title: Severe SAR-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting indysregulation of eicosanoid immune mediators

text: The COVID-19 pandemic has affected more than 10 million people worldwide with mortality exceeding half a million patients. Risk factors associated with severe disease and mortality include advanced age,hypertension, diabetes, and obesity. Clear mechanistic understanding of how these comorbidities converge to enable severe infection is lacking. Notably each of these risk factors pathologically disrupts the lipidome and this disruption may be a unifying feature of severe COVID-19. Here we provide the first in depth interrogation of lipidomic changes, including structural-lipids as well as the eicosanoids and docosanoids lipid mediators (LMs), that mark COVID-19 disease severity. Our data reveal that progression from moderate to severe disease is marked by a loss of specific immune regulatory LMs and increased pro-inflammatory species. Given the important immune regulatory role of LMs, these data provide mechanistic insight into the immune balance in COVID-19 and potential targets for therapy with currently approved pharmaceuticals.


title: Peculiarities of Student Distance Learning in Emergency Situation Condition

text: The article outlines the contemporary issues of distance learning and the use of the Internet by students during the outbreak of pandemic The conducted research demonstrates student attitude towards distance learning, its advantages and disadvantages, student perception and acquisition of lecture and seminar material, implementation of online trainings and practical classes The purpose of this article is to investigate student behavioral, cognitive and emotional reactions to forced distance learning conditions The authors assume that students, being members of Generation Z, can easily adapt to the new learning environment, quickly organize the learning process, as well as choose preferable online learning platforms The research proves that 66% of students need from 2 to 4 hours for distance learning;22% spend from 4 to 6 hours studying remotely and only 12% spend less than 2 hours a day studying in a new way One third of students (36%) consider the distance learning system quite comfortable, 8% - very comfortable, while a quarter of the respondents (25%) have neutral attitude towards online learning technologies Students choose the following distance learning platforms the most often: Google Meet (94%) and Moodle (70%) They also use Zoom, Skype, Viber and Telegram in order to keep in touch with teachers and fulfil studying purposes 19% of students regard distance learning as of a high quality, whereas 75% are currently neutral about this way of learning and only 6% of the respondents consider these necessary innovations ineffective


title: Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

text: Background The burden and impact of healthcare-associated COVID-19 infections is unknown. We aimed to examine the utility of rapid sequencing of SARS-CoV-2 combined with detailed epidemiological analysis to investigate healthcare-associated COVID-19 infections and to inform infection control measures. Methods We set up rapid viral sequencing of SARS-CoV-2 from PCR-positive diagnostic samples using nanopore sequencing, enabling sample-to-sequence in less than 24 hours. We established a rapid review and reporting system with integration of genomic and epidemiological data to investigate suspected cases of healthcare-associated COVID-19. Results Between 13 March and 24 April 2020 we collected clinical data and samples from 5191 COVID-19 patients in the East of England. We sequenced 1000 samples, producing 747 complete viral genomes. We conducted combined epidemiological and genomic analysis of 299 patients at our hospital and identified 26 genomic clusters involving 114 patients. 66 cases (57.9%) had a strong epidemiological link and 15 cases (13.2%) had a plausible epidemiological link. These results were fed back clinical, infection control and hospital management teams, resulting in infection control interventions and informing patient safety reporting. Conclusions We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and demonstrated the benefit of combined genomic and epidemiological analysis for the investigation of healthcare-associated COVID-19 infections. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection control interventions to reduce further healthcare-associated infections.


title: Teacher uses quarantine time to max out credits

text: In the wake of the COVID-19 global pandemic changing the face of the world and causing, in the United States, shelter-in-place measures, Tara Lopez Donohoe has decided to put her time in self-isolation to good use: She's going back to (online) campus


title: Variation in False Negative Rate of RT-PCR Based SARS-CoV-2 Tests by Time Since Exposure

text: SARS-CoV-2 RT-PCR based tests are being used to rule out infection among high-risk individuals such as exposed inpatients and healthcare workers. It is critical to understand how the predictive value of the test varies with time from exposure and symptom onset in order to avoid being falsely reassured by negative tests. As such, the goal of our study was to estimate the false negative rate by day since infection. We used previously published data on RT-PCR sensitivity on samples derived from nasal swabs by day since symptom onset (n=633) and fit a cubic polynomial spline to calculate the false negative rate by day since exposure and symptom onset. Over the four days of infection prior to the typical time of symptom onset (day 5) the probability of a false negative test in an infected individual falls from 100% on day one (95% CI 69-100%) to 61% on day four (95% CI 18-98%), though there is considerable uncertainty in these numbers. On the day of symptom onset, the median false negative rate was 39% (95% CI 16-77%). This decreased to 26% (95% CI 18-34%) on day 8 (3 days after symptom onset), then began to rise again, from 27% (95% CI 20-34%) on day 9 to 61% (95% CI 54-67%) on day 21. Care must be taken when interpreting RT-PCR tests for SARS-CoV-2 infection, particularly if performed early in the course of infection, when using these results as a basis for removing precautions intended to prevent onward transmission. If there is high clinical suspicion, patients should not be ruled out on the basis of RT-PCR alone, and the clinical and epidemiologic situation should be carefully considered.


title: Sensitivity and specifity of prediction models based on gustatory disorders in diagnosing COVID-19 patients: a case-control study.

text: Abstract Objective: to quantitatively assess disturbances of sweet, sour and salty and bitter tastes in a group of young, asymptomatic or oligosymptomatic COVID-19 patients; establish a reliable, sensitive and specific test that can diagnose COVID-19 on the basis of taste disorders and publish the results according to STARD 2015 statement (Standards for Reporting Diagnostic Accuracy). Design: case-control study Setting: isolated rooms in the Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw (which had been transformed into an infectious hospital) and a dormitory in one of Warsaw universities. Participants: 52 SARS-CoV-2 positive (51 men, mean age 21.7 years) and 36 negative students (34 men, mean age 20.8 years). Main outcome measures: a gustatory function assessment (sweet, salty, sour and bitter taste), with flavour concentrations established previously in healthy subjects was conducted for all subjects. Each participant received one tasteless reference and nine flavour tablets with sucrose concentrations of 40, 80 and 106.4 mg/ml; NaCl at 13.5, 17 and 27 mg/ml; ascorbic acid at 6.25 and 12.5 mg/ml and grapefruit extract at 40 mg/ml. Results: the only taste that was impaired significantly more frequently in COVID-19 patients was the sweet taste at the lowest flavour concentration (40 mg/ml, p = 0.002). Different screening and diagnostic models were constructed using the examined variables. The highest accuracy screening test consisted of the positive result of a three-question questionnaire (self-reported loss of taste, self-reported loss of smell, or fever within the last month (positive if at least one present) and/or ageusia of sweet taste at a sucrose concentration of 40 mg/ml. The sensitivity of the model was 94% with a specificity of 55%. The highest accuracy diagnostic test consisted of ageusia of sweet taste at a sucrose concentration of 106.4 mg/ml or/and ageusia of salty taste at an NaCl concentration of 13.5 or 17 mg/ml. The specificity of the test was found to be 100%, and the sensitivity was 34%. Conclusion: as the most effective way of controlling the present pandemic involves testing the wider population for symptomatic, oligosymptomatic and asymptomatic carriers of SARS-CoV-2 and isolating or hospitalising infected subjects, in the present study, an inexpensive, simple, fast and sensitive (94%) screening test that can be used for such a purpose is proposed. In addition, a specific (100%) diagnostic test that could be used to refer patients to quarantine in the case of limited availability of genetic or serological tests is proposed.


Sport in the face of the COVID-19 pandemic: towards an agenda for research in the sociology of sport


title: Gender Differences in Patients With COVID-19: Focus on Severity and Mortality

text: Objective: The recent outbreak of Novel Coronavirus Disease (COVID-19) is reminiscent of the SARS outbreak in 2003. We aim to compare the severity and mortality between male and female patients with COVID-19 or SARS. Study Design and Setting: We extracted the data from: (1) a case series of 43 hospitalized patients we treated, (2) a public data set of the first 37 cases of patients who died of COVID-19 and 1,019 patients who survived in China, and (3) data of 524 patients with SARS, including 139 deaths, from Beijing in early 2003. Results: Older age and a high number of comorbidities were associated with higher severity and mortality in patients with both COVID-19 and SARS. Age was comparable between men and women in all data sets. In the case series, however, men's cases tended to be more serious than women's (P = 0.035). In the public data set, the number of men who died from COVID-19 is 2.4 times that of women (70.3 vs. 29.7%, P = 0.016). In SARS patients, the gender role in mortality was also observed. The percentage of males were higher in the deceased group than in the survived group (P = 0.015). Conclusion: While men and women have the same prevalence, men with COVID-19 are more at risk for worse outcomes and death, independent of age.


title: COVID-19 and depressive symptoms in students before and during lockdown

text: The lockdown due to coronavirus pandemic may exacerbate depressive symptoms, experts argue. Here we evidence that students, a high-risk category for mental disorders, report on average worse depressive symptoms than 6 months before isolation. The prospective data reported herein should alert clinician of a possible aggravation as well as new-onsets of depressive symptoms in students.


title: Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.

text: Importance: There are growing concerns that the UK COVID-19 lockdown has reduced opportunities to maintain health through physical activity, placing individuals at higher risk of chronic disease and leaving them more vulnerable to severe sequelae of COVID-19. Objective: To examine whether the UK's lockdown measures have had disproportionate impacts on intensity of physical activity in groups who are, or who perceive themselves to be, at heightened risk from COVID-19. Designs, Setting, Participants: UK-wide survey of adults aged over 20, data collected between 2020-04-06 and 2020-04-22. Exposures: Self-reported doctor-diagnosed obesity, hypertension, type I/II diabetes, lung disease, cancer, stroke, heart disease. Self-reported disabilities and depression. Sex, gender, educational qualifications, household income, caring for school-age children. Narrative data on coping strategies. Main Outcomes and Measures: Change in physical activity intensity after implementation of UK COVID-19 lockdown (self-reported). Results: Most (60%) participants achieved the same level of intensity of physical activity during the lockdown as before the epidemic. Doing less intensive physical activity during the lockdown was associated with obesity (OR 1.21, 95% CI 1.02-1.41), hypertension (OR 1.52, 1.33-1.71), lung disease (OR 1.31,1.13-1.49), depression (OR 2.02, 1.82-2.22) and disability (OR 2.34, 1.99-2.69). Participants who reduced their physical activity intensity also had higher odds of being female, living alone or having no garden, and more commonly expressed sentiments about personal or household risks in narratives on coping. Conclusions and relevance: Groups who reduced physical activity intensity included disproportionate numbers of people with either heightened objective clinical risks or greater tendency to express subjective perceptions of risk. Policy on exercise for health during lockdowns should include strategies to facilitate health promoting levels of physical activity in vulnerable groups, including those with both objective and subjective risks.


title: Modeling risk of infectious diseases: a case of Coronavirus outbreak in four countries

text: Background The novel coronavirus (2019-nCOV) outbreak has been a serious concern around the globe. Since people are in tremor due to the massive spread of Coronavirus in the major parts of the world, it requires to predict the risk of this infectious disease. In this situation, we develop a model to measure the risk of infectious disease and predict the risk of 2019-nCOV transmission by using data of four countries - United States, Australia, Canada and China. Methods The model underlies that higher the population density, higher the risk of transmission of infectious disease from human to human. Besides, population size, case identification rate and travel of infected passengers in different regions are also incorporated in this model. Results According to the calculated risk index, our study identifies New York State in United States (US) to be the most vulnerable area affected by the novel Coronavirus. Besides, other areas (province/state/territory) such as Hubei (China, 2nd), Massachusetts (US, 3rd), District of Columbia (US, 4th), New Jersey (US, 5th), Quebec (Canada, 20th), Australian Capital Territory (Australia, 29th) are also found as the most risky areas in US, China, Australia and Canada. Conclusion The study suggests avoiding any kind of mass gathering, maintaining recommended physical distances and restricting inbound and outbound flights of highly risk prone areas for tackling 2019-nCOV transmission.


title: A simple, safe and sensitive method for SARS-CoV-2 inactivation and RNA extraction for RT-qPCR

text: The SARS-CoV-2 pandemic has created an urgent need for large amounts of diagnostic tests to detect viral RNA, which commercial suppliers are increasingly unable to deliver. In addition to the lack of availability, the current methods do not always fully inactivate the virus. Together, this calls for the development of safer methods for extraction and detection of viral RNA from patient samples that utilise readily available reagents and equipment present in most standard laboratories. We present a rapid and straightforward RNA extraction protocol for inactivating the SARS-CoV-2 virus that uses standard lab reagents. This protocol expands analysis capacity as the inactivated samples can be used in RT-qPCR detection tests at laboratories not otherwise classified for viral work. The method circumvents the need for commercial RNA purification kits, takes about 30 minutes from swab to PCR-ready viral RNA, and enables downstream detection of SARS-CoV-2 by RT-qPCR with very high sensitivity (~4 viral RNA copies per RT-qPCR). In summary, we present a rapid, safe and sensitive method for high-throughput detection of SARS-CoV-2, that can be conducted in any laboratory equipped with a qPCR machine.


title: Reduction and Functional Exhaustion of T Cells in Patients with Coronavirus Disease 2019 (COVID-19)

text: BACKGROUND The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed great threat to human health, which has been declared a public health emergency of international concern (PHEIC) by the WHO. T cells play a critical role in antiviral immunity but their numbers and functional state in COVID-19 patients remain largely unclear. METHODS We retrospectively reviewed the counts of total T cells, CD4+, CD8+ T cell subsets, and serum cytokine concentration from inpatient data of 522 patients with laboratory-confirmed COVID-19, admitted into two hospitals in Wuhan from December 2019 to January 2020, and 40 healthy controls, who came to the hospitals for routine physical examination. In addition, the expression of T cell exhaustion markers PD-1 and Tim-3 were measured by flow cytometry in the peripheral blood of 14 COVID-19 cases. RESULTS The number of total T cells, CD4+ and CD8+ T cells were dramatically reduced in COVID-19 patients, especially among elderly patients (≥60 years of age) and in patients requiring Intensive Care Unit (ICU) care. Counts of total T cells, CD8+T cells or CD4+T cells lower than 800/μL, 300/μL, or 400/μL, respectively, are negatively correlated with patient survival. Statistical analysis demonstrated that T cell numbers are negatively correlated to serum IL-6, IL-10 and TNF-α concentration, with patients in decline period showing reduced IL-6, IL-10 and TNF-α concentrations and restored T cell counts. Finally, T cells from COVID-19 patients have significantly higher levels of the exhausted marker PD-1 as compared to health controls. Moreover, increasing PD-1 and Tim-3 expression on T cells could be seen as patients progressed from prodromal to overtly symptomatic stages, further indicative of T cell exhaustion. CONCLUSIONS T cell counts are reduced significantly in COVID-19 patients, and the surviving T cells appear functionally exhausted. Non-ICU patients, with total T cells, CD8+T cells CD4+T cells counts lower than 800/μL, 300/μL, and 400/μL, respectively, may still require aggressive intervention even in the immediate absence of more severe symptoms due to a high risk for further deterioration in condition.


4S-DT: Self Supervised Super Sample Decomposition for Transfer learning with application to COVID-19 detection


title: ‘It will not be easy.’ As labs begin to reopen, enormous challenges remain

text: Russell Hopcroft spent much of April hunkered down in Fairbanks, Alaska, plotting how he’d return to research once the state ended its lockdown Late last week, he finally got the call—or rather, the Zoom: The National Science Foundation was granting Hopcroft, a biological oceanographer at the University of Alaska, Fairbanks, permission to set sail on his ecological expedition to collect data on critical Gulf of Alaska fishing grounds But there would be some big caveats When the vessel left port yesterday, it held only three researchers, instead of the typical 24 The voyage is limited to 1 week, not two, meaning the scientists will not be able to conduct their usual surveys of birds and marine mammals And everyone on board is wearing face masks and physical distancing, not a simple task for crews accustomed to working hands-on in close quarters


title: Epidemiological investigation of the first 135 COVID-19 cases in Brunei: Implications for surveillance, control, and travel restrictions

text: Background Studies on the early introduction of SARS-CoV-2 in a naive population have important epidemic control implications. We report findings from the epidemiological investigation of the initial 135 COVID-19 cases in Brunei and describe the impact of control measures and travel restrictions. Methods Epidemiological and clinical information were obtained for all confirmed COVID-19 cases in Brunei, whose symptom onset was from March 9 to April 5, 2020 (covering the initial 5 weeks of the epidemic). Transmission-related measures such as reproduction number (R), incubation period, serial interval were estimated. Time-varying R was calculated to assess the effectiveness of control measures. Results A total of 135 cases were detected, of which 53 (39.3%) were imported. The median age was 36 years (range = 0.5 to 72). 41 (30.4%) and 13 (9.6%) were presymptomatic and asymptomatic cases respectively. The median incubation period was 5 days (IQR = 5, range = 1 to 11), and the mean serial interval was 5.39 days (sd = 4.47; 95% CI: 4.25, 6.53). R0 was between 3.88 and 5.96, and the doubling time was 1.3 days. By the 13th day of the epidemic, the Rt was under one (Rt = 0.91; 95% credible interval: 0.62, 1.32 ) and the epidemic was under control. Conclusion Epidemic control was achieved through a combination of public health measures, with emphasis on a test-isolate-trace approach supplemented by travel restrictions and moderate physical distancing measures but no actual lockdown. To maintain suppression, regular and ongoing testing of high-risk groups can supplement the existing surveillance program.


title: Impact of emerging mutations on the dynamic properties the SARS-CoV-2 main protease: an in silico investigation

text: The new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mpro dimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averaged betweenness centrality and geometry calculations. Domains from each Mpro protomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants. A mirrored interprotomer pocket was found to be correlated to the catalytic site using compaction dynamics, and can be a potential allosteric target. The high number of titratable amino acids of Mpro may indicate an important role of pH on enzyme dynamics, as previously reported for SARS-CoV. Independent coarse-grained Monte Carlo simulations suggest a link between rigidity/mutability and enzymatic function.


title: CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

text: The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 24 samples at a time. There is a need for a higher throughput method to reduce cost per genome. Here we present CoronaHiT, a method capable of multiplexing up to 95 small genomes on a single Nanopore flowcell, which uses transposase mediated addition of adapters and PCR based addition of symmetric barcodes. We demonstrate the method using 48 and 94 SARS-CoV-2 genomes per flowcell, amplified using the ARTIC protocol, and compare performance with Illumina and ARTIC ONT sequencing. Results demonstrate that all sequencing methods produce inaccurate genomes when the RNA extract from SARS-CoV-2 positive clinical sample has a cycle threshold (Ct) >= 32. Results from set same set of 23 samples with a broad range of Cts show that the consensus genomes have >90% coverage (GISAID criteria) for 78.2% of samples for CoronaHiT-48, 73.9% for CoronaHiT-94, 78.2% for Illumina and 73.9% for ARTIC ONT, and all have the same clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 94 SARS-CoV-2 genomes per nanopore flowcell without compromising the quality of the resulting genomes while reducing library preparation complexity and significantly reducing cost. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.


title: Determinants of cardiac adverse events of chloroquine and hydroxychloroquine in 20 years of drug safety surveillance reports

text: Chloroquine (CQ) and hydroxychloroquine (HCQ) are on the World Health Organization's List of Essential Medications for treating non-resistant malaria, rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In addition, both drugs are currently used off-label in hospitals worldwide and in numerous clinical trials for the treatment of SARS-CoV-2 infection. However, CQ and HCQ use has been associated with cardiac side effects, which is of concern due to the higher risk of COVID-19 complications in patients with heart related disorders, and increased mortality associated with COVID-19 cardiac complications. In this study we analyzed over thirteen million adverse event reports form the United States Food and Drug Administration Adverse Event Reporting System to confirm and quantify the association of cardiac side effects of CQ and HCQ. Additionally, we identified several confounding factors, including male sex, NSAID coadministration, advanced age, and prior diagnoses contributing to the risk of drug related cardiotoxicity. These findings may help guide therapeutic decision making and ethical trial design for COVID-19 treatment.


title: COVID-19 outbreak: Application of multi-gene genetic programming to country-based prediction models

text: Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a novel coronavirus that has infected more than 2,900,000 individuals worldwide. The widespread of coronavirus 2019 (COVID-19) brings about the need for a prediction model to adopt appropriate evidence-based strategies. In this study, multi-gene genetic programming (MGGP), as one of the artificial intelligence models, has been proposed for the first time for predicting the COVID-19 outbreak. Although this is a challenging task due to significant fluctuations of daily confirmed cases, the results achieved by MGGP are promising. To be more specific, the predicted confirmed cases are acceptably close to the observed values for seven countries considered in this study. Thus, MGGP is suggested for developing estimation models of COVID-19. Furthermore, similarities and differences between the proposed prediction models are presented. Finally, it is discussed why a country-based prediction model is recommended.


title: A data-driven assessment of early travel restrictions related to the spreading of the novel COVID-19 within mainland China

text: Two months after it was firstly reported, the novel coronavirus disease COVID-19 has already spread worldwide. However, the vast majority of reported infections have occurred in China. To assess the effect of early travel restrictions adopted by the health authorities in China, we have implemented an epidemic metapopulation model that is fed with mobility data corresponding to 2019 and 2020. This allows to compare two radically different scenarios, one with no travel restrictions and another in which mobility is reduced by a travel ban. Our findings indicate that i) travel restrictions are an effective measure in the short term, however, ii) they are ineffective when it comes to completely eliminate the disease. The latter is due to the impossibility of removing the risk of seeding the disease to other regions. Our study also highlights the importance of developing more realistic models of behavioral changes when a disease outbreak is unfolding.


title: The Covid-19 Pandemic and the social life of English Premier League Football Fandom in Eldoret, Kenya

text: English Premier League Football Fandom (hereafter referred to EPLFF) has infiltrated the everyday life of the ordinary people in Eldoret, working its way into the communal and commercial aspects of life here. Studies have shown that this trend is popular in many parts of sub-Saharan Africa as well. In this study we argue that this essentially global cultural form has been affected by the Covid-19 Virus Pandemic in ways that resonate with its social function and that this varies from one locality to another. Using data from a long-term ethnographic study of EPLFF and sociological introspection on lived experience here in Eldoret, the authors revisit the normally active sites of EPLFF-dominant social sites to capture and reflect on the social function of this popular cultural practice that is now changed because of the social impact of the Covid-19 Pandemic.


title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning

text: Accurate diagnostic strategies to rapidly identify SARS-CoV-2 positive individuals for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results of this test are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours. Here we present a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,346 SARS-CoV-2 RT-PCR tested patients (1,394 positive and 1,952 negative) evaluated at a large metropolitan hospital. The model achieved an area under the receiver operating characteristic curve (AUC) of 0.853 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within two days. Overall, this model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-COV-2 infected patients before their RT-PCR results are available. This may facilitate patient care and quarantine, indicate who requires retesting, and direct personal protective equipment use while awaiting definitive RT-PCR results.


title: Glycoinformatics approach for identifying target positions to inhibit initial binding of SARS-CoV-2 S1 protein to the host cell

text: COVID-19 outbreak is still threatening the public health. Therefore, in the middle of the pandemic, all kind of knowledge on SARS-CoV-2 may help us to find the solution. Determining the 3D structures of the proteins involved in host-pathogen interactions are of great importance in the fight against infection. Besides, post-translational modifications of the protein on 3D structure should be revealed in order to understand the protein function since these modifications are responsible for the host-pathogen interaction. Based on these, we predicted O-glycosylation and phosphorylation positions using full amino acid sequence of S1 protein. Candidate positions were further analyzed with enzyme binding activity, solvent accessibility, surface area parameters and the positions determined with high accuracy rate were used to design full 3D glycoprotein structure of the S1 protein using carbohydrate force field. In addition, the interaction between the C-type lectin CD209L and α-mannose residues was examined and carbohydrate recognition positions were predicted. We suggest these positions as a potential target for the inhibition of the initial binding of SARS-CoV-2 S1 protein to the host cell.


title: Conjunctival polymerase chain reaction-tests of 2019 novel coronavirus in patients in Shenyang,China

text: Purpose: The 2019 novel coronavirus(COVID-19) mainly transmitted by person-to-person through inhalation of respiratory droplets. We report the laboratory results of conjunctival PCR-tests and some clinical features of these patients in shenyang China. Design: This is a cross-sectional non-randomized study. Subjects: The study include 14 confirmly diagnosed cases, 16 suspected cases and some medical observed patients. Methods: All patients with diagnosed and suspected COVID-19 were admitted to a designated hospital in Shenyang,China. We collected conjunctival samples of these patients to do the laboratory tests by real time RT-PCR.Medical observed patients were enrolled if they had clinical symptoms. Then we analysed the PCR results and clinical data from eletronic medical records in order to find some relationships. Main Outcome Measures: Clinical condition and PCR results of conjunctival swabs compared with other specimens. Results: One of the identified case coverted from suspected case without typical clinical symptoms. Twenty-two medical observed cases were removed because none of them converted to identified cases.One of the suspected converted to identified case recently.The included cases in our study are imported cases with less underlying diseases and the severity of their infection was relatively moderate. All the conjunctival results of PCR-test were negative. Two cases had typical clinical symptoms but were finally confirmed by repeated pharynx swab tests. Conclusion: Conjunctiva may be a transmission way of COVID-19. And ocular conjunctival swabs in combination with PCR test could be a non-invasive,convenient and feasible diagnostic method for identifying the infection of COVID-19. Emphasis on the false-negative results is vital.


title: Protecting our health care workers while protecting our communities during the COVID-19 pandemic: a comparison of approaches and early outcomes in two Italian regions, Italy, 2020

text: Introduction Italy, which has been hard-hit by the COVID-19 pandemic, has an overriding national strategy, but its 21 regions have adapted their response based on the organization of their curative and public health services. In this paper, we compare outcomes for two northern Italian regions which had almost simultaneous initial outbreaks: Lombardy, which had a patient-centered approach that relied on primary care physicians and hospital care, and Veneto, which focused on community-based diagnosis and care. Methods We used numerator and denominator data from public Italian government sources to calculate reported rates of COVID-19 testing/1000, COVID-19 cases/100,000 overall and for health care workers (HCWs) and non-HCWs, deaths per 100,000, and the percent of cases admitted to hospitals and ICUs for February 24-April 1, 2020. Results As of April 1, 2020, Lombardy experienced 44,733 cases and 7,539 deaths; for Veneto, the corresponding values were 9,625 and 499. The cumulative case rate was 445/100,000 for Lombardy and 196/100,000 for Veneto, a 2.3-fold difference. Mortality rates were 7.5 times higher in Lombardy than in Veneto (75/100,000 and 10/100,000, respectively). Cumulative rates of testing were nearly twice as high in Veneto and were 2.7 times higher in the first week of the epidemic. In Lombardy, 51.5% of patients were admitted, including, 5.2% to intensive care units; for Veneto, the corresponding figures were 25.1% and 4.3%, respectively. HCWs account for 14.3% of all cases in Lombardy compared with 4.4% in Veneto. In Lombardy, the rate among HCWs was 19.1 times higher than in the general population (6,924 versus 362 per 100,000), while in Veneto it was 3.9 times higher (676 versus 172/100,000). Discussion The community-based approach in Veneto appears to be associated with substantially reduced rates of cases, hospitalizations, deaths, and infection in HCWs compared with the patient-centered approach in Lombardy. Our findings suggest that the impact of COVID-19 can be reduced through strong and aggressive public health efforts to confirm and isolate cases and contacts in a timely way and to minimize unnecessary contact between HCWs and cases through home-based testing and pro-active home follow-up.


title: The more I fear about COVID-19, the more I wear medical masks: A survey on risk perception and medical masks uses

text: The legal behaviors in using medical masks in public have been finally promulgated by the Vietnamese Government after 47 days since the WHO declared the Public Health Emergency of International Concern (PHEIC) due to the COVID-19 pandemic. From a sample of 345 Vietnamese respondents aged from 15 to 47 years, this brief note found that the risk perception of COVID-19 danger significantly increases the likelihood of wearing the medical masks. In addition, there is a weak evidence about the differences in age under the COVID-19 outbreaks. More noticeably, those who use masks before COVID-19 pandemic tend to maintain their behaviors. Our results offer the insightful into Vietnamese citizens responses in terms of using medical masks; even the uses of this method are still controversial. Our results are robust by performing Exploratory Factor Analysis for five features and further regressions.


title: A special case of COVID-19 with long duration of viral shedding for 49 days

text: Prolonged viral shedding is associated with severe status and poor prognosis of COVID-19 patients. Unexpectedly, here we report a non-severe patient with the longest duration of viral shedding. According to the investigation on the clinical and epidemiological information of this case, we concluded that this type of virus might have a low toxicity and transmissibility, but have a prolonged infective ability and was hardly to be eliminated in the body with regular therapy. However, infusion of plasma from recovered patients showed high efficiency in elimination of this virus. Our findings might shed light on the management of COVID-19.


title: Flattening the curve is not enough, we need to squash it. An explainer using a simple model

text: Background: Around the world there are examples of both very good and effective control (e.g., South Korea, Japan) and slower, less aggressive control (e.g., Italy, Spain, United States) of COVID-19 with dramatic differences in the consequent epidemic curves. Models agree that flattening the curve without controlling the epidemic completely is insufficient and will lead to an overwhelmed health service. A recent model, calibrated for the UK and US, demonstrated this starkly. Methods: We used a simple compartmental deterministic model of COVID-19 transmission in Australia, to illustrate the dynamics resulting from shifting or flattening the curve versus completely squashing it. Results: We find that when the reproduction number is close to one, a small decrease in transmission leads to a large reduction in burden (i.e., cases, deaths and hospitalisations) but achieving this early in the epidemic through social distancing interventions also implies that the community will not reach herd immunity. Conclusions: Australia needs not just to shift and flatten the curve but to squash it by getting the reproduction number below one. This will require Australia to achieve for transmission rates at least two thirds lower than those seen in the most severely affected countries.


title: Using Deep Image Colorization to Predict Microstructure-Dependent Strain Fields

text: Abstract The microstructure of a material governs mechanical properties such as strength and toughness. Various finite element analysis (FEA) software packages are used to perform structural analyses such as predicting the flow of strain or strain fields in a microstructure. Engineers frequently operate these software packages to evaluate mechanical behavior and predict failure. Even though these FEA software packages provide highly accurate analyses, they are computationally intensive, taking a significant amount of time to produce a solution. The time required by the FEA software packages to achieve accurate results largely depends on microstructure details and mesh resolution, thus providing a trade-off between fidelity and computation time. This research proposes the use of Deep Learning algorithms to achieve a significant reduction in the time required to predict high-accuracy strain fields in a two-dimensional microstructure with defects. This work presents a foundation for developing deep neural networks to conduct structural analyses, thus reducing the exclusive use of computationally demanding FEA software and augmenting the analytical capabilities of scientists and engineers.


title: Activation of bone marrow adaptive immunity in type 2 diabetes: rescue by co-stimulation modulator Abatacept

text: Hypothesis Type 2 diabetes (T2D) is characterized by low-grade inflammation. Here, we investigated the state of adaptive immunity in bone marrow (BM) of patients and mice with T2D. We also tested if inhibition T cell co-stimulation by Abatacept could rescue the immune profile of T2D mice. Methods Flow-cytometry and cytokine analyses were performed on BM samples from patients with or without T2D. Moreover, we studied the immune profile of db/db and control wt/db mice. A cohort of db/db mice was randomized to receive Abatacept or vehicle for 4 weeks, with endpoints being immune cell profile and indexes of insulin sensitivity and heart performance. Results T2D patients showed increased frequencies of BM CD4+ (2.8-fold, p=0.001) and CD8+ T cells (1.8-fold, p=0.01), with upregulation of the activation marker CD69 and homing receptor CCR7 in CD4+ (1.64-fold, p=0.003 and 2.27-fold, p=0.01, respectively) and CD8+ fractions (1.79-fold, p=0.05 and 1.69-fold, p=0.02, respectively). CCL19 (CCR7 receptor ligand) and CXCL10/11 (CXCR3 receptor ligands), implicated in T cell migration and activation, were the most differentially modulated chemokines. Studies in mice confirmed the activation of adaptive immunity in T2D. Abatacept reduced the activation of T cells and levels of pro-inflammatory chemokines and cytokines. Additionally, Abatacept improved indexes of cardiac systolic function, but not insulin sensitivity. Conclusions These novel findings support the concept of BM adaptive immune activation in T2D. Modulation of T cell co-stimulation could represent an attractive and immediately available modality to dampen inappropriate activation of adaptive immune response and protect from target organ damage.


A Role for Metal-Based Drugs in Fighting COVID-19 Infection? The Case of Auranofin


title: Risk factors for hospital admission related to COVID-19 in inflammatory rheumatic diseases

text: OBJECTIVES: To describe patients with inflammatory rheumatic diseases (IRD) who had COVID-19; to compare patients who need hospital admission versus those that did not and assess risk factors of hospital admission related to COVID-19. METHODS: We performed a prospective observational study, from 1st March 2020 until the 24th of April. All patients being attended at the rheumatology outpatient clinic of a tertiary hospital of Madrid, with medical diagnosis of inflammatory rheumatic disease, and with symptomatic COVID-19 disease were included. Main variable was the hospital admission related to COVID-19. Covariates: sociodemographic, clinical and treatments. We performed a multivariate logistic regression model to assess risk factors of hospital admission. RESULTS: 123 patients with IRD and COVID-19 disease were identified and included. We found 54 patients that need hospital admission, 59.2% were women, with a mean age at hospital admission of 69.7 (15.7) years, and a median lag time from symptoms onset to hospital admission of 5 (3-10) days. The median length of stay was 9 (6-14) days. A total of 12 patients died (22%) during their hospital admission. Factors independently associated with hospital admission were being older (OR 1.08; p=0.00), and type of diagnosis (OR 3.55; p=0.01), compared to those who were ambulatory. DMARDs dropped from the model. Male sex, associated comorbidities and glucocorticoids use showed a tendency risk (p<0.2) CONCLUSION: Our results suggests that age, comorbidities and having an autoimmune systemic condition increased the risk of hospital admission, whereas disease modifying agents were not associated with hospital admission.


title: Postmastectomy Breast Reconstruction in the Time of the Novel Coronavirus Disease 2019 (COVID-19) Pandemic

text: Background Breast reconstruction has a well-documented positive impact on the psychosocial well-being of women recovering from breast cancer Rates of breast cancer diagnoses are rising, and more women are seeking mastectomy as treatment and as prophylaxis Methods: Postmastectomy breast reconstruction often begins at the time of mastectomy in coordination with the oncologic breast surgeons Immediate breast reconstruction increases complication rate (11% vs 4%) and unplanned reoperation rate (7% vs 4%), requiring more personnel and resources used during the preoperative, intraoperative, and postoperative phases of patient care Discussion: In the setting of global pandemics such as coronavirus disease 2019 (COVID-19), breast reconstruction demands a unique and nuanced approach, as most forms of breast reconstruction can occur successfully in a delayed fashion While this may prolong the overall time until completion of reconstruction, other factors come into play in the setting of a communicable (potentially deadly) illness Factors that must be considered include allocation of essential resources and protection of patients and families from disease transmission Conclusions: Plastic surgeons performing breast reconstruction must take these factors into account when counseling their patients, colleagues, and institutions and be proactive in determining which procedures are time-critical and which should be postponed until the disaster situation has relieved Published online 9 June 2020 Received for publication May 15, 2020;accepted May 19, 2020 Disclosure: The authors have no financial interest to declare in relation to the content of this article Clara Lee is supported by a grant from the Agency for Healthcare Research and Quality, R18 HS026699-01A1 Matthew D Chetta, MD, FACS Department of Plastic and Reconstructive Surgery The Ohio State University 915 Olentangy River Rd, Ste 2100 Columbus, OH 43212 E-mail: matthew chetta@osumc edu This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4 0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited The work cannot be changed in any way or used commercially without permission from the journal Copyright © 2020 The Authors Published by Wolters Kluwer Health, Inc on behalf of the American Society of Plastic Surgeons All rights reserved


title: 3 Developmental and Inherited Liver Disease

text: Abstract A new section on the approach to diagnostic histological interpretation, is the overture to this chapter on inherited and developmental disorders. This initial section is split chronologically into the early neonatal and infantile period and later childhood and adulthood; with the intention of reflecting clinical practice as closely and succinctly as possible. Disorders of the biliary tree, bile formation and secretion, and hepatocyte metabolism are the core of this chapter, a merger of chapters 3 and 4 of the previous edition. Considerations on the pathogenetic and/or clinical overlap between developmental, genetic and metabolic disorders were the rationale behind this change. The complexity of hepatocyte metabolism is reflected into the miriad of related pathological conditions. Recent technological advances, particularly in genomics in the last five years, have resulted in a plethora of new entities and changes in terminology, challenging the authors to balance detail and application to clinical practice. Tables and figures from previous editions have been largely kept due to their quality and contemporary relevance, whilst new ones have been added to accommodate new advances (e.g. classification of mitochondrial disorders), a compromise to bridge between the two editions for the accustomed reader. Liver involvement in immunodeficiency and miscellaneous disorders precede the final section on anatomical anomalies. Vascular anomalies are now included in the chapters on vascular disorders.


title: Did pangolins help spread SARS-CoV-2?

text: Since the novel coronavirus, SARS-CoV-2, was first detected late last year, researchers have been trying to understand how the virus passed to humans in the first place Although bats are thought to be the origin of the virus, bat coronaviruses differ from SARS-CoV-2 in some key ways In particular, the spike proteins, which bind to receptors on the surface of cells to gain access, are different in the two viruses Authorities in China quickly shut down a market linked to the outbreak Closing the market prevented researchers from examining the animals sold there for coronaviruses So a team led by Yan-Ling Hu of Guangxi Medical University and Yi Guan of the University of Hong Kong turned to a small number of pangolins—also called scaly anteaters—seized in antismuggling raids in 2017 and 2018 The team found that coronavirus RNA isolated from those pangolins encodes spike proteins that are closely related to [truncated ]


title: High Filtration Efficiency Face Masks made from Sterilization Wraps

text: COVID-19 pandemic has spawned the need for mass production of N-95 respirators. We used Sterilization Wraps to produce face masks which maintained 93% particle capture efficacy post sterilization. This ubiquitously available material could be explored for production of high quality face masks at a cost less than 30 US cents.


title: On the digital frontier: Stakeholders in rural areas take on educational technology and schooling

text: Even in the most remote U.S. rural contexts today technology is a part of schooling. This article explores stakeholders’ perceptions of educational technology as it relates to schooling in six rural districts in the state of Idaho. Stakeholder descriptions were collected using sondeo style focus groups with seven specific groups (students, parents, teachers, support staff, community members, principals, boards, and superintendents) in each district (n = 42). Stakeholders believe the educational technology in their schooling environments is both necessary and welcome in their districts; however, their assessments indicated that despite a decades-long policy push aimed at increasing educational equity, augmenting schooling facilities with technology presents complex resourcing challenges. The conclusion explores how different experiences and conceptualizations of context shape individuals’ understanding and implementation of educational technology. We argue that a more contextualized view of technology-oriented change is needed. One that better positions rural place as something to be protected (as opposed to overcome) in order to leverage the best of both what technology and place have to offer in changing rural communities.


title: Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing

text: COVID-19 caused by SARS-CoV-2 has recently affected over 200,000 people and killed more than 8000. Immune system dysregulation such as lymphopenia and inflammatory cytokine storm has been observed in COVID-19 patients, but it remains unclear for the change of key immune cell subsets and their states during COVID-19. Here, we applied single-cell technology to comprehensively characterize transcriptional changes of peripheral blood mononuclear cells in ten patients recovered from COVID-19. Compared with healthy control, COVID-19 induced a unique signature of immune cells in humans, especially in the early recovery stage (ERS). In ERS patients, T cells were decreased remarkably, while monocytes were increased. A detailed analysis of monocytes showed that there was an increased ratio of classical CD14++ monocytes with highly inflammatory genes expression, as well as a greater abundance of CD14++IL1B+ monocytes. For nature killer (NK) cells and T cells, CD4+ T cells were significantly decreased and expressed high level of inflammatory markers, while NK cells were increased. In addition, T cells were highly expanded clone, especially in CD4+ T memory cells and CD8+ T cells. Among B cells, plasma cells were increased remarkably, and naïve B cells were reduced. Our study also identified several novel B cell receptor (BCR) changes (such as IGHV1-8 and IGHV3-7), and confirmed isotypes (IGKV3-11 and IGHV3-21) previously used for virus vaccine development. The strongest pairing frequencies, IGHV3-23+IGHJ4, indicated a monoclonal state associated with SARS-CoV-2 specificity. Furthermore, integrated analysis predicated that IL-1B and M-CSF may be novel candidate target gene for inflammatory storm, and TNFSF13, IL-18 and IL-4 may be benefit for the recovery of COVID-19 patients. Our study provides the first evidence of inflammatory immune signature in early recovery stage, suggesting that the COVID-19 patients are still vulnerable after hospital discharge. Our identification of novel BCR signaling may lead to the development of vaccine and antibodies for the treatment of COVID-19.


title: The natural history of symptomatic COVID-19 in Catalonia, Spain: a multi-state model including 109,367 outpatient diagnoses, 18,019 hospitalisations, and 5,585 COVID-19 deaths among 5,627,520 people

text: Background The natural history of Coronavirus Disease 2019 (COVID-19) has yet to be fully described, with most previous reports focusing on hospitalised patients. Using linked patient-level data, we set out to describe the associations between age, gender, and comorbidities and the risk of outpatient COVID-19 diagnosis, hospitalisation, and/or related mortality. Methods A population-based cohort study including all individuals registered in Information System for Research in Primary Care (SIDIAP). SIDIAP includes primary care records covering > 80% of the population of Catalonia, Spain, and was linked to region-wide testing, hospital and mortality records. Outpatient diagnoses of COVID-19, hospitalisations with COVID-19, and deaths with COVID-19 were identified between 1st March and 6th May 2020. A multi-state model was used, with cause-specific Cox survival models estimated for each transition. Findings A total of 5,664,652 individuals were included. Of these, 109,367 had an outpatient diagnosis of COVID-19, 18,019 were hospitalised with COVID-19, and 5,585 died after either being diagnosed or hospitalised with COVID-19. Half of those who died were not admitted to hospital prior to their death. Risk of a diagnosis with COVID-19 peaked first in middle-age and then again for oldest ages, risk for hospitalisation after diagnosis peaked around 70 years old, with all other risks highest at oldest ages. Male gender was associated with an increased risk for all outcomes other than outpatient diagnosis. The comorbidities studied (autoimmune condition, chronic kidney disease, chronic obstructive pulmonary disease, dementia, heart disease, hyperlipidemia, hypertension, malignant neoplasm, obesity, and type 2 diabetes) were all associated with worse outcomes. Interpretation There is a continued need to protect those at high risk of poor outcomes, particularly the elderly, from COVID-19 and provide appropriate care for those who develop symptomatic disease. While risks of hospitalisation and death are lower for younger populations, there is a need to limit their role in community transmission. These findings should inform public health strategies, including future vaccination campaigns.


title: Identifying SARS-CoV-2 entry inhibitors through drug repurposing screens of SARS- S and MERS-S pseudotyped particles

text: While vaccine development will hopefully quell the global pandemic of COVID-19 caused by SARS-CoV-2, small molecule drugs that can effectively control SARS-CoV-2 infection are urgently needed. Here inhibitors of two coronavirus spike proteins (S) were identified by screening a library of approved drugs with SARS-S and MERS-S pseudotyped particle entry assays. Using high-throughput screening technology, we discovered three compounds (cepharanthine, abemaciclib and trimipramine) to be broad spectrum inhibitors for spike-mediated entry. This work should contribute to the development of effective treatments against the initial stage of viral infection, thus reducing viral burden in COVID-19 patients.


title: Controversial issues in obstetric management of women with novel coronavirus disease covid-19 during pregnancy and childbirth

text: The new coronavirus infection, which was identified in Wuhan (Hubei province, China) in late 2019, caused an outbreak of severe pneumonia. The disease quickly spread throughout China and was followed by a dramatic increase in number of new cases in other countries of the world. Certain population groups that require particular attention include pregnant women due to the fact that pneumonia is the third-leading indirect cause of maternal mortality. Among the controversial issues in the management of pregnant women with COVID-19, special attention should be paid to the tactics of prolonging pregnancy and approaches to childbirth. The available scientific and clinical data are currently insufficient to perform a complete assessment of perinatal outcomes in pregnant women with COVID-19. Researchers and practical healthcare specialists have more questions than answers due to the limited time and number of studies, lack of evidence of vertically transmitted infection from mother to fetus, absence of clear understanding of viral pathogenesis during pregnancy, as well as the level and degree of initiation of SARS-CoV-2 pathological processes in the mother and fetus that can have a negative influence on the perinatal This review is devoted to the analysis of pregnancy and childbirth outcomes, presentation of current approaches to the management of women with novel coronavirus infection COVID-19 during pregnancy and childbirth on the basis of the available literature data in the domestic and foreign clinical guidelines.


The utility of high-flow nasal cannula oxygen therapy in the management of respiratory failure secondary to COVID-19 pneumonia


title: Triphosphates of the Two Components in DESCOVY and TRUVADA are Inhibitors of the SARS-CoV-2 Polymerase

text: SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 pandemic. We previously demonstrated that four nucleotide analogues (specifically, the active triphosphate forms of Sofosbuvir, Alovudine, AZT and Tenofovir alafenamide) inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Tenofovir and emtricitabine are the two components in DESCOVY and TRUVADA, the two FDA-approved medications for use as pre-exposure prophylaxis (PrEP) to prevent HIV infection. This is a preventative method in which individuals who are HIV negative (but at high-risk of contracting the virus) take the combination drug daily to reduce the chance of becoming infected with HIV. PrEP can stop HIV from replicating and spreading throughout the body. We report here that the triphosphates of tenofovir and emtricitabine, the two components in DESCOVY and TRUVADA, act as terminators for the SARS-CoV-2 RdRp catalyzed reaction. These results provide a molecular basis to evaluate the potential of DESCOVY and TRUVADA as PrEP for COVID-19.


title: Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system

text: The causative agent of the current pandemic and coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1. Understanding how SARS-CoV-2 enters and spreads within human organs is crucial for developing strategies to prevent viral dissemination. For many viruses, tissue tropism is determined by the availability of virus receptors on the surface of host cells2. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as a host receptor, yet, their tropisms differ3-5. Here, we found that the cellular receptor neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, which was inhibited by a monoclonal blocking antibody against the extracellular b1b2 domain of NRP1. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial cells and in the epithelial cells facing the nasal cavity. Neuropathological analysis of human COVID-19 autopsies revealed SARS-CoV-2 infected NRP1-positive cells in the olfactory epithelium and bulb. In the olfactory bulb infection was detected particularly within NRP1-positive endothelial cells of small capillaries and medium-sized vessels. Studies in mice demonstrated, after intranasal application, NRP1-mediated transport of virus-sized particles into the central nervous system. Thus, NRP1 could explain the enhanced tropism and spreading of SARS-CoV-2.


title: COVID-19 and olfactory dysfunction - an ENT perspective to the current COVID-19 pandemic

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title: Tracking the Effect of the COVID-19 Pandemic on American Households

text: Since March 10, 2020, we have been tracking effects of the COVID-19 pandemic on respondents to the nationally representative Understanding America Study (UAS). After an initial survey that covered March 10–31, 2020, we launched tracking surveys every two weeks. Every day, about 500 respondents are invited to take the survey for a total of about 7,000 respondents over a two-week period. Results are shared in a variety of ways. About 3,000 graphs are updated every night, with the corresponding tab-delimited text files available for download. The underlying micro-data are available for registered researchers after the end of each four-week field period. The paper describes the set-up of the tracking survey, lists the main topics covered and highlights a number or early results. Our ambition is to keep tracking the experiences of U.S. households for as along as the pandemic lasts.


title: Act early, save lives: managing COVID-19 in Greece

text: Abstract Objectives: To assess the impact of the implemented social distancing interventions (SD) in Greece. Study Design: A dynamic, discrete time, stochastic individual-based model was developed to simulate COVID-19 transmission. Methods: We fit the transmission model to the observed trends in deaths and ICU beds use. Results: If Greece had not implemented the SD measures, the healthcare system would have been overwhelmed between 30 March and 4 of April. Additionally, the SD interventions averted 4360 deaths and prevent the healthcare system from overwhelmed. Conclusions: The fast reflexes of the Greek government limit the burden of the Covid-19 outbreak.


title: Tocilizumab is associated with reduction of the risk of ICU admission and mortality in patients with SARS-CoV-2 infection

text: Background In some patients the immune response triggered by SARS-CoV-2 is unbalanced, presenting an acute respiratory distress syndrome which in many cases requires intensive care unit (ICU) admission. The limitation of ICU beds has been one of the major burdens in the management around the world, therefore, clinical strategies to avoid ICU admission are needed. Objective We aimed to describe the influence of tocilizumab on the need of transfer to ICU or death in non-critically ill patients. Methods A retrospective study of 171 patients with SARS-CoV-2 infection that did not qualify as requiring transfer to ICU during the first 24h after admission to a conventional ward, were included. The criteria to receive tocilizumab was radiological impairment, oxygen demand or an increasing of inflammatory parameters, however, the ultimate decision was left to the attending physician judgement. The primary outcome was the need of ICU admission or death whichever came first. Results 77 patients received tocilizumab and 94 did not. The tocilizumab group had less ICU admissions (10.3% vs. 27.6%, P= 0.005) and need of invasive ventilation (0 vs 13.8%, P=0.001). In the multivariable analysis, tocilizumab remained as a protective variable (OR: 0.03, CI 95%: 0.007-0*1, P=0.0001) of ICU admission or death. Conclusions Tocilizumab in the early stages of the inflammatory flare, could avoid an important number of ICU admissions and mechanical ventilation use. The mortality rate of 10.3% among patients receiving tocilizumab appears to be lower than other reports.


title: Diagnostic accuracy of Faecal Immunochemical Testing for patients with symptoms of colorectal cancer: a retrospective cohort study of 14,487 consecutive test requests from English primary care.

text: Objective: To ascertain the diagnostic performance of faecal immunochemical test (FIT) in symptomatic primary care patients, to provide objective data on which to base referral guidelines. Design: Stool samples from routine primary care practice in Oxfordshire, UK were analysed using the HM-JACKarc FIT method between March 2017 to March 2020. Clinical details described on the test request were recorded. Patients were followed up for up-to 36 months in linked hospital records for evidence of benign and serious (colorectal cancer, high-risk adenomas and bowel inflammation) colorectal disease. The diagnostic accuracy of FIT is reported by gender, age, and FIT threshold. Results: In 9,896 adult patients with at least 6 months of follow-up, a FIT result [≥]10 ug/g had an overall sensitivity for colorectal cancer of 90.5% (95% CI 84.9%-96.1%), women 90.0 (80.7-99.3), men 90.8 (83.7-97.8); overall specificity 91.3 (90.8-91.9), women 92.4 (91.8-93.1), men 89.8 (88.8-90.7); overall Positive Predictive Value (PPV) 10.1 (8.15-12.0), women 7.64 (5.24-10.0), men 12.5 (9.52-15.5)); and an overall Negative Predictive Value (NPV) 99.9 (99.8-100.0), women 99.8 (99.7-100.), men 99.9 (99.9-100.0). The PPV and specificity of FIT were higher for serious colorectal disease combined and the sensitivity and NPV were lower than for colorectal cancer alone. The Area Under the Curve (AUC) for all patients did not change substantially by increasing the minimum age of testing. In this population, 10% would be further investigated to detect 91% of the cancers at 10ug/g and 3% further investigated to detect 54% of the cancers at 150ug/g. The number needed to scope to detect one cancer at was ten using FIT at 10ug/g. Conclusion: A FIT threshold of 10ug/g is appropriate to triage adult patients presenting to primary care with symptoms of serious colorectal disease. FIT may provide an appropriate approach to reprioritising patients colorectal cancer symptoms whose tests have been delayed by the COVID-19 pandemic.


title: Outbreak of COVID-19 and Interventions in One of the Largest Jails in the United States: Cook County, IL, 2020

text: Background: Correctional and detention facilities are disproportionately affected by COVID-19 due to shared space, contact between staff and detained persons, and movement within facilities of detained persons, many with pre-existing medical conditions. On March 18, 2020, Cook County Jail, one of the United States' largest, identified its first suspected case of COVID-19 in a detained person. Methods: This analysis includes SARS-CoV-2 cases confirmed by molecular detection among detained persons and Cook County Sheriff's Office staff. We examined occurrence of symptomatic cases in each building and proportions of asymptomatic detained persons testing positive. We describe timing of interventions including social distancing, mask use, and expanded testing and show outbreak trajectory in the jail versus contemporaneous case counts in Chicago. Results: During March 1-April 30, 907 symptomatic and asymptomatic cases of SARS-CoV-2 infection were detected among detained persons (n = 628) and staff (n = 279), with nine deaths. Symptomatic cases occurred in all housing divisions; in 9/13 buildings, staff cases occurred first. Among asymptomatic detained persons in quarantine, 23.6% tested positive. Programmatic activity and visitation stopped March 9, cells were converted into single occupancy beginning March 26, and universal masking was implemented for staff (April 2) and detained persons (April 13). Cases at the jail declined while cases in Chicago increased. Conclusion: Aggressive intervention strategies coupled with widespread diagnostic testing of detained and staff populations can limit introduction and mitigate transmission of SARS-CoV-2 infection in correctional and detention facilities.


title: Is the Current N95 Respirator Filtration Efficiency Test Sufficient for Evaluating Protection Against Submicrometer Particles Containing SARS-CoV-2?

text: Previous researchers measured the Overall Filtration Efficiency using sodium chloride testing aerosol with aerosol photometer to analyze the reuse of respirators after sterilization. However, this study showed that the Overall Filtration Efficiency would significantly overestimate the respirators' ability to protect against submicrometer particles containing SARS-CoV-2. For example, after three cycle H2O2 vaporous sterilizations, the most penetrating particle size for the N95 level respirators was from 250 nm to 500 nm, which carried the peak concentration of the SARS-CoV-2 in hospitals. The Size Specific Filtration Efficiency (250 nm to 500 nm) dropped to 56%{+/-}4%, however, the Overall Filtration Efficiency was still 86%{+/-}5%. In order to protect health care personnel adequately, we recommend measuring the Size Specific Filtration Efficiency to evaluate the reuse of respirators.


title: An integrated planning framework for sustainable water and energy supply

text: This study aims to reveal the economic, technical, and environmental impacts of different system configurations (centralized or decentralized, components, and technologies) on transition plans to achieve a higher share of renewable energy and desalination supplies for regions facing water scarcity. The main contribution of this research is the comparative evaluation of on-grid decentralized or distributed renewable-powered desalination systems for sustainable water and energy supply planning. Applying a novel nexus approach, an interactive multi-period planning model is developed to highlight synergies and to identify conflicts of planning both energy and water sectors at the same time as endogenous subsystems of one overall system. For studying these synergies in this study, the pace of technology deployment and the path of decline in overall costs are assumed to be a function of experience and knowledge as two-factor learning curves. Using data from 81 projects, the levelized cost and capacity factor of utility-scale photovoltaic and wind supplies in the Middle East were calculated. The results indicate that a scenario with a decentralized water sector and renewable-powered multiple-effect distillation technology has the best overall performance among the proposed scenarios.


title: Silk fabric as a protective barrier for personal protective equipment and as a functional material for face coverings during the COVID-19 pandemic

text: Background The worldwide shortage of single-use N95 respirators and surgical masks due to the COVID-19 pandemic has forced many health care personnel to prolong the use of their existing equipment as much as possible. In many cases, workers cover respirators with available masks in an attempt to extend their effectiveness against the virus. Due to low mask supplies, many people instead are using face coverings improvised from common fabrics. Our goal was to determine what fabrics would be most effective in both practices. Methods and findings We examined the hydrophobicity of fabrics (silk, cotton, polyester), as measured by their resistance to the penetration of small and aerosolized water droplets, an important transmission avenue for the virus causing COVID-19. We also examined the breathability of these fabrics and their ability to maintain hydrophobicity despite undergoing repeated cleaning. Tests were done when fabrics were fashioned as an overlaying barrier and also when constructed as do-it-yourself face coverings. As a protective barrier and face covering, silk is more effective at impeding the penetration and absorption of droplets due to its greater hydrophobicity relative to other tested fabrics. Silk face coverings repelled droplets as well as masks, but unlike masks they are hydrophobic and can be readily sterilized for immediate reuse. Conclusions Silk is an effective hydrophobic barrier to droplets, more breathable than other fabrics that trap humidity, and are readily re-useable via cleaning. Therefore, silk can serve as an effective material for protecting respirators under clinical conditions and as a material for face coverings.


title: A Multicentre Study of 2019 Novel Coronavirus Disease Outcomes of Cancer Patients in Wuhan, China

text: Background: At present, there is a global pandemic of coronavirus disease 2019 (COVID-19) pneumonia. Two previous case series from China have suggested that cancer patients are at a higher risk of COVID-19 pneumonia, but the reports were limited by small numbers and few clinical information. Objective: To study clinical characteristics and outcomes of cancer patients infected with COVID-19. Design: Retrospective study. Setting: Four designated COVID-16 hospitals in Wuhan, Hubei province, China. Participants: Medical records of 67 cancer patients admitted to hospitals between Jan 5, 2020 to Feb 18, 2020 were included. Measurements: Demographic, clinical, laboratory, radiological and treatment data were collected. Survival data of the cohort was cut-off on Mar 10, 2020. Results: Of the 67 patients (median age: 66 years), the median age of patients who had severe illness was older than that of patients who had mild symptoms (P<0.001). Forty-three (64.2%) patients had other concurrent chronic diseases, and the proportion of severe patients had co-morbidities was higher than patients with mild disease (P=0.004). Twenty-three (34.3%) patients were still at the anticancer treatment phase, but no tumour progression and recurrence was observed for all the patients during the treatment of COVID-19 pneumonia. About 70% of these patients had fever (n=53, 79.1%) and/or cough (n=50, 74.6%). Lymphocytopenia was the main laboratory finding accompanying increased C-reactive protein and procalcitonin in cancer patients, especially in severe cases. By Mar 10, 2020, 18 (26.9%) patients died from COVID-19, and 39 (58.2%) patients have been discharged. The median age of survivors was younger than that of deaths (P=0.014). Lung cancer (n=15, 22.4%) with COVID-19 was the most common cancer type and accounted for the highest proportion COVID-19 resulted deaths (33.3%, 5/15). We observed a tendency that patients at the follow-up phase had a better prognosis than that at anticancer treatment phase (P=0.095). Limitation: This is a retrospective study with only 67 cases from four hospitals. And some specific clinical information was insufficient. Conclusion: This study showed COVID-19 patients with cancer seem to have a higher proportion of severe cases and poorer prognosis. The tendency of poor prognosis was more obvious in patients at anticancer treatment phase. We should pay more intensive attentions to cancer patients infected with COVID-19.


title: Exponential damping: The key to successful containment of COVID-19

text: Due to its excessively high capacity for human-to-human transmission, the 2019 novel coronavirus disease (COVID-19), first reported in Wuhan in China, spread rapidly to the entire nation and beyond, and has now been declared a global public health emergency. Understanding the transmission pattern of the virus and the efficacy of transmission control measures is crucial to ensuring regional and global disease control. Here we propose a simple model based on exponential infectious growth, but with a time-varying, largely damping, transmission rate. This model provides an excellent fit to the existing data from the 102 countries and regions which have reported cases for more than 6 days, and, we think, has largely captured the transmission patterns of the COVID-19 outbreak under a variety of intervention and control measures. We found that the damping rate, defined as the rate of the exponential decline in transmission rate, ranged from -0.125 to 0.513 d-1 globally (a negative damping rate represents acceleration in spread). The estimated peak time (when the fastest spread occurs) and the final number of infections were found to be greatly affected by the damping rate. Successful control measures, such as those implemented in China and South Korea, have resulted in a clear pattern of exponential damping in the viral spread (also shown during the 2003 outbreak of Severe Acute Respiratory Syndrome, SARS). The damping rate, therefore, could be used as an indicator for the efficacy of implemented control measures. Our model suggests that the COVID-19 outbreak is currently accelerating worldwide, especially rapidly in certain countries (e.g. USA and Australia) where exponential damping is yet to emerge. Consistent with the message from the World Health Organisation (WHO), we thus strongly suggest all countries to take active measures to contain this global pandemic. Slight increments in the damping rate from additional control efforts, especially in countries showing weak or no exponential damping in COVID-19 transmission, could lead to a radically more positive outcome in the fight to contain the pandemic.


title: Effects of city-size heterogeneity on epidemic spreading in a metapopulation: A reaction-diffusion approach

text: We review and introduce a generalized reaction-diffusion approach to epidemic spreading in a metapopulation modeled as a complex network. The metapopulation consists of susceptible and infected individuals that are grouped in subpopulations symbolising cities and villages that are coupled by human travel in a transportation network. By analytic methods and numerical simulations we calculate the fraction of infected people in the metaopoluation in the long time limit, as well as the relevant parameters characterising the epidemic threshold that separates an epidemic from a non-epidemic phase. Within this model, we investigate the effect of a heterogeneous network topology and a heterogeneous subpopulation size distribution. Such a system is suited for epidemic modeling where small villages and big cities exist simultaneously in the metapopulation. We find that the heterogeneous conditions cause the epidemic threshold to be a non-trivial function of the reaction rates (local parameters), the network's topology (global parameters) and the cross-over population size that separates"village dynamics"from"city dynamics".


title: SARS-CoV-2 Detection in Istanbul Wastewater Treatment Plant Sludges

text: Following the announcement of SARS-CoV-2 worldwide pandemic spread by WHO on March 11, 2020, wastewater based epidemiology received great attention in several countries: The Netherlands [Medama et al., 2020; K-Lodder et al., 2020], USA [Wu et al., 2020; Memudryi et al., 2020], Australia [Ahmed et al., 2020], France [Wurtzer et al., 2020], China [Wang et al., 2020], Spain [Randazzo et al., 2020; Walter et al., 2020], Italy (La Rosa et al., 2020; Rimoldi et al., 2020) and Israel [Or et al., 2020], performed analysis in wastewaters by using different virus concentration techniques. Turkey took its place among these countries on 7th of May, 2020 by reporting SARS-CoV-2 RT-qPCR levels at the inlet of seven (7) major municipal wastewater treatment plants (WWTPs) of Istanbul [Alpaslan Kocamemi et al., 2020], which is a metropole with 15.5 million inhabitants and a very high population density (2987 persons/km2) and having about 65 % of Covid-19 cases in Turkey. Sludges that are produced in WWTPs should be expected to contain SARS-CoV-2 virus as well. There has not yet been any study for the fate of SAR-CoV-2 in sludges generated from WWTPs. Knowledge about the existing of SARS-CoV-2 in sludge may be useful for handling the sludge during its dewatering, stabilizing and disposal processes. This information will also be valuable in case of sludges that are used as soil conditioners in agriculture or sent to landfill disposal. In wastewater treatment plants, generally two different types of sludges are generated; primary sludge (PS) and waste activated sludge (WAS). PS forms during the settling of wastewater by gravity in the primary settling tanks. Little decomposition occurs during primary sludge formation. Since most of the inorganic part of the wastewater is removed in the earlier grit removal process, the PS consists of mainly organic material that settles. The PS is about 1-2 % solids by weight. In the biological treatment part of the WWTPs, the biomass that forms in the anaerobic, anoxic and oxic zones of the process is settled in final clarifiers by gravity and returned to the beginning of the biological process so that it is not washed off. The waste activated sludge (WAS) is the excess part of the biomass that grows in this secondary treatment process. It has to be removed from the process not to increase the mixed liquor suspended solids concentration (bacteria concentration) in the secondary process more than a fixed value. The WAS is about 0.6 - 0.9 % solids by weight. This work aims to find whether SARS-CoV-19 is present in the PS and WAS before it is dewatered and sent to anaerobic or aerobic digester processes or to thermal drying operations. For this purpose, on the 7th of May 2020, two (2) PS samples were collected from Ambarl and Tuzla WWTPs, seven (7) WAS samples were collected from Terkos, Ambarl, Atakoy I & II, Pasakoy II, Buyukcekmece and Tuzla I WWTPs. Polyethylene glycol 8000 (PEG 8000) adsorption [Wu et al., 2020] SARS-Cov-2 concentration method was used for SARS-CoV-2 concentration after optimization. [Alpaslan Kocamemi et al., 2020]. Real time RT-PCR diagnostic panel validated by US was used to quantify SARS-CoV-2 RNA in primary and waste activated sludge samples taken from WWTPs in Istanbul. All samples were tested positive. Titers of SARS-CoV-2 have been detected ranging copies between 1.17E4 to 4.02x104 per liter.


title: Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection

text: Background: Currently, there is a pandemic caused by the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes Covid-19. We wanted to compare specimen types and collection methods to explore if a simpler to collect specimen type could expand access to testing. Methods: We recruited individuals recently tested for SARS-CoV-2 infection through a testing program (drive-through). In homes of participants, we assessed the performance of self-collected oral fluid swab specimens with and without clinician supervision, clinician-supervised self-collected mid-turbinate (nasal) swab specimens, and clinician-collected nasopharyngeal swab specimens. We tested specimens with a validated reverse transcription-quantitative polymerase chain reaction assay for the detection of SARS-CoV-2 and measured cycle threshold values. Symptom status and date of onset of symptoms was also recorded for each participant. Results: We recruited 45 participants. The median age of study participant was 42 years old (Interquartile range, 31 to 52 years). Of the participants, 29 had at least one specimen test positive for SARS-CoV-2. Of those, 21 (73%) of 29 reported active symptoms. By specimen type and home-based collection method, clinician-supervised self-collected oral fluid swab specimens detected 26 (90%) of 29 infected individuals, clinician-supervised self-collected nasal swab specimens detected 23 (85%) of 27, clinician-collected posterior nasopharyngeal swab specimens detected 23 (79%) of 29, and unmonitored self-collected oral fluid swab specimens detected 19 (66%) of 29. Despite nasopharyngeal swabs being considered the gold standard, 4 participants tested negative by clinician-collected nasopharyngeal swab and positive by the 3 other specimen types. Additionally, false negative results by each sample type were seen to generally not overlap. Conclusions: Supervised self-collected oral fluid and nasal swab specimens performed similarly to, if not better than clinician-collected nasopharyngeal swab specimens for the detection of SARS-CoV-2 infection. No sample type captured all SARS-CoV-2 infections, suggesting potential heterogeneity in the distribution of viral load in different parts of the respiratory tract between individuals. Supervised self-collection performed comparably to clinician collection and would allow for rapid expansion of testing capacity in the United States by reducing the need for trained healthcare workers, reducing exposure of healthcare workers, and reducing the amount of PPE (personal protective equipment) being used for testing during a critical shortage.


title: In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

text: Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N=80 samples from persons with RT-PCR confirmed SARS-CoV2 infection), and a specificity of 97.2% (N=106 control samples).


Scathing COVID-19 book from Lancet editor - rushed but useful


title: Logistic Approach to COVID - 19 Epidemic Evolution in Brazil

text: We study in this work the temporal evolution of local and global contaminated population by coronavirus. We access those information analytically and numerically using a logistic model. It is shown, using diferent data from The Brazilian Ministry of Health (MS), The World Health Organization - WHO, and The Niteroi Health Foundation (FMS), the contaminated population ramping-up curves, the population inflection, the population saturation - plateau regime, and also the time related to these population evolution regimes. Based on the simulations, approaches are proposed at this more advanced phase of the pandemic, which might generate effectiveness at the actions of society in general, in a way that those actions could generate effective and efficient results, and this means a more organized war against this pandemic, a better way to induce the economy resumption, and also to create a more intense public awareness on the contamination hubs and surges that may emerge due to the reduction of social isolation.


title: The impact of social distancing and epicenter lockdown on the COVID-19 epidemic in mainland China: A data-driven SEIQR model study

text: The outbreak of coronavirus disease 2019 (COVID-19) which originated in Wuhan, China, constitutes a public health emergency of international concern with a very high risk of spread and impact at the global level. We developed data-driven susceptible-exposed-infectious-quarantine-recovered (SEIQR) models to simulate the epidemic with the interventions of social distancing and epicenter lockdown. Population migration data combined with officially reported data were used to estimate model parameters, and then calculated the daily exported infected individuals by estimating the daily infected ratio and daily susceptible population size. As of Jan 01, 2020, the estimated initial number of latently infected individuals was 380.1 (95%-CI: 379.8~381.0). With 30 days of substantial social distancing, the reproductive number in Wuhan and Hubei was reduced from 2.2 (95%-CI: 1.4~3.9) to 1.58 (95%-CI: 1.34~2.07), and in other provinces from 2.56 (95%-CI: 2.43~2.63) to 1.65 (95%-CI: 1.56~1.76). We found that earlier intervention of social distancing could significantly limit the epidemic in mainland China. The number of infections could be reduced up to 98.9%, and the number of deaths could be reduced by up to 99.3% as of Feb 23, 2020. However, earlier epicenter lockdown would partially neutralize this favorable effect. Because it would cause in situ deteriorating, which overwhelms the improvement out of the epicenter. To minimize the epidemic size and death, stepwise implementation of social distancing in the epicenter city first, then in the province, and later the whole nation without the epicenter lockdown would be practical and cost-effective.


title: Effects of a blend of essential oils in milk replacer on performance, rumen fermentation, blood parameters and health scores of dairy heifers

text: The objective of this study was to evaluate how the inclusion of a blend of essential oils in milk replacer (MR) affects different outcomes of dairy heifers. The outcomes evaluated: feed intake, performance, body development, blood cells and metabolites, insulin-like growth factor-1 (IGF-1), rumen fermentation, fecal scores and respiratory scores. All outcomes were evaluated during pre-weaning (4 – 60 d of age), and carryover effects on post-weaning (61 – 90 d of age) periods. The experimental units utilized were 29 newborn Holstein × Gyr crossbred dairy heifers, with genetic composition of 5/8 or more Holstein and 3/8 or less Gyr and body weight (BW) at birth of 32.2 ± 5.2 kg. Experimental units were randomly assigned to either a control group (CON, n = 15) or a treatment group, consisting of supplementation of a blend of essential oils (BEO, n = 14) with1 g/d/calf (Apex Calf, Adisseo, China). During the pre-weaning phase, all heifers were fed 5 L of MR/d reconstituted at 15% (dry matter basis), divided into two equal meals. Water and starter were provided ad libitum. During the post-weaning, animals received a maximum 3 kg of starter/d, and ad libitum corn silage, divided into two meals. The outcomes feed intake, fecal and respiratory scores were evaluated daily. BW was measured every three days, while body development was recorded weekly. Blood samples were collected on 0, 30 and 60 d of age for total blood cell count, weekly to determinate ß-hydroxybutyrate, urea and glucose, and biweekly for IGF-1. Ruminal parameters (pH, volatile fatty acids, ammonia-N and acetate:proprionate proportion - C2:C3) were measured each 14 days. A randomized complete block design with an interaction between treatment and week was the experimental method of choice to test the hypothesis of effect of BEO on all outcomes. An ANOVA procedure was used for continuous outcomes and a non-parametric test was used for the ordered categorical outcomes both adopting a C.I. = 95%. Results indicated that there was not enough evidence to accept the alternative hypothesis of effect of BEO in MR on: feed intake, performance, body development and blood metabolites during both pre-weaning and post-weaning periods. However, results indicated that the inclusion of BEO in MR significantly affects the proportion of C2:C3 during pre and post-weaning (P ≤ 0.05). Similarly, the effect is significant for basophil (P ≤ 0.001) and platelet (P ≤ 0.05) counts in pre-weaning. The interaction between week and treatment was also significant for lymphocytes (P ≤ 0.001), revealing a long-term treatment immunological effect. Lastly, the effect on fecal scores was also significant (P ≤ 0.05) during pre-weaning, with lower values for BEO. BEO contributed for ruminal manipulation on pre-weaning and carry over effect on post-weaning; immunity improvement and a decrease morbidity of neonatal diarrhea in pre-weaning phase.


title: Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

text: Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical in tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequential supply strain. Therefore, alternative specimen types have been investigated, that provide similar detection sensitivity with reduced health care exposure and potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS, using matched specimens from two outpatient cohorts in New York State (total n = 463). The first cohort showed only a 5.4% positivity but the second cohort (n=227) had a positivity rate of 41%, with sensitivity in NPS, NS and saliva of 97.9%, 87.1%, and 87.1%, respectively. Whether the reduced sensitivity of NS or saliva is acceptable must be assessed in the settings where they are used. However, we sought to improve on it by validating a method to mix the two sample types, as the combination of nasal swab and saliva resulted in 94.6% SARS-CoV-2 detection sensitivity. Spiking experiments showed that combining them did not adversely affect the detection sensitivity in either. Virus stability in saliva was also investigated, with and without the addition of commercially available stabilizing solutions. The virus was stable in saliva at both 4C and room temperature for up to 7 days. The addition of stabilizing solutions did not enhance stability and in some situations reduced detectable virus levels.


title: Simplified model of Covid-19 epidemic prognosis under quarantine and estimation of quarantine effectiveness

text: A simplified model of Covid19 epidemic dynamics under quarantine conditions and criteria to estimate quarantine effectiveness is developed. The model is based on the growth rate of new infection cases when total number of infected cases is significantly smaller than population size of infected country or region. The model is developed on collected epidemiological data of Covid19 pandemic, which shows that the growth rate of new infection cases has tendency of linearly decrease until its constant value during imposed quarantine according to effectiveness of quarantine actions. The growth rate of new infection cases can be used as criteria to estimate quarantine effectiveness.


The Impact of the Current SARS-CoV-2 Pandemic on Neonatal Care


title: Early CPAP reduced mortality in covid-19 patients. Audit results from Wrightington, Wigan and Leigh Teaching Hospitals NHS Foundation Trust.

text: COVID-19 infection typically causes pneumonia with bilateral changes on Chest radiograph. There is significant hypoxia and use of oxygen for patients admitted to hospital is standard. The use of Continuous Positive Airway Pressure (CPAP) in patients with COVID-19 has now become established as a common clinical practice based on recent experience. It is given as part of best endeavours treatment in the absence of sufficient evidence to guide best practice. The use of CPAP as a step up in clinical care is now common but has a poor evidence base. Using routinely collected data, the use of CPAP as a supportive non-invasive ventilatory treatment is described in 35 patients with COVID infection. Patients given early CPAP and in particular within 48 hours of admission, are shown to have a better outcome (a significant probability of lower mortality) than patients who received late CPAP (more than 48 hours after admission). Although the analysis is affected by a small sample size, the results have shown good evidence that supports the early use of CPAP in patients with COVID-19 infection.