinfectant properties, but this requires further confirmation.


title: Periodic Graphics: How does immunity work?

text: Chemical educator and Compound Interest blogger Andy Brunning explains how our bodies fight foreign invaders like coronaviruses To download a pdf of this article, visit http://cenm ag/immunity References used to create this graphic:Centers for Disease Control and Prevention Understanding How Vaccines Work Last updated July 2018 Janeway, Charles A , Jr , Paul Travers, Mark Walport, and Mark J Shlomchik “The Distribution and Functions of Immunoglobulin Isotypes ” In Immunobiology: The Immune System in Health and Disease 5th ed New York: Garland Science, 2001 Li, Geng, Yaohua Fan, Yanni Lai, et al “Coronavirus Infections and Immune Responses ”J Med Virol (Jan 2020) DOI: 10 1002/jmv 25685 National Institute of Allergy and Infectious Diseases and National Cancer Institute Understanding the Immune System: How It Works US Department of Health and Human Services, National Institutes of Health, 2003 Siegrist , Claire-Anne “Vaccine Immunology ” In Plotkin’s Vaccines 7th ed Edited by Stanley A Plotkin, Walter A Orenstein, Paul A Offit, and


title: TEG Max Clot Strength is Consistently Elevated and May Be Predictive of COVID-19 Status at the Time of ICU Admission

text: Background: Hypercoagulability is becoming widely recognized as a major complication of COVID-19 infection as evidenced by high levels of fibrinogen degradation products and microthrombi identified within the lungs and kidneys of autopsy specimens from these patients. We report thromboelastography (TEG) testing on a cohort of patients with suspected COVID-19 infection at the time of admission to the intensive care unit. Methods: TEG testing was performed using the TEG 6s analyzer near or at the time of ICU admission. We also report the results of other coagulation or inflammatory related indices such as platelet count, prothrombin time, fibrinogen, D-dimer, C-reactive protein, ferritin, and procalcitonin. All laboratory testing was performed at the discretion of the attending physician in the course of normal patient care and retrospectively reviewed. Results: We found that maximum clot strength was consistently elevated in COVID-19 patients while normal in all patients found to be negative. We did not encounter significant prolongations of coagulation assays outside of those expectedly prolonged by heparin therapy nor was meeting the criteria for disseminated intravascular coagulation encountered. Conclusions: We postulate that elevated maximum clot strength by TEG testing is predictive of COVID-19 status as within our cohort this perfectly predicted patients COVID-19 status despite a high level of suspicion in negative patients with normal TEG results. While these results require a larger cohort for confirmation, we feel that TEG testing could improve confidence in negative COVID-19 testing results in suspected patients possibly allowing for earlier de-escalation of infectious precautions and personal protective equipment utilization.


title: COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM

text: Motivation The first cases of the COVID-19 pandemic emerged in December 2019. Until the end of February 2020, the number of available genomes was below 1,000, and their multiple alignment was easily achieved using standard approaches. Subsequently, the availability of genomes has grown dramatically. Moreover, some genomes are of low quality with sequencing/assembly errors, making accurate re-alignment of all genomes nearly impossible on a daily basis. A more efficient, yet accurate approach was clearly required to pursue all subsequent bioinformatics analyses of this crucial data. Results hCoV-19 genomes are highly conserved, with very few indels and no recombination. This makes the profile HMM approach particularly well suited to align new genomes, add them to an existing alignment and filter problematic ones. Using a core of ∼2,500 high quality genomes, we estimated a profile using HMMER, and implemented this profile in COVID-Align, a user-friendly interface to be used online or as standalone via Docker. The alignment of 1,000 genomes requires less than 20mn on our cluster. Moreover, COVID-Align provides summary statistics, which can be used to determine the sequencing quality and evolutionary novelty of input genomes (e.g. number of new mutations and indels). Availability https://covalign.pasteur.cloud, hub.docker.com/r/evolbioinfo/covid-align Contacts olivier.gascuel@pasteur.fr, frederic.lemoine@pasteur.fr Supplementary information Supplementary information is available at Bioinformatics online.


title: CoVID-19 in Singapore: Impact of Contact Tracing and Self-awareness on Healthcare Demand

text: Background. A great concern around the globe now is to mitigate the COVID-19 pandemic via contact tracing. Analyzing the control strategies during the first five months of 2020 in Singapore is important to estimate the effectiveness of contacting tracing measures. Methods. We developed a mathematical model to simulate the COVID-19 epidemic in Singapore, with local cases stratified into 5 categories according to the conditions of contact tracing and self-awareness. Key parameters of each category were estimated from local surveillance data. We also simulated a set of possible scenarios to predict the effects of contact tracing and self-awareness for the following month. Findings. During January 23 - March 16, 2020, the success probabilities of contact tracing and self-awareness were estimated to be 31% (95% CI 28%-33%) and 54% (95% CI 51%-57%), respectively. During March 17 - April 7, 2020, several social distancing measures (e.g., limiting mass gathering) were introduced in Singapore, which, however, were estimated with minor contribution to reduce the non-tracing reproduction number per local case (R_(l,2)). If contact tracing and self-awareness cannot be further improved, we predict that the COVID-19 epidemic will continue to spread in Singapore if R_(l,2)[≥]1.5. Conclusion. Contact tracing and self-awareness can mitigate the COVID-19 transmission, and can be one of the key strategies to ensure a sustainable reopening after lifting the lockdown.


title: A Fully Automated Deep Learning-based Network ForDetecting COVID-19 from a New And Large Lung CT ScanDataset

text: COVID-19 is a severe global problem that has crippled many industries and killed many people around the world. One of the primary ways to decrease the casualties is the infected person's identification at the proper time. AI can play a significant role in these cases by monitoring and detecting infected persons in early-stage so that it can help many organizations. In this paper, we aim to propose a fully-automated method to detect COVID-19 from the patient's CT scan without needing a clinical technician. We introduce a new dataset that contains 48260 CT scan images from 282 normal persons and 15589 images from 95 patients with COVID-19 infection. Our proposed network takes all the CT scan image sequences of a patient as the input and determines if the patient is infected with COVID-19. At the first stage, this network runs an image processing algorithm to discard those CT images that inside the lung is not properly visible in them. This helps to reduce the number of images that shall be identified as normal or COVID-19, so it reduces the processing time. Also, running this algorithm makes the deep network at the next stage to analyze only the proper images and thus reduces false detections. At the next stage, we propose a modified version of ResNet50V2 that is enhanced by a feature pyramid network for classifying the selected CT images into COVID-19 or normal. If enough number of chosen CT scan images of a patient be identified as COVID-19, the network considers that patient, infected to this disease. The ResNet50V2 with feature pyramid network achieved 98.49% accuracy on more than 7996 validation images and correctly identified almost 237 patients from 245 patients.


title: Evaluation of Ultraviolet-C Light for Rapid Decontamination of Airport Security Bins in the Era of SARS-CoV-2

text: BACKGROUND: Contaminated surfaces are a potential source for spread of respiratory viruses including SARS-CoV-2. Ultraviolet-C (UV-C) light is effective against RNA and DNA viruses and could be useful for decontamination of high-touch fomites that are shared by multiple users. METHODS: A modification of the American Society for Testing and Materials standard quantitative carrier disk test method (ASTM E-2197-11) was used to examine the effectiveness of UV-C light for rapid decontamination of plastic airport security bins inoculated at 3 sites with methicillin-resistant Staphylococcus aureus (MRSA) and bacteriophages MS2, PhiX174, and Phi6, an enveloped RNA virus used as a surrogate for coronaviruses. Reductions of 3 log(10) on inoculated plastic bins were considered effective for decontamination. RESULTS: UV-C light administered as 10-, 20-, or 30-second cycles in proximity to a plastic bin reduced contamination on each of the test sites, including vertical and horizontal surfaces. The 30-second cycle met criteria for decontamination of all 3 test sites for all the test organisms except bacteriophage MS2 which was reduced by greater than 2 log(10) PFU at each site. CONCLUSIONS: UV-C light is an attractive technology for rapid decontamination of airport security bins. Further work is needed to evaluate the utility of UV-C light in real-world settings and to develop methods to provide automated movement of bins through a UV-C decontamination process.


title: Estimation of global case fatality rate of coronavirus disease 2019 (COVID-19) using meta-analyses: Comparison between calendar date and days since the outbreak of the first confirmed case.

text: Since the outbreak of the coronavirus disease 2019 (COVID-19) in December of 2019 in China, the estimation of the pandemic case fatality rate (CFR) has been the focus and interest of many stakeholders. In this manuscript, we prove that the method of using the cumulative CFR is static and does not reflect the trend according to the daily change per unit of time. A proportion meta-analysis was carried out on CFR in every country reporting COVID-19 cases. Based on the results, we performed a meta-analysis for global COVID-19 CFR. Each analysis was performed on two different calculations of CFR: according to calendar date and according to days since the outbreak of the first confirmed case. We thus explored an innovative and original calculation of CFR concurrently based on the date of the first confirmed case as well as on a daily basis. For the first time, we showed that using meta-analyses, according to calendar date and days since the outbreak of the first confirmed case were different. We propose that CFR according to days since the outbreak of the first confirmed case might be a better predictor of the current CFR of COVID-19 and its kinetics. Keywords: COVID-19, case fatality rate, proportion meta-analysis, calendar date, days since first confirmed case.


title: Efficacy of Corticosteroids in Non-Intensive Care Unit Patients with COVID-19 Pneumonia from the New York Metropolitan region

text: Introduction: The role of systemic corticosteroid as a therapeutic agent for patients with COVID19 pneumonia is controversial. Objective: The purpose of this study was to evaluate the effect of corticosteroids in non-intensive care unit (ICU) patients with COVID19 pneumonia complicated by acute hypoxemic respiratory failure (AHRF). Methods: This was a single center retrospective cohort study, comprising of 205 patients admitted to the general wards with COVID19 pneumonia. The primary outcome was a composite of ICU transfer, intubation, or inhospital mortality. Cox proportional hazard regression was implemented. Result: Among 205 patients, 60 (29.27%) were treated with corticosteroid. The mean age was ~57 years, and ~75% were men. Thirteen patients (22.41%) developed a primary composite outcome in the corticosteroid cohort vs. 54 (37.5%) patients in the non-corticosteroid cohort (P=0.039). The adjusted hazard ratio (HR) for the development of the composite primary outcome was 0.15 (95% CI, 0.07 to 0.33; P <0.001). The adjusted hazard ratio for ICU transfer was 0.16 (95% CI, 0.07 to 0.34; P < 0.001), intubation was 0.31 (95% CI, 0.14 to 0.70; P=0.005), death was 0.53 (95% CI, 0.22 to 1.31; P=0.172), and discharge was 3.65 (95% CI, 2.20 to 6.06; P<0.001). The corticosteroid cohort had increasing SpO2/FiO2 over time compared to the non-corticosteroid cohort who experience decreasing SpO2/FiO2 over time. Conclusion: Among non-ICU patients hospitalized with COVID-19 pneumonia complicated by AHRF, treatment with corticosteroid was associated with a significantly lower risk of the primary composite outcome of ICU transfer, intubation, or inhospital death.


title: What constitutes urgent endoscopy? A social media snapshot of gastroenterologists’ views during the COVID-19 pandemic

text: Background and study aims There is a consensus among gastroenterology organizations that elective endoscopic procedures should be deferred during the COVID-19 pandemic. While the decision to perform urgent procedures and to defer entirely elective procedures is mostly evident, there is a wide “middle ground” of time-sensitive but not technically urgent or emergent endoscopic interventions. We aimed to survey gastroenterologists worldwide using Twitter to help elucidate these definitions using commonly encountered clinical scenarios during the COVID-19 pandemic. Methods A 16-question survey was designed by the authors to include common clinical scenarios that do not have clear guidelines regarding the timing or urgency of endoscopic evaluation. This survey was posted on Twitter. The survey remained open to polling for 48 hours. During this time, multiple gastroenterologists and fellows with prominent social media presence were tagged to disseminate the survey. Results The initial tweet had 38,795 impressions with a total of 2855 engagements. There was significant variation in responses from gastroenterologists regarding timing of endoscopy in these semi-urgent scenarios. There were only three of 16 scenarios for which more than 70 % of gastroenterologists agreed on procedure-timing . For example, significant variation was noted in regard to timing of upper endoscopy in patients with melena, with 44.5 % of respondents believing that everyone with melena should undergo endoscopic evaluation at this time. Similarly, about 35 % of respondents thought that endoscopic retrograde cholangiopancreatography should only be performed in patients with choledocholithiasis with abdominal pain or jaundice. Conclusion Our analysis shows that there is currently lack of consensus among gastroenterologists in regards to timing of semi-urgent or non-life-threatening procedures during the COVID-19 pandemic. These results support the need for the ongoing development of societal guidance for these “semi-urgent” scenarios to help gastroenterologists in making difficult triage decisions.


title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results

text: Improper nasopharyngeal swab collection could contribute to false-negative COVID-19 results. In support of this, specimens from confirmed or suspected COVID-19 cases that tested negative or indeterminate (i.e. suspected false-negatives) contained less human DNA (a stable molecular marker of sampling quality) compared to a representative pool of specimens submitted for testing.


title: Efficacy and safety of interferon beta-1a in treatment of severe COVID-19: A randomized clinical trial

text: Objectives: To the best of our knowledge, there is no published study regarding use of IFN beta-1a in the treatment of severe COVID-19. In this randomized clinical trial efficacy and safety of IFN {beta}-1a has been evaluated in patients with severe COVID-19. Methods: Forty-two patients in the interferon group received IFN beta-1a in addition to the standard of care. Each 44 micrograms/ml (12 million IU/ml) of interferon beta-1a was subcutaneously injected three times weekly for two consecutive weeks. The control group received only the standard of care. Primary outcome of study was time to reach clinical response. Secondary outcomes duration of hospital stay, length of ICU stay, 28-day mortality, effect of early or late administration of IFN on mortality, adverse effects and complications during the hospitalization. Results: As primary outcome, time to the clinical response was not significantly different between the IFN and the control groups (9.7 +/- 5.8 vs. 8.3 +/- 4.9 days respectively, P=0.95). On day 14, 66.7% vs. 43.6% of patients in the IFN group and the control group were discharged, respectively (OR= 2.5; 95% CI: 1.05- 6.37). The 28-day overall mortality was significantly lower in the IFN then the control group (19% vs. 43.6% respectively, p= 0.015). Early administration significantly reduced mortality (OR=13.5; 95% CI: 1.5-118). Conclusion: Although did not change time to reach the clinical response, adding to the standard of care significantly increased discharge rate on day 14 and decreased 28-day mortality. Clinical Trial Registration ID #IRCT20100228003449N28.


title: Chinese expert brief consensus on newborn screening of inherited metabolic disorders during the novel coronavirus infection epidemic

text: Novel coronavirus (2019-nCov) infection (COVID-19) rapidly spread across China and 25 countries in the worldwide, which infected not only adults but also children, even neonates. Each year, about 15 million newborns are delivered in China. Newborn screening (NBS) helps effectively prevent some mental retardation, premature death, and adverse outcomes in the early stage of baby, which could detect some inherited metabolic disorders (IMDs). During this COVID-19 epidemic, how to balance the risk of infected 2019-nCov and the risk of disability and teratogenesis of IMDs. Expert members of NBS extra quality assessment in National Clinical Center of Laboratory (NCCL) give a brief consensus for NBS of IMDs in the COVID-2019 epidemic, hoping that the brief consensus could be reference for NBS of IMDs in the other epidemic areas or periods all over the world.


title: Monitoring and predicting viral dynamics in SARS-CoV-2-infected Patients

text: This manuscript is based on the a simple but robust model we developed urgently to accurately monitor and predict viral dynamics for each SARS-CoV-2-infected patient, given the limited number of RT-PCR tests and the complexity of each individual's physical health situation. In this study, we used the mathematical model to monitor and predict the changes of viral loads from different nasal and throat swab of clinical specimens collected from diagnosed patients. We also tested our real time model by using the data from the SARS-CoV-2-infected patients with different severity. By using this personal model, we can predict the viral dynamics of patients, minimize false-negative test results, and screen the patients who are at risk of testing positive again after recovery. We sincerely thank those who are on the front lines battling SARS-CoV-2 virus. We hope this model will be useful for SARS-CoV-2-infected patients.


title: COVID-19 Epidemic in Algeria: Assessment of the implemented preventive strategy

text: Abstract Since the spread of the COVID-19 epidemic in China, several preventive strategies have been implemented worldwide to fight against the spread of the virus, in Algeria the control actions have been mainly social distancing, movement restriction, quarantine and lockdown. In order to assess the preventive strategy adopted in Algeria, we studied three zones whole Algeria, Blida region, and whole Algeria except Blida, we used as a indicator the basic reproduction number R0, we compared the mean R0-before and R0-after the implementation of the mitigation measures using bivariate analysis, then we used the results we found to estimate the number of COVID-19 cases avoided by these measures, then after, we predicted the peak of the first wave of the epidemic. We note that the decrease in R0 after the preventive measures implementation was statistically significant, p value < 10-4, in the three areas, thus, the preventive strategy in Algeria has been effective in its entirety. Our projection revealed that 15613 cases of COVID-19 were avoided in 14 days, from April 6, to April 19, 2020, in the whole country, and 1747 cases were prevented in Blida during the same period. We estimate that the peak of the first wave of the epidemic in Algeria will be reached with herd immunity of 15.93% as of November 2020, however, at least 56% of people with protective immunity would be needed to be sufficient to avoid a second wave. The used method to carry out the evaluation has given us a good overview, but, R0 is not the only factor to consider when estimating the burden of the epidemic, to do that, the number of daily admissions to intensive care units and hospitalizations remain good indicators. In order to better the epidemic control in Algeria, it is possible to act on contact efficacy rate by adding an instruction to wear medical mask by ordinary population outside, this measure has been reported to be effective in some countries. To conclude, it is good to keep in mind that a new way of life based on good hygiene habits and social distancing must therefore be in place and adopted by the population for at least several months, otherwise the demand for health care will exceed the availability. Keywords: COVID-19, Algeria, preventive strategy assessment, R0, epidemic peak.


title: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity

text: Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and raises the alarm that the ongoing vaccine development may become futile in future epidemic if more mutations were identified. Highlights Based on the currently available genome sequence data, we proved that SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak. The spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. We confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020.


title: Currently prescribed drugs in the UK that could up or downregulate ACE2 in COVID-19 disease: A systematic review

text: Objective: To review evidence on routinely prescribed drugs in the UK that could up or downregulate Angiotensin Converting Enzyme 2 (ACE2) and potentially affect COVID-19 disease Design: Systematic review Data source: MEDLINE, EMBASE, CINAHL, the Cochrane Library and Web of Science Study selection: Any design with animal or human models examining a currently prescribed UK drug compared to a control, placebo or sham group, and reporting an effect on ACE2 level, activity or gene expression. Data extraction and synthesis: MEDLINE, EMBASE, CINAHL, the Cochrane Library, Web of Science and OpenGrey from inception to 1st April 2020. Methodological quality was assessed using the SYRCLE's risk of bias tool for animal studies and Cochrane risk of bias tool for human studies. Results: We screened 3,360 titles and included 112 studies with 21 different drug classes identified as influencing ACE2 activity. Ten studies were in humans and 102 were in animal models None examined ACE2 in human lungs. The most frequently examined drugs were Angiotensin Receptor Blockers (ARBs) (n= 55) and Angiotensin-Converting Enzyme- Inhibitors (ACE-I) (n= 22). More studies reported upregulation than downregulation with ACE-I (n=22), ARBs (n=55), insulin (n=8), thiazolidinedione (n=7) aldosterone agonists (n=3), statins (n=5), oestrogens (n=5) calcium channel-blockers (n=3) GLP-1 agonists (n=2) and NSAIDs (n=2). Conclusions: There is an abundance of academic literature and media reports on the potential of drugs that could attenuate or exacerbate COVID-19 disease. This is leading to trials of repurposed drugs and uncertainty amongst patients and clinicians concerning continuation or cessation of prescribed medications. Our review indicates that the impact of currently prescribed drugs on ACE2 has been poorly studied in-vivo, particularly in human lungs where the SARS-CoV-2 virus appears to enact its pathogenic effects. We found no convincing evidence to justify starting or stopping currently prescribed drugs to influence outcomes of COVID-19 disease.


title: Microbial and autoantibody immunogenic repertoires in TIF1γ autoantibody positive dermatomyositis

text: We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. Increased microbial diversity was observed in dermatomyositis. Viruses were over-represented and species of the Poxviridae family were significantly enriched. The autoantibodies identified recognised a large portion of the human proteome, including interferon regulated proteins; these proteins were clustered in specific biological processes. Apart from TRIM33, autoantibodies against eleven further TRIM proteins, including TRIM21, were identified. Some of these TRIM proteins shared epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a significant role in the pathogenesis of dermatomyositis.


Temporal Association Between Particulate Matter Pollution and Case Fatality Rate of COVID-19 in Wuhan, China


title: Performance of temporal artery temperature measurement in ruling out fever: implications for COVID-19 screening.

text: The use of non-invasive temperature testing methods like temporal artery thermometers (TATs) is growing exponentially in the face of the ongoing COVID-19 pandemic. We performed a retrospective analysis of over 1.8 million emergency department electronic health records to identify assess the performance of TAT measurement using patients with near-contemporaneous temperature measurements taken via rectal or oral approaches. Using over 17,000 matched measurements, we show poor fever sensitivity using TAT. We show that sensitivity is significantly improved by lowering the fever threshold and describe limits of agreement between methods of measurement. Our findings suggest that private, public, and healthcare delivery organizations may need to reconsider how we perform high-volume screening during this time of crisis and has implications for return-to-work protocols.


title: Deep Learning Based Approach for Identifying Conventional Machining Processes from CAD Data

text: Abstract Manufacturing has evolved to become more automated in pursuit of higher quality, better productivity and lower cost. However, industrial logistics between the end customer and manufacturing supply chain still demands human labor and intelligence. This logistic work requires engineers with experienced knowledge to identify machining processes from the CAD model provided by customers at the beginning, and later sourcing for qualified manufacturing suppliers according to identified manufacturing processes. Developing an efficient automatic Machining Process Identification (MPI) system becomes a pivotal problem for logistic automation. In this paper, a novel MPI system is presented based on 3D Convolutional Neural Networks (CNN) and Transfer learning. The proposed system admits triangularly tessellated surface (STL) models as inputs and outputs machining process labels (e.g. milling, turning etc.) as the results of classification of the neural network. Computer-synthesized workpiece models are utilized in training the neural network. In addition to the MPI system, a portable framework was developed for future applications in related fields. The MPI system shows more than 98% accuracy for both synthesized models and real workpiece models which verifies its robustness and real-time reliability.


title: Trend analysis, modelling and impact assessment of COVID-19 in Nepal

text: With continued global expansion of COVID-19 transmission and mounting threat of the disease, the timely analysis of its trend in Nepal and forecasting the potential situation in the country has been deemed necessary. We analyzed the trend, modelling and impact assessment of COVID-19 cases of Nepal from 23rd January 2020 to 30th April 2020 to portray the scenario of COVID-19 after the first phase of lockdown. Exponential smoothing state-space and autoregressive integrated moving average (ARIMA) models were constructed to forecast the cases. Susceptible-infectious-recovered (SIR) model was fit to estimate the basic reproduction number (Ro) of COVID-19 in Nepal. There has been increase in the number of cases but the overall growth in COVID-19 was not high. Statistical modelling has shown that COVID-19 cases may continue to increase exponentially in Nepal. The basic reproduction number in Nepal being maintained at low level of 1.08 for the period of 23rd January to 30th April 2020 is an indication of effectiveness of lockdown in containing the COVID-19 spread. The models further suggest that COVID-19 might persist until December 2020 with peak cases in August 2020. On the other hand, basic reproduction number of 1.25 was computed for total cases reported for the 22nd March to 30th April 2020 period implying that COVID-19 may remain for at least for a year in the country. Thus, maintaining social distance and stay home policy with an implementation of strict lockdown in COVID-19 affected district is highly recommended.


Der Run auf die Virentests


title: The behaviour changes in response to COVID-19 pandemic within Malaysia

text: The novel coronavirus infection, COVID-19, is a pandemic that currently affects the whole world. During this period, Malaysians displayed a variety of behaviour changes as a response to COVID-19, including panic buying, mass travelling during movement restriction and even absconding from treatment facilities. This article attempts to explore some of these behaviour changes from a behaviourist perspective in order to get a better understanding of the rationale behind the changes.


title: Towards nexus-based governance_ defining interactions between economic activities and Sustainable Development Goals (SDGs)

text: The success of the Sustainable Development Goals (SDGs) depends on solving the ‘nexus’ challenge: how can positive interactions between SDGs be optimised, and negative interactions minimised, in order to create co-benefits and reduce trade-offs? Due to their varying impacts on the SDGs, the economic activities undertaken by organisations present a key lever for operationalising this SDG-nexus. Yet the interactions between individual economic activities and the economic, social, and environmental dimensions of sustainable development have not been systematically assessed, thus creating a vital operational bottleneck to achieving the SDGs. This paper conducts a systematic review of 876 articles published between 2005 and 2019 to study the nexus between individual economic activities, sustainable development in general, and the SDGs in specific. It finds that studies on agricultural, industrial, and manufacturing activities predominantly report negative impacts on environmental development, while literature on services activities highlight economic and social contributions. Overall, economic activities are expected to positively impact industrialisation, infrastructure, and innovation [SDG 9], economic productivity [SDG 8], housing and transport [SDG 11], energy [SDG 7], and waste management [SDG 6]. However, negative impacts are widespread, afflicting ecosystems [SDGs 14 and 15], climate change [SDG 13] and human health [SDG 3]. We synthesise positive and negative interactions between individual economic activities and SDG targets and discuss implications for: integrated (nexus) governance approaches to the SDGs; the role of the private sector in promoting sustainable development; and for improving statistical classifications to monitor economic activities’ SDG impacts.


title: INTRAREGIONAL PROPAGATION OF COVID-19 CASES IN PARA, BRAZIL. ASSESSMENT OF ISOLATION REGIME TO LOCKDOWN.

text: Due to the high incidence of COVID-19 case numbers internationally, the World Health Organization (WHO) declared a Public Health Emergency of global relevance, advising countries to follow protocols to combat pandemic advance through actions that can reduce spread and consequently avoid a collapse in the local health system. On March 18, 2020, Para notified the first case of COVID-19. After seven weeks, the number of confirmed cases reached 4,756 with 375 deaths. Knowing that infected people may be asymptomatic, the disease symptomatology absence and the population's neglect of isolation influence the spread, and factors such as chronic pneumonia, high age, obesity, chronic kidney diseases and other comorbidities favor the mortality rate. On the other hand, social isolation, quarantine and lockdown seek to contain the intraregional contagion advance. This study analyzes the dynamics of COVID-19 new cases advance among municipalities in the state of Para, Brazil. The results show it took 49 days for 81% of the state's municipalities to register COVID-19 cases. The association between social isolation, quarantine and lockdown as an action to contain the infection was effective in reducing the region's new cases registration of COVID-19 in the short-term.


title: Characterizing COVID-19 case detection utilizing influenza surveillance data in the United States, January-March, 2020

text: COVID-19 reached the US in January, 2020, but state and local case detection efforts varied in timing and scale. We conducted a state-level ecological analysis of COVID-19 epidemiology alongside CDC influenza surveillance data and policy timelines. Our findings show wide variation in COVID-19 case detection and influenza-like-illness activity between states.


title: Now-casting the COVID-19 epidemic: The use case of Japan, March 2020

text: Background Reporting delays in disease surveillance impair the ability to assess the current dynamic of an epidemic. In continuously updated epidemic curves, case numbers for the most recent epidemic week or day usually appear to be lower than the previous, suggesting a decline of the epidemic. In reality, the epidemic curve may still be on the rise, because reporting delay prevents the most recent cases to appear in the case count. In context of the COVID-19 epidemic and for countries planning large international gatherings, such as the Summer Olympic Games in Japan 2020, the ability to assess the actual stage of an epidemic is of outmost importance. Methods We applied now-casting onto COVID-19 data provided by the nCoV-2019 Data Working Group to evaluate the .true count of cases, by taking into account reporting delays occurring between date of symptom onset and date of confirmation. Findings We calculated a decrease of reporting delay, from a median delay of ten days in calendar week four 2020 to six days in calendar week eight, resulting in an overall mean of 4.3 days. The confidence intervals of the now-casting indicated an increase of cases in the last reporting days, while case country in that same time period suggested a decline. Interpretation As a specific use case this tool may be of particular value for the challenging risk assessment and risk communication in the context of the Summer Olympic Games in Japan 2020 and similar situations elsewhere.


title: Philippine Teachers’ Practices to Deal with Anxiety amid COVID-19

text: School closures, home quarantine, and social distancing implemented worldwide can cause a sudden anxiety even among teachers. A designed online survey collected data from Filipino teachers’ practices on how they deal with anxiety due to the COVID-19 outbreak. The practices include information seeking, preventive measures, and other coping mechanisms to deal with anxiety during the quarantine period. Results revealed that teachers practice virtual learning, communicate with the professional community, adhere to quarantine requirements, and find purposeful activities to deal with anxiety due to the suspension of national school-related activities in the country brought by the pandemic.


title: Evaluation the auxiliary diagnosis value of antibodies assays for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19)

text: Background: The spread of an novel coronavirus (SARS-CoV-2, previously named 2019-nCoV) has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks. Elucidating the diagnostic value of different methods, especially the auxiliary diagnosis value of antibodies assays for SARS-CoV-2 infection is helpful for improving the sensitivities of pathogenic-diagnosis, providing timely treatment, and differentiating the infected cases from the healthy, thus preventing further epidemics. Methods: Medical records from 38 patients with confirmed SARS-CoV-2 infection in the Second People's Hospital of Fuyang from January 22, 2020 to February 28, 2020 were collected and retrospectively analyzed. Specimens including throat swabs, sputum and serum were collected during the hospitalization period, viral RNAs and serum IgM-IgG antibodies to SARS-CoV-2 were measured respectively. The detectability of different methods as well as the auxiliary diagnosis value of antibodies test for SARS-CoV-2 infection were analyzed. Results: Among 38 patients, the total seropositive rate for IgM and IgG was 50.0% and 92.1%, respectively. Two patients remained seronegative throughout the course of illness. In the early phase of illness, the RNA test for sputum specimens possessed the highest detectability(92.3%), followed by the the RNA test for throat swabs (69.2%), and the antibodies assays presented lower positive rates(IgM, 23.0%, IgG, 53.8%). While, the sensitivity of antibodies assays overtook that of RNA test since day 8 after onset (IgM, 50.0%; IgG, 87.5%). Of note, the positive rate of throat swabs was only 13.0% for cases in later phase(≥15 d.a.o), and the sensitivities of IgM and IgG rose to 52.2% and 91.3%, respectively. Combined use of antibodies assay and qRT-PCR at the same time was able to improve the sensitivities of pathogenic-diagnosis, especially for the throat swabs group at the later stage of illness. Moreover, most of these cases with undetectable viral RNA in throat swabs specimens at the early stage of illness were able to be IgM/IgG seropositive after 7 days. Conclusions: The antibodies detection against SARS-CoV-2 offers vital clinical information for physicians, and could be used as an effective supplementary indicator for suspected cases of negative viral nucleic acid detection or in conjunction with nucleic acid detection in the diagnosis of suspected cases.


title: Method for Active Pandemic Curve Management (MAPCM)

text: The COVID-19 pandemic of 2020 prompted stringent mitigation measures to "flatten the curve" quickly leading to an asphyxiated US economy as a national side effect. There are severe drawbacks to this strategy. The resulting flattened curve remains exponential and always under utilizes available healthcare capacity with a chance of still overburdening it. Moreover, while a mitigation strategy involving isolation and containment can scale down infections, it not only prolongs the outbreak significantly, but also leaves a susceptible population in its wake that's ripe for a secondary outbreak. Since economic activity is inversely proportional to mitigation, curtailing the outbreak with sustained mitigation can stifle the economy severely with disastrous repercussions. Full mitigation for the duration of an outbreak is therefore unsustainable and, overall, a poor solution with potentially catastrophic consequences that could've been avoided. A new strategy, coined a "Method for Active Pandemic Curve Management", abbreviated MAPCM, presented herein can shape the outbreak curve in a controlled manner for optimal utilization of healthcare resources during the pandemic, while drastically shortening the outbreak duration compared to mitigation by itself without trading off lives. This method allows mitigation measures to be relaxed gradually from day one, which enables economic activity to resume gradually from the onset of a pandemic. Since outbreak curves (such as hospitalizations) can be programmed using this method, they can also be shaped to accommodate changing needs during the outbreak; and to build herd immunity without the damaging side effects. The method can also be used to ease out of containment. MAPCM is a method and not a model. It is compatible with any appropriate outbreak model; and herein it is illustrated in examples using a hybrid logistic model.


title: Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) System for Rapid Viral DNA Sensing

text: A fully Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) system is developed for viral DNA detection. This powerful system is patterned with high-aspect ratio micropillars to enhance reporter probe binding. After surface modification and probe immobilization, CRISPR Cas12a/crRNA complex is injected into the fully enclosed system. With the presence of double-stranded DNA target, the CRISPR enzyme is activated and non-specifically cleaves the ssDNA reporters initially immobilized on the micropillars. This collateral cleavage releases fluorescence dyes into the assay, and the intensity is linearly proportional to the target DNA concentration ranging from 0.1 to 10 nM. Importantly, this system does not rely on traditional dye-quencher labeled probe thus eliminating the fluorescence background presented in the assay. Furthermore, our one-step detection protocol is performed at isothermal conditions (37°C) without using complicated and time-consuming off-chip probe hybridization and denaturation. This miniaturized and fully packed IMPACT chip demonstrates rapid, sensitive, and simple nucleic acid detection and is an ideal candidate for the next generation molecular diagnostic platform for point-of-care (POC) applications, responding to emerging and deadly pathogen outbreaks.


title: Fiscal Responses to COVID‐19: Evidence from Local Governments and Nonprofits

text: The rate of expansion and breadth of COVID‐19 caught the world by surprise. From the perspective of nonprofit and public entities responsible for service provision, this pandemic is also unprecedented. We offer a RISE framework for navigating the fiscal effects of COVID‐19 and rely on recent surveys to assess local governments’ and nonprofit organizations’ response strategies. We find that many nonprofits were hit the fastest and hardest by the pandemic and that local governments are, essentially, trying to figure out their financial condition moving into the next budget cycle.