title: Suppress, and not just flatten:Strategies for Rapid Suppression of COVID19 transmission in Small World Communities

text: Many countries have introduced Lockdowns to contain the COVID19 epidemic. Lockdowns, though an effective policy for containment, imposes a heavy cost on the economy as it enforces extreme social distancing measures on the whole population. The objective of this note is to study alternatives to Lockdown which are either more targeted or allows partial opening of the economy. Cities are often spatially organized into wards. We introduce Multi-lattice small world (MLSW) network as a model of a city where each ward is represented by a 2D lattice and each vertex in the latex represents an agent endowed with SEIR dynamics. Through simulation studies on MLSW we examine a variety of candidate suppression policies and find that restricting lockdowns to infected wards can indeed out-perform global Lockdowns in both reducing the attack rate and also shortening the duration of the epidemic. Even policies such as partial opening of the economy, such as Two Day Work Week, can be competitive if augmented with extensive Contact Tracing.


title: (Dis)embeddedness and (de)commodification: COVID-19, Uber, and the unravelling logics of the gig economy

text: The ride-hailing giant Uber has long circumvented labour regulations and commodified its drivers’ labour by existing at the conjuncture of multiple geographies – being simultaneously embedded and disembedded from the places where it operates. In this commentary, we argue that the COVID-19 pandemic has destabilised Uber’s ‘conjunctural’ existence and forced the company to become more embedded in the locations where it operates, bringing about a – perhaps temporary – turn towards the decommodification of its drivers’ labour.


title: What can a Pandemic Teach Us about Competency Based Medical Education?

text: Medical education is moving towards competency-based medical education (CBME) where learning and assessment are focused on predefined abilities and outcomes. While medical student and residency training have defined competencies and objectives that trainees need to achieve, training remains time -based. Students and residents graduate based on a preset length of training. The COVID -19 pandemic is disrupting educational and clinical environments and in some regions the workforce may not be adequate to respond to the needs of the community. This, therefore, presents an opportunity for the medical education community to reconsider time-based training and embrace a competency-based progression to accelerate entry into the workforce. This commentary discusses undergraduate and graduate medical education response to workforce pressures of COVID-19. On one hand, some medical schools are moving towards competency-based (early) graduation from medical school. On the other hand, residency programs have generally held to time -based completion of training. In the context of this clinical and educational disruption, there are two challenges to CBME progression of trainees. The first challenge is whether there is trust in competency-based assessment to permit time independent progression. The second involves a number of logistical issues to competency-based progression.


title: Dual-Histamine Blockade with Cetirizine - Famotidine Reduces Pulmonary Symptoms in COVID-19 Patients

text: Background: The COVID-19 pandemic due to SARS-CoV-2 infection can produce Acute Respiratory Distress Syndrome as a result of a pulmonary cytokine storm. Antihistamines are safe and effective treatments for reducing inflammation and cytokine release. Combinations of Histamine-1 and Histamine-2 receptor antagonists have been effective in urticaria, and might reduce the histamine-mediated pulmonary cytokine storm in COVID-19. Can a combination of Histamine-1 and Histamine-2 blockers improve COVID-19 inpatient outcomes? Methods: A physician-sponsored cohort study of cetirizine and famotidine was performed in hospitalized patients with severe to critical pulmonary symptoms. Pulmonologists led the inpatient care in a single medical center of 110 high-acuity patients that were treated with cetirizine 10 mg and famotidine 20 mg b.i.d. plus standard-of-care. Results: Of all patients, including those with Do Not Resuscitate directives, receiving the dual-histamine blockade for at least 48 hours, the combination drug treatment resulted in a 16.4% rate of intubation, a 7.3% rate of intubation after a minimum of 48 hours of treatment, a 15.5% rate of inpatient mortality, and 11.0 days duration of hospitalization. The drug combination exhibited reductions in symptom progression when compared to published reports of COVID-19 patients. Concomitant medications were assessed and hydroxychloroquine was correlated with worse outcomes. Conclusions: This physician-sponsored cohort study of cetirizine and famotidine provides proof-of-concept of a new safe and effective method to reduce the progression in symptom severity, presumably by minimizing the histamine-mediated cytokine storm. Further clinical studies in COVID-19 are warranted of the repurposed off-label combination of two historically-safe histamine blockers.


title: The feasibility of convalescent plasma therapy in severe COVID-19 patients: a pilot study

text: Currently, there are no approved specific antiviral agents for 2019 novel coronavirus disease (COVID-19). In this study, ten severe patients confirmed by real-time viral RNA test were enrolled prospectively. One dose of 200 mL convalescent plasma (CP) derived from recently recovered donors with the neutralizing antibody titers above 1:640 was transfused to the patients as an addition to maximal supportive care and antiviral agents. The primary endpoint was the safety of CP transfusion. The second endpoints were the improvement of clinical symptoms and laboratory parameters within 3 days after CP transfusion. The median time from onset of illness to CP transfusion was 16.5 days. After CP transfusion, the level of neutralizing antibody increased rapidly up to 1:640 in five cases, while that of the other four cases maintained at a high level (1:640). The clinical symptoms were significantly improved along with increase of oxyhemoglobin saturation within 3 days. Several parameters tended to improve as compared to pre-transfusion, including increased lymphocyte counts (0.65*109/L vs. 0.76*109/L) and decreased C-reactive protein (55.98 mg/L vs. 18.13 mg/L). Radiological examinations showed varying degrees of absorption of lung lesionswithin 7 days. The viral load was undetectable after transfusion in seven patients who had previous viremia. No severe adverse effects were observed. This study showed CP therapy was welltolerated and could potentially improve the clinical outcomes through neutralizing viremia in severe COVID-19 cases. The optimal dose and time point, as well as the clinical benefit of CP therapy, needs further investigation in larger well-controlled trials.


title: COVID-19 pandemic: examining the faces of spatial differences in the morbidity and mortality in sub-Saharan Africa, Europe and USA.

text: Background: COVID-19, the disease associated with the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently a global pandemic with several thousands of confirmed cases of infection and death. However, the death rate across affected countries shows variation deserving of critical evaluation. Methods: In this study, we evaluated differentials in COVID-19 confirmed cases of infection and associated deaths of selected countries in Sub-Sahara Africa (Nigeria and Ghana), South Africa, Europe (Italy, Spain, Sweden and UK) and USA. Data acquired for various standard databases on mutational shift of the SARS-CoV-2 virus based on geographical location, BCG vaccination policy, malaria endemicity, climatic conditions (temperature), differential healthcare approaches were evaluated over a period of 45 days from the date of reporting the index case. Results: The number of confirmed cases of infection and associated deaths in Sub-Sahara Africa were found to be very low compared to the very high values in Europe and USA over the same period. Recovery rate from COVID-19 is not correlated with the mutational attributes of the virus with the sequenced strain from Nigeria having no significant difference (p>0.05) from other geographical regions. Significantly higher (p<0.05) infection rate and mortality from COVID-19 were observed in countries (Europe and USA) without a current universal BCG vaccination policy compared to those with one (Sub-Sahara African countries). Countries with high malaria burden had significantly lower (p<0.05) cases of COVID-19 than those with low malaria burden. A strong negative correlation (-0.595) between mean annual temperature and COVID-19 infection and death was observed with 14.8% variances between temperature and COVID-19 occurrence among the countries. A clear distinction was observed in the COVID-19 disease management between the developed countries (Europe and USA) and Sub-Sahara Africa. Conclusions: The study established that the wide variation in the outcome of the COVID-19 disease burden in the selected countries are attributable largely to climatic condition (temperature) and differential healthcare approaches to management of the disease. We recommend consideration and mainstreaming of these findings for urgent intervention and management of COVID-19 across these continents.


COVID-19: a challenge for oncology services


title: Epidemiological features after emergency declaration in Hokkaido and report of 15 cases of COVID-19 including 3 cases requiring mechanical ventilation

text: The ongoing spread of coronavirus disease (COVID-19) is a worldwide crisis Hokkaido Prefecture in Japan promptly declared a state of emergency following the rapid increase of COVID-19 cases, and the policy became an example to mitigate the spread of COVID-19 We herein report 15 cases of COVID-19 including 3 cases requiring mechanical ventilation Based on review of our cases, among patients over 50 years of age with underlying diseases such as hypertension and diabetes mellitus, and those who required oxygen administration tended to deteriorate These cases highlight the importance of understanding the background and clinical course of severe cases to predict prognosis


title: The emergence of novel-coronavirus and its replication cycle - An overview

text: Recently, a new viral-based infection has emerged as a respiratory disease caused by a novel (new) coronavirus that was first detected in Wuhan City, China. With any or many reasons, this newly emerged novel-Coronavirus (2019-nCoV) has now been recognized in more than 70 locations around the globe. The disease caused by 2019-nCoV has been named as “coronavirus disease 2019 - COVID-19”. Due to the rising number of confirmed 2019-nCoV infected cases and widespread detection, the World Health Organization (WHO) has announced 2019-nCoV as a threatening health concern, and urgent robust actions are of supreme interest to tackle this global health emergency. Owing to this new emergence, we know relatively little about 2019-nCoV, which is a highly pathogenic human pathogen. To completely overcome this life-threatening 2019-nCoV pathogen, further in-depth studies are needed to gain insight and complete understanding about its fast mode spread, replication, and pathogenesis. Since the first appearance and detection of 2019-nCoV and COVID-19, respectively, the current literature lacks the global perspective and replication cycle of 2019-nCoV. Thus, herein, an effort has been made to cover this literature gap. A proper understanding of the 2019-nCoV replication will further insight and strengthen the infection control measures, transmission prevention, and vaccine development, effectively.


title: In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins

text: COVID 19 is disease caused by novel corona virus, SARS-CoV2 originated in China most probably of Bat origin. Till date, no specific vaccine or drug has been discovered to tackle the infections caused by SARS-CoV2. In response to this pandemic, we utilized bioinformatics knowledge to develop efficient vaccine candidate against SARS-CoV2. Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes were antigenic in nature non-toxic and probably non-allergen. Modelled and refined tertiary structure was predicted as valid for further use. Protein-Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. Designed multiepitope vaccine has induced cell mediated and humoral immunity along with increased interferon gamma response. Macrophages and dendritic cells were also found increased over the vaccine exposure. In silico codon optimization and cloning in expression vector indicates that vaccine can be efficiently expressed in E. coli. In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity.


title: A hybrid multi-scale model of COVID-19 transmission dynamics to assess the potential of non-pharmaceutical interventions

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that emerged in Wuhan, China in December 2019. It has caused a global outbreak which represents a major threat to global health. Public health resorted to non-pharmaceutical interventions such as social distancing and lockdown to slow down the spread of the pandemic. However, the effect of each of these measures remains hard to quantify. We design a multi-scale model that simulates the transmission dynamics of COVID-19. We describe the motion of individual agents using a social force model. Each agent can be either susceptible, infected, quarantined, immunized or deceased. The model considers both mechanisms of direct and indirect transmission. We parameterize the model to reproduce the early dynamics of disease spread in Italy. We show that panic situations increase the risk of infection transmission in crowds despite social distancing measures. Next, we suggest that pre-symptomatic transmission could be a significant driver of the infection spread. Then, we show that the restricted movement of the individuals flattens the epidemic curve. Finally, model predictions suggest that measures stricter than social distancing and lockdown were used to control the epidemic in Wuhan, China.


title: Pandemic leadership: Lessons from New Zealand’s approach to COVID-19

text: This case study analyses the leadership approach and practices of the New Zealand government, led by Prime Minister Jacinda Ardern, in the response thus far to the COVID-19 pandemic. It reports on how a shared sense of purpose has been established, that of minimizing harm to lives and livelihoods, for which the government has sought – and secured – New Zealanders’ commitment. Key leadership practices comprise the government’s willingness to themselves be led by expertise, its efforts to mobilise the population, and to enable coping, all of which serve to build the trust in leadership needed for transformative, collective action such as the pandemic demands. At the time of writing, New Zealand appears well on track to achieve its ambitious goal of achieving rapid and complete control over the COVID-19 outbreak – not just ‘flattening the curve’ as other countries are struggling to do – at least in part due to these leadership contributions. A framework of good practices for pandemic leadership is offered drawn from this case study, in the hope transferable lessons can be taken to aid others in the continuing struggle to limit the harm COVID-19 poses to lives and livelihoods throughout the world.


title: Social distancing strategies for curbing the COVID-19 epidemic

text: The SARS-CoV-2 pandemic is straining healthcare resources worldwide, prompting social distancing measures to reduce transmission intensity. The amount of social distancing needed to curb the SARS-CoV-2 epidemic in the context of seasonally varying transmission remains unclear. Using a mathematical model, we assessed that one-time interventions will be insufficient to maintain COVID-19 prevalence within the critical care capacity of the United States. Seasonal variation in transmission will facilitate epidemic control during the summer months but could lead to an intense resurgence in the autumn. Intermittent distancing measures can maintain control of the epidemic, but without other interventions, these measures may be necessary into 2022. Increasing critical care capacity could reduce the duration of the SARS-CoV-2 epidemic while ensuring that critically ill patients receive appropriate care.


title: Ambient air pollutants, meteorological factors and their interactions affect confirmed cases of COVID-19 in 120 Chinese cities

text: Emerging evidences have confirmed effects of meteorological factors on novel coronavirus disease 2019 (COVID-19). However, few studies verify the impact of air pollutants on this pandemic. This study aims to explore the association of ambient air pollutants, meteorological factors and their interactions effect confirmed case counts of COVID-19 in 120 Chinese cities. Here, we collected total confirmed cases of COVID-19 by combining with meteorological factors and air pollutants data from 15th January 2020 to 18th March 2020 in 120 Chinese cities. Spearman correlation analysis was employed to estimate the association between two variables; univariate and multivariate negative binomial regression analysis were applied to explore the effect of air pollutants and meteorological parameters on the COVID-19 confirmed cases. Positive associations were found between the confirmed cases of COVID-19 and carbon monoxide (CO), aerodynamic particulate matter with aerodynamic diameter [≤]2.5 um (PM2.5), relative humidity (RH) and air pressure (AP). And negative association was found for sulfur dioxide (SO2). In addition, multivariate negative binomial regression analysis suggested that confirmed cases of COVID-19 was positively correlated with ozone (O3) in lag 0 day while it was negatively associated with wind velocity (WV) in lag 14 days, and the pollutants-meteorological factors interactions also associate with COVID-19. In conclusions, air pollutants and meteorological factors and their interactions all associate with COVID-19.


title: Clinical features and the maternal and neonatal outcomes of pregnant women with coronavirus disease 2019

text: BACKGROUND There is little information about the coronavirus disease 2019 (Covid-19) during pregnancy. This study aimed to determine the clinical features and the maternal and neonatal outcomes of pregnant women with Covid-19. METHODS In this retrospective analysis from five hospitals, we included pregnant women with Covid-19 from January 1 to February 20, 2020. The primary composite endpoints were admission to an intensive care unit (ICU), the use of mechanical ventilation, or death. Secondary endpoints included the clinical severity of Covid-19, neonatal mortality, admission to neonatal intensive care unit (NICU), and the incidence of acute respiratory distress syndrome (ARDS) of pregnant women and newborns. RESULTS Thirty-three pregnant women with Covid-19 and 28 newborns were identified. One (3%) pregnant woman needed the use of mechanical ventilation. No pregnant women admitted to the ICU. There were no moralities among pregnant women or newborns. The percentages of pregnant women with mild, moderate, and severe symptoms were 13 (39.4%),19(57.6%), and 1(3%). One (3.6%) newborn developed ARDS and was admitted to the NICU. The rate of perinatal transmission of SARS-CoV-2 was 3.6%. CONCLUSIONS This report suggests that pregnant women are not at increased risk for severe illness or mortality with Covid-19 compared with the general population. The SARS-CoV-2 infection during pregnancy might not be associated with as adverse obstetrical and neonatal outcomes that are seen with the severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) infection during pregnancy. (Funded by the National Key Research and Development Program.)


title: COVID 19 in Bangladesh: Assumption of possible infection and death

text: Abstract: It is a painful job to predict the death of people. But sometimes it is important to predict the future and concern the government. A furious future is waiting for Bangladesh. Objective: Objective of the study is to assume the number of positive case and death till 30th December, 2020 in Bangladesh. Study design: This study was designed with systematic review and data analysis. Method: The study was completed by analyzing data available on website. First COVID 19 case in Bangladesh was identified on 8th March. Analyzing the data increasing rate/common ratio of infection and death has been identified. Then this common ratio has been used in the formula of multiplication series. Data of China, Iran, Italy and the USA was also analyzed to assume how the death and case number increased. Social issues of Bangladesh were also analyzed. Considering all these the assumption was made. Result: It has been assumed that by the 43rd week (on 30th December, 2020) of first identification the total case can be 17024322 and total death can be 86265 by 30 December, 2020. As this is an assumption this can be true, partially true or false. But the base of assumption is strong enough so the possibility of being true or nearly true is higher. Policy Suggestion: Government should choose properly one between two options. Either government should declare curfew or let people lead normal life. A very weak lock down for a long time does not make any sense.


title: D614G Spike Variant Does Not Alter IgG, IgM, or IgA Spike Seroassay Performance

text: Emergence of a new variant of spike protein (D614G) with increased infectivity and transmissibility has prompted many to analyze the potential role of this variant in the SARS-CoV-2 pandemic. When a new variant emerges, there is a concern regarding whether an individual exposed to one variant of a virus will have cross-reactive immune memory to the second variant. Accordingly, we analyzed the serologic reactivity of D614 (original) and G614 variant spike proteins. We found that antibodies from a high-incidence population in New York City reacted both toward the original D614 spike and the G614 spike variant. These data suggest that patients who have been exposed to either SARS-CoV-2 variant have humoral immunity that can respond against both variants. This is an important finding both for SARS-CoV-2 disease biology and for potential antibody-based therapeutics.


title: A simple Covid-19 Epidemic Model and Containment Policy in France

text: We show that the standard SIR model is not effective to predict the 2019-20 coronavirus pandemic propagation. We propose a new model where the logarithm of the detected population number follows a linear dynamical system. We estimate the parameters of this system and compare models obtained with data observed from different countries. Based on the given estimator and results obtained with the Pr. Raoult s treatment, we affirm with a reasonable degree of confidence that his test-treat-noconfine policy was less expensive in human lives than the confine and wait for a proved treatment policy adopted by the French government.


title: COVID‐US: A simplified approach to cardiopulmonary ultrasound in suspected and confirmed COVID‐19 patients in surge crisis

text: The severe acute respiratory syndrome coronavirus 2 (COVID‐19) pandemic has placed an unprecedented challenge on healthcare systems across the globe. Rapid assessment of the cardiorespiratory function to monitor disease progression and guide treatment is essential. Therefore, we have designed the COVID‐US: a simplified cardiopulmonary ultrasound approach to use in suspected and confirmed COVID‐19 patients, to aid front‐line health workers in their decision‐making in a surge crisis.


title: Practical Challenges of Mask-to-Mask Encounters with Patients with Head and Neck Cancers Amid the COVID-19 Pandemic

text: The coronavirus disease 2019 (COVID-19) pandemic has forced a re-design of care in radiation oncology. Perhaps more than any other disease site we commonly see, the evaluation and treatment of head and neck cancer has posed the greatest risk of COVID-19 transmission between patients and radiotherapy providers. In our early experience with the novel coronavirus, several staff members were exposed to a COVID-positive patient and this caused us to devise policies and procedures to mitigate further risk in a way that could practically be employed across a large health system while not compromising care delivery. Here, we formulate a concise summary of simple steps, including a novel thermoplastic mask fitting technique and procedures for intraoral immobilization devices, to guide practices and provide new layers of protection for both patients and staff.


title: Water Scarcity: A Big Challenge to Slums in Africa to Fight against COVID-19

text: In the light of the current situation regarding the COVID-19 disease, a discussion is attempted on the need for focusing on water scarcity in Africa and the important considerations to conserving water to fight against SARS-CoV-2 virus.


title: Communicating with patients and families about difficult matters: A rapid review in the context of the COVID-19 pandemic

text: Background: Pandemics pose significant challenges for healthcare systems, including an increase in difficult discussions about future illness progression and end of life. Objectives: To synthesise existing evidence about communication practices used to discuss difficult matters, including prognosis and end of life, and to use this evidence to make recommendations for clinical practice. The aim of this study was to use rapid review methods to update findings from a previous systematic review published in 2014. Data sources: MEDLINE, EMBASE, CINAHL, PsycINFO, Sociological Abstracts, Web of Science, Scopus, ASSIA and Amed. Study eligibility criteria: Studies using conversation analysis or discourse analysis to examine recordings of actual conversations about difficult matters relating to future illness progression and end of life. Study appraisal and synthesis methods: Data appraisal and extraction procedures used in the 2014 review were modified for this rapid review. Results: Following screening, 18 sources were deemed to meet eligibility criteria, which were added to the 19 sources included in the 2014 systematic review. Synthesis of study findings identified 11 communication practices: providing opportunities for patient or family members to propose matters to discuss (7 out of 37 included sources); seeking a patient or family member's perspective (6/37); discussing the future indirectly (11/37); discussing the future explicitly (7/37) linking to something previously said or done (11/37); using hypothetical scenarios (13/37); framing a difficult matter as universal (5/37); acknowledging uncertainty (3/37); exploring options (2/37); displaying sensitivity (7/37); emphasising the positive (7/37). Limitations: Dividing work amongst the study authors to enable rapid review may have created inconsistencies. Conclusions and implications of key findings: This synthesis of high-quality evidence from actual clinical practice supports a series of recommendations for communicating about difficult matters during and beyond the COVID-19 pandemic.


title: Global trends in air travel: implications for connectivity and resilience to infectious disease threats

text: Background: Increased connectivity via air travel can facilitate the geographic spread of infectious diseases. The number of travelers alone does not explain risk; passenger origin and destination will also influence risk of disease introduction and spread. We described trends in international air passenger numbers and connectivity between countries with different capacities to detect and respond to infectious disease threats. Methods: We used the Fragile States Index (FSI) as an annual measure of country-level resilience and capacity to respond to infectious disease events. Countries are categorized as: Sustainable, Stable, Warning, or Alert, in order of increasing fragility. We included data for 177 sovereign states for the years 2007 to 2016. Annual inbound and outbound international air passengers for each country were obtained for the same time period. We examined trends in FSI score, trends in worldwide air travel, and the association between a state's FSI score and air travel. Results: Among countries included in the FSI rankings, the total number of passengers increased from 0.791 billion to 1.28 billion between 2007 and 2016. Increasing fragility was associated with a decrease in travel volumes, with a 2.9% (95% CI: 2.3-3.5%) reduction in passengers per 1-unit increase in FSI score. Overall, travel between countries of different FSI categories either increased or remained stable. The greatest increase was observed for travel to Warning countries from Warning countries, with an annual increase of 8,967,623 passengers (95%CI: 6,546,494 to 11,388,753) over the study period. Conclusions: The world's connectivity via air travel has increased dramatically over the past decade. There has been notable growth in travel from Warning and Stable countries, which comprise more than three-quarters of international air travel passengers. These countries may have suboptimal capacity to detect and respond to infectious disease threats that emerge within their borders.


title: Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

text: COVID-19 caused by a novel coronavirus SARS-CoV-2 emerged in Wuhan, Hubei province since December 2019, and caused a rapid outbreak throughout China and globally. Cities outside Hubei are also facing great challenge and require implementing of effective and feasible strategy in precision diagnosing novel coronavirus pneumonia (NCP). We described a multicenter prospective study on diagnostic strategy of suspected NCP patients from January 22nd to February 9th, 2020 in Eastern China cities. Nasopharyngeal swabs were collected from the patients. The epidemiological characteristics, clinical symptoms, laboratory assessments, and computed tomographic (CT) scans were obtained. Pathogen screen were performed including RT-PCR, multiplex PCR, rapid flu antigen tests and mNGS. We enrolled 53 suspected NCP patients, among whom 20 were laboratory-confirmed. Fourteen (70%) and 3 (15%) patients were positive for the first and second SARS-CoV-2 RT-PCR test, respectively. All NCP patients were positive for mNGS. Chest CT images and the symptoms of early stage NCP patients were similar to other viral pneumonia patients. We identified 11 of 20 co-infections in NCP cases, including regular respiratory virus, fungi and bacteria synchronously. Genomic analysis showed that 8 of 10 cases had no mutation in virus genome, while 2 cases had only one single mutation in N gene. Our study discovered that a combination of chest CT, SARS-CoV-2 RT-PCR and multi-plex PCR is recommended in regions outside Hubei province. Co-infection of other pathogens with SARS-CoV-2 exists and should be acknowledged. Repeated sampling, change of specimen type or metagenomics sequencing could further facilitate during critical clinical cases.


title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

text: The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.


Epidemiological Data From the COVID-19 Outbreak in Spain for the Promotion of Tobacco Smoking Cessation Policies


title: Mixed Chinese herbs and Western medicine for novel coronavirus disease 2019 (COVID-19): a mixed method review

text: Background: Coronavirus disease 2019 (COVID-19) is a pandemic affecting millions around the world. There is no existing pharmaceutical treatment that is known to be effective. Preliminary data shows that San Yao San Fang (SYSF) has clinical benefits in patients with COVID-19. The aim of this paper is to review existing data regarding the use of formulas within San Yao San Fang in the treatment of COVID-19 Search Strategy: We searched through 5 databases for studies on SYSF and patients with COVID-19 through April 2020. Eligibility Criteria: We included studies that included formulas within San Yao San Fang with or without Western interventions against Western interventions. Main results: We included 7 studies involving 532 patients. SYSF combined with Western interventions improved the recovery rate of symptoms such as fever (Risk Ratio (RR) 0.40 (95% CI 0.24 to 0.66, P < 0.01)), cough (RR 0.56 (95% CI 0.38 to 0.82, P < 0.01)) and fatigue (RR 0.61 (95% CI 0.47 to 0.78, P < 0.01)) and other symptoms such as headache, gastrointestinal symptoms, myalgia, dyspnoea and chest tightness (RR 0.63 (95% CI 0.47 to 0.83, P < 0.01)) as compared to the control group. SYSF combined with Western interventions reduced the duration of fever as compared to the control group. (Mean difference (MD) -1.18 (95% CI -1.45 to -0.91, P < 0.01)) In regards to adverse events, there is no statistical difference between the treatment group and the control group. (RR 1.62 (95% CI 0.83 to 3.17, P = 0.16)). SYSF combined with Western interventions did not show to significantly reduce duration of hospitalisation as compared to the control group. (MD -0.73 (95% CI -5.19 to 3.73, P = 0.75)) Conclusion: SYSF appears to be clinically effective and safe. Further research is required to ensure the efficacy of SYSF.


title: Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data

text: Pockets of susceptibility resulting from spatial or social heterogeneity in vaccine coverage can drive measles outbreaks, as cases imported into such pockets are likely to cause further transmission and lead to large transmission clusters. Characterising the dynamics of transmission is essential for identifying which individuals and regions might be most at risk. As data from detailed contact tracing investigations are not available in many settings, we combined age, location, genotype, and onset date of cases in order to probabilistically reconstruct the importation status and transmission clusters within a newly developed R package called o2geosocial. We compared our inferred cluster size distributions to 737 transmission clusters identified through detailed contact-tracing in the United States between 2001 and 2016. We were able to reconstruct the importation status of the cases and found good agreement between the inferred and reference clusters. The results were improved when the contact-tracing investigations were used to set the importation status before running the model. Spatial heterogeneity in vaccine coverage is difficult to measure directly. Our approach was able to highlight areas with potential for local transmission using a minimal number of variables and could be applied to assess the intensity of ongoing transmission in a region.


title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Mimicking as Pulmonary Tuberculosis in an Inmate

text: Coronavirus disease 2019 (COVID-19) is an emerging global infectious disease with emerging medical knowledge. Clinical presentation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is very variable amongst patients, and the literature about unusual presentations is growing rapidly. This lack of knowledge leads to diagnostic, therapeutic, and management challenges in such patients. Here, we describe a case of SARS-CoV-2 infection in a low prevalence area which was initially diagnosed and managed as pulmonary tuberculosis (TB) in a high-risk inmate population. These ambiguous presentations can lead to mismanagement of such patients resulting in potentially fatal outcomes and public health crises in confined facilities. This also highlights the significance of a high index of clinical suspicion for SARS-CoV-2 especially in high risk and vulnerable populations.


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title: Cardiopulmonary Ultrasonography for Severe Coronavirus Disease 2019 Patients in Prone Position


title: A human monoclonal antibody blocking SARS-CoV-2 infection

text: The emergence of the novel human coronavirus SARS-CoV-2 in Wuhan, China has caused a worldwide epidemic of respiratory disease (COVID-19). Vaccines and targeted therapeutics for treatment of this disease are currently lacking. Here we report a human monoclonal antibody that neutralizes SARS-CoV-2 (and SARS-CoV). This cross-neutralizing antibody targets a communal epitope on these viruses and offers potential for prevention and treatment of COVID-19.


title: Critical limitations of digital epidemiology: Why COVID-19 apps are useless

text: During the current COVID-19 pandemic, “digital epidemiology” has been proposed to comple-ment traditional reporting and surveillance systems. Instruments such as smartphone contact apps, fitness trackers, and apps for voluntary reporting are intended to be used to monitor or limit the spread of COVID-19. The methodological drawbacks and limitations of these instruments and devices are insufficiently addressed in the public discussion. Therefore, we review these weaknesses and limitations, using the Total Survey Error framework to address sampling and non-sampling errors of these approaches. We argue that no useful results can be obtained by any of the suggested methods of digital epidemiology for COVID-19 research. Finally, we suggest feasible alternative data sources for valid and population covering COVID-19 indicator systems.


title: Stranded College Students amid Corona Virus Disease 2019 Pandemic: An Existential Phenomenology

text: This paper explores the lived experiences of college students who are stranded in the middle of the Corona Virus Disease 2019 (COVID-19) crisis. It follows the approach of Heideggerian existential phenomenology in studying ontology or what it means to be. Five college students were purposively selected to participate in the study. The researcher gained insight into each world of the students using interview procedures and thematic analysis. The results are presented through emerging themes and contextual ground. A conceptual structure that depicts the essence of the lived experiences of the stranded college students is offered in the end of the paper.


title: Project design of a device for express analysis for Coronaviridae antigens based on Omron industrial programmable logic controller

text: — Coronaviruses take the lead in gastrointestinal pathologies of animals and are spread all around the world. Causative agents of coronaviruses belong to Nidovirales order, Coronaviridae family which includes 2 subfamilies: Toroviridna (genera Torovirus and Bafinivirus) and Coronaviridna (genera Alphavirus, Betavirus, Gammavirus). Dividing of the latter by genera (groups I-III) was based on serological cross-reactions. Group I includes pathogens causing diseases in animals, such as swine coronavirus, feline infectious peritonitis virus. Group II includes pathogens of veterinary importance, such as BCoV, porcine hemagglutinating encephalomyelitis virus, horse coronavirus, viruses infecting mice and rats, as well as human coronaviruses that cause respiratory damage. Group III includes at the moment only avian coronaviruses. Coronavirus got its name in 1968 because of its special structure and appearance – it has spikes which resemble solar corona. In humans, coronavirus was first isolated by D. Tyrrell and M. Bynoe in 1965 from a patient with acute respiratory disease. Severe acute respiratory syndrome (SARS) in 2002, and then Middle East respiratory syndrome (MERS) in 2012 made specialists significantly increase the level of epidemic danger of coronaviruses. Due to its high virulence, virus multiplication rate in macrophages, pathogen replication, and antibody production increase significantly. At the end of 2019, coronavirus strain 2019-nCoV of Betacoronavirus genus was found in patients with pneumonia in China, and by early 2020 it spread all around the world. In animals, coronavirus leads to damage to mucous membranes. The amount of economic damage associated with disease caused by coronavirus is significant and includes death of animals, decreased meat and dairy productivity, decreased weight gain, culling, loss from abortion and infertility. In this regard, a demand arose for developing project of a device for express analysis for Coronaviridae antigen for the early diagnosis of coronaviruses. Based on the express analysis technique using solid-phase immunochromatographic medium, a project for express analysis for Coronaviridae antigen based on Omron industrial programmable logic controller was developed; it includes process chart for equipment, functional diagram and logical equations.


title: ESTIMATING R0 OF SARS-COV-2 IN HEALTHCARE SETTINGS

text: To date, no specific estimate of R0 for SARS-CoV-2 is available for healthcare settings. Using inter-individual contact data, we highlight that R0 estimates from the community cannot translate directly to healthcare settings, with pre-pandemic R0 values ranging 1.3-7.7 in three illustrative healthcare institutions. This has implications for nosocomial Covid-19 control.


title: Extrapolation of Infection Data for the CoVid-19 Virus and Estimate of the Pandemic Time Scale.

text: Predictions about the further development of the Corona pandemic are widely diverging. Here, a simple yet powerful algorithm is introduced for extrapolating infection rate and number of total infections from available data. The calculation predicts that under present conditions the infection rate in Germany will culminate in a few weeks and decrease to low values by mid-June 2020. Total number of infections will reach several 100,000 though.


title: Smoking and the risk of COVID-19 infection in the UK Biobank Prospective Study

text: Several studies suggest a lower prevalence of smoking than expected among adults with coronavirus disease (COVID-19). We conducted logistic regression analyses of the UK Biobank prospective study of 0.5 million adults followed for an average of 11 years. Compared to women, men were more likely to be tested and to test positive. In sex-stratified analyses, current smokers had higher adjusted Odds Ratios (OR) for being tested (male OR 1.60, 95%CI 1.32-1.95 and female OR 1.50, 1.21-.1.86). Current smokers were more slightly more likely than never smokers to test positive for COVID-19. Further examination of smoking as a risk factor for COVID-19 is required. These must take into account reverse causality, where smokers quit to avoid disease as well as prior diseases.


Working remotely if you are visually impaired


title: Using epidemic simulators for monitoring an ongoing epidemic

text: Prediction of infection trends, estimating the efficacy of contact tracing, testing or impact of influx of infected are of vital importance for administration during an ongoing epidemic. Most effective methods currently are empirical in nature and their relation to parameters of interest to administrators are not evident. We thus propose a modified SEIRD model that is capable of modeling effect of interventions and in migrations on the progress of an epidemic. The tunable parameters of this model bear relevance to monitoring of an epidemic. This model was used to show that some of the commonly seen features of cumulative infections in real data can be explained by piece wise constant changes in interventions and population influx. We also show that the data of cumulative infections from twelve Indian states between mid March and mid April 2020 can be generated from the model by applying interventions according to a set of heuristic rules. Prediction for the next ten days based on this model, reproduced real data very well. In addition, our model also reproduced the time series of recoveries and deaths. Our work constitutes an important first step towards an effective dashboard for the monitoring of epidemic by the administration, especially in an Indian context.


title: Endotoxemia and circulating bacteriome in severe COVID-19 patients

text: Background: When severe, COVID-19 shares many clinical features with bacterial sepsis. Yet, secondary bacterial infection is uncommon. However, as epithelium are injured and barrier function is lost, bacterial products entering the circulation might contribute to the pathophysiology of COVID-19. Methods: We studied 19 adults, severely ill patients with COVID-19 infection, who were admitted to King Chulalongkorn Memorial Hospital, Bangkok, Thailand, between 13th March and 17th April 2020. Blood samples on day 1, 3, and 7 of enrollment were analyzed for endotoxin activity assay (EAA), Beta-D-Glucan (BG), and 16S rRNA gene sequencing to determine the circulating bacteriome. Findings: Of the 19 patients, 14 were in intensive care and 10 patients received mechanical ventilation. We found 8 patients with high EAA ([≥] 0.6) and about half of the patients had high serum BG levels which tended to be higher in later in the illness. Although only 1 patient had a positive blood culture, 18 of 19 patients were positive for 16S rRNA gene amplification. Proteobacteria was the most abundant phylum. The diversity of bacterial genera was decreased overtime. Interpretation: Bacterial DNA and toxins were discovered in virtual all severely ill COVID-19 pneumonia patients. This raises a previously unrecognized concern for significant contribution of bacterial products in the pathogenesis of this disease.


title: Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

text: We enrolled 53 consecutive in-patients with COVID-19 at six hospitals in Toronto, Canada, and tested one nasopharyngeal swab/saliva sample pair from each patient for SARS-CoV-2. Overall, sensitivity was 89% for nasopharyngeal swabs and 77% for saliva (p=NS); difference in sensitivity was greatest for sample pairs collected later in illness.


title: Effects of temperature and humidity on the spread of COVID-19: A systematic review.

text: Background: Faced with the global pandemic of COVID-19, declared by World Health Organization (WHO) on March 11th 2020, and the need to better understand the seasonal behavior of the virus, our team conducted this systematic review to describe current knowledge about the emergence and replicability of the virus and its correlation with different weather factors such as temperature and relative humidity. Methods: The review was registered with the PROSPERO database. The electronic databases PubMed, Scopus, Web of Science, Cochrane Library, LILACS, OpenGrey and Google Scholar were examined with the searches restricted to the years 2019 and 2020. Risk of bias assessment was performed using the Joanna Briggs Institute (JBI) Critical Appraisal Checklist tool. The GRADE tool was used to assess the quality of the evidence. Results: The initial screening identified 517 articles. After examination of the full texts, seventeen studies met the review's eligibility criteria. Great homogeneity was observed in the findings regarding the effect of temperature and humidity on the seasonal viability and transmissibility of COVID-19. Cold and dry conditions were potentiating factors on the spread of the virus. After quality assessment, four studies had a high risk of bias and thirteen studies were scored as moderate risk of bias. The certainty of evidence was graded as low for both outcomes evaluated. Conclusion: Considering the existing scientific evidence, warm and wet climates seem to reduce the spread of COVID-19. The certainty of the evidence generated was graded as low. However, these variables alone could not explain most of the variability in disease transmission.


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title: Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site

text: We found, in our 788 confirmed COVID-19 patients, the decreased rate of severe/critical type, increased liver/kidney damage and prolonged period of nuclear acid positivity during virus dissemination, when compared with Wuhan. To investigate the underlining mechanism, we isolated one strain of SARS- CoV-2 (ZJ01) in mild COVID-19 patient and found the existence of 35 specific gene mutation by gene alignment. Further phylogenetic analysis and RSCU heat map results suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 strains of viruses worldwide (C/T type) based on the base (C or T) at positions 8824 and 28247. ZJ01 were both T at these two sites, becoming the only TT type currently identified in the world. The prediction of Furin cleavage site (FCS) and the sequence alignment of virus family indicated that FCS may be an important site of coronavirus evolution. ZJ01 had mutations near FCS (F1-2), which caused changes in the structure and the electrostatic distribution of the S protein surface, further affecting the binding capacity of Furin. Single cell sequencing and ACE2-Furin co-expression results confirmed that Furin level was higher in the whole body, especially in glands, liver, kidney and colon while FCS may help SARS-CoV-2 infect these organs. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 (the source of FCS sequence-PRRA) caused influenza, further showing potential in differentiating into mild COVID-19 subtypes.


title: On the reliability of model-based predictions in the context of the current COVID epidemic event: impact of outbreak peak phase and data paucity

text: The pandemic spread of the COVID-19 virus has, as of 20th of April 2020, reached most countries of the world. In an effort to design informed public health policies, many modelling studies have been performed to predict crucial outcomes of interest, including ICU solicitation, cumulated death counts, etc... The corresponding data analyses however, mostly rely on restricted (openly available) data sources, which typically include daily death rates and confirmed COVID cases time series. In addition, many of these predictions are derived before the peak of the outbreak has been observed yet (as is still currently the case for many countries). In this work, we show that peak phase and data paucity have a substantial impact on the reliability of model predictions. Although we focus on a recent model of the COVID pandemics, our conclusions most likely apply to most existing models, which are variants of the so-called 'Susceptible-Infected-Removed' or SIR framework. Our results highlight the need for performing systematic reliability evaluations for all models that currently inform public health policies. They also motivate a plea for gathering and opening richer and more reliable data time series (e.g., ICU occupancy, negative test rates, social distancing commitment reports, etc).


title: Polymorphisms in the ACE2 Locus Associate with Severity of COVID-19 Infection

text: The mechanisms underlying risk of developing severe outcomes due to COVID-19 have not yet been fully elucidated. The SARS-CoV-2 virus has a marked affinity to the human angiotensin-converting enzyme 2 (ACE2) receptor. The ACE2 locus is highly polymorphic, and this genetic variability may affect COVID-19 disease severity. Here, we analyzed associations between polymorphisms in the ACE2 locus and COVID-19 severity in 62 patients found to be COVID-19 positive by polymerase chain reaction. Of these patients, 23 required hospitalization due to COVID-19 infection. Of 61 ACE2 single nucleotide polymorphisms (SNPs) genotyped in this patient cohort, 10 were significantly associated with tissue expression of ACE2. Logistic regression adjusted for age and sex identified six of these ten SNPs to be significantly associated with hospitalization. These results provide preliminary evidence of a link between the ACE2 genotype and COVID-19 disease severity and suggest that the ACE2 genotype may inform COVID-19 risk stratification and need for more intense therapy.


title: Propagation, inactivation, and safety testing of SARS-CoV-2

text: In late 2019, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, the capital of the Chinese province Hubei. Since then, SARS-CoV-2 has been responsible for a worldwide pandemic resulting in over 4 million infections and over 250,000 deaths. The pandemic has instigated widespread research related to SARS-CoV-2 and the disease that it causes, COVID-19. Research into this new virus will be facilitated by the availability of clearly described and effective procedures that enable the propagation and quantification of infectious virus. Because work with the virus is recommended to be performed at biosafety level 3, validated methods to effectively inactivate the virus to enable safe study of RNA, DNA and protein from infected cells are also needed. Here, we report methods used to grow SARS-CoV-2 in multiple cell lines and to measure virus infectivity by plaque assay using either agarose or microcrystalline cellulose as an overlay as well as a SARS-CoV-2 specific focus forming assay. We also demonstrate effective inactivation by TRIzol, 10% neutral buffered formalin, beta propiolactone, and heat.


title: An Analysis of SARS-CoV-2 Using ViReport

text: The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of cases and hundreds of thousands of deaths. Given the current lack of treatments or vaccines available, it may be useful to trace the evolu-tion and spread of the virus to better develop methods of preventative intervention. In this study, we analyzed over 4,000 full genome sequences of human SARS-CoV-2 using novel tool ViReport [13], an automated workflow for performing phylogenetic analyses on viral sequences and generating comprehensive molecular epidemiologi-cal reports. The complete ViReport output can be found at https://github.com/mirandajsong/ViReport-SARS-CoV-2.


COPD at the time of COVID-19: A COPD foundation perspective


title: Swab Tests and COVID 19, Italy case studied using Artificial Intelligence, Statistical Analysis and MLR

text: Abstract: Objectives: The outbreak of the new Coronavirus (COVID-19) pandemic has prompted investigations on various aspects. This research aims to study the possible correlation between the numbers of swab tests and confirmed cases of infection, with special attention to the sickness level. Study Design: The study is carried out with reference to the Italian case, but the result is of more general importance, in particular for countries with limited availability of ICUs (intensive care units). Methods: The statistical analysis shows correlation between the number of swab tests and those of daily positive cases, mild cases admitted to hospital, intensive care cases, recovery, and death rate, and provides a basis to carry on an AI study. The results were validated using a multivariate linear regression (MLR) approach. Results: Our main result is the identification of a significant statistical effect of reduction of the pressure on the Health system as result of the increase of the tests. The relevance of this result is not confined to the COVID-19 outbreak, because the high demand of hospitalizations and ICU treatments due to this pandemic has an indirect effect on the possibility of guaranteeing an adequate treatment for other high-fatality disease, such as e.g. cardiological, and oncological. Conclusions: Our results show that swab testing may play a major role to decrease the stress on the Health system of a country. Therefore, this case study is relevant in particular for the planning of the control of the pandemic in countries with a limited capacity of admission to ICU s units.


title: Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States

text: Detection of SARS-CoV-2 infections to date has relied on RT-PCR testing. However, a failure to identify early cases imported to a country, bottlenecks in RT-PCR testing, and the existence of infections which are asymptomatic, sub-clinical, or with an alternative presentation than the standard cough and fever have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how publicly available CDC influenza-like illness (ILI) outpatient surveillance data can be repurposed to estimate the detection rate of symptomatic SARS-CoV-2 infections. We find a surge of non-influenza ILI above the seasonal average and show that this surge is correlated with COVID case counts across states. By quantifying the number of excess ILI patients in March relative to previous years and comparing excess ILI to confirmed COVID case counts, we estimate the syndromic case detection rate of SARS-CoV-2 in the US to be less than 13%. If only 1/3 of patients infected with SARS-CoV-2 sought care, the ILI surge would correspond to more than 8.7 million new SARS-CoV-2 infections across the US during the three week period from March 8 to March 28. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to be doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID epidemic in the US in which rapid spread across the US are combined with a large population of infected patients with presumably mild-to-moderate clinical symptoms. We emphasize the importance of testing these findings with seroprevalence data, and discuss the broader potential to use syndromic time series for early detection and understanding of emerging infectious diseases.


title: Depression and anxiety during 2019 coronavirus disease pandemic in Saudi Arabia: a cross-sectional study

text: Background: COVID 19 outbreak in 2020 was associated with a high rate of depression and anxiety among individuals in the affected countries. The aim of this study is to explore the influence of the COVID 19 epidemic on the psychological distress of residents of the Kingdom of Saudi Arabia. Methods: A cross sectional study using an online survey was conducted in Saudi Arabia between 27th of March and 27th of April 2020. The Patient Health Questionnaire (PHQ 9) and Generalized Anxiety Disorder-7 (GAD 7) were used to assess depression and anxiety. Logistic regression analysis was used to identify predictors of depression and anxiety. Results: The prevalence of depression and anxiety among the entire study participants was 9.4% and 7.3%, respectively. Non-Saudi residents, aged 50 years and above, divorced, retired, university students, and those with income (2000 to 10,000 RS) were at higher risk of developing depression. Saudi individuals, married, unemployed, and those with high income (> 10,000 RS) were at higher risk of developing anxiety. Conclusions: There is a wide range of the Saudi residents who are at higher risk of mental illness during COVID 19 pandemic. Policymakers and mental healthcare providers are advised to provide continuous monitoring of the psychological consequences during this pandemic, and provide mental support.


title: SARS-CoV-2 seroprevalence trends in healthy blood donors during the COVID-19 Milan outbreak

text: Objectives: The Milan metropolitan area in Northern Italy was among the most severely hit by the SARS-CoV-2 outbreak. The epidemiological trends of mild COVID-19 are however still unknown. The aim of this study was to examine the seroprevalence of SARS-CoV-2 infection in healthy asymptomatic adults, the risk factors, and laboratory correlates. Design: We conducted a cross-sectional study during the outbreak. Presence of anti-SARS-CoV-2 IgM/IgG antibodies against the Nucleocapsid protein was assessed by a lateral flow immunoassay. Setting: Blood center at a leading academic hospital serving as COVID-19 referral center. Participants: We considered a random sample of blood donors since the start of the outbreak (February 24th to April 8th 2020, n=789). Main outcome measures: The main outcome was the prevalence of IgG/IgM anti-SARS-CoV-2 antibodies . Results: The test had a 98.3% specificity and 100% sensitivity, and for IgG was validated in a subset by an independent ELISA against the Spike protein (N=34, P<0.001). At the start of the outbreak, the overall seroprevalence of SARS-CoV-2 was 4.6% (2.3 to 7.9; P<0.0001 vs. 120 historical controls). During the study period characterized by a gradual implementation of social distancing measures, there was a progressive increase in seroprevalence to 7.1% (4.4 to 10.8), due to a rise in IgG+ to 5% (2.8 to 8.2; P=0.004 for trend, adjusted weekly increase 2.7, SE 1.3%), but not of IgM+ (P=NS). At multivariate logistic regression analysis, seroconversion to IgG was more frequent in younger (P=0.043), while recent infections (IgM+) in older individuals (P=0.002). IgM+ was independently associated with higher triglycerides, eosinophils, and lymphocytes (P<0.05). Conclusions: SARS-CoV-2 infection was already circulating in Milan at the outbreak start. Social distancing may have been more effective in younger individuals, and by the end of April 4.4-10.8% of healthy adults had evidence of seroconversion. Asymptomatic infection may affect lipid profile and blood count.


title: Questionnaire assessment helps the self-management of patients with inflammatory bowel disease during the outbreak of Coronavirus Disease 2019

text: Background and Aims: The outbreak of Coronavirus Disease 2019 (COVID-19) may affect the disease status of patients with inflammatory bowel disease (IBD). This study aimed to assess the disease status of IBD patients in Hubei province by questionnaire online and guide to the self-management of IBD patients during this epidemic. Methods: A questionnaire was designed containing the Harvey-Bradshaw Index (HBI), the Partial Mayo Score (PMS), the short inflammatory bowel disease questionnaire (SIBDQ) and distributed to Hubei IBD patients online within one month of traffic control after the outbreak of COVID-19. This questionnaire also included some questions about patients' self-report disease conditions and their epidemiological history of COVID-19. Results: A total of 102 eligible questionnaires were included in the analysis. No patient reported infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in our study. Our result showed that 69.64% of patients with ulcerative colitis (UC) and 80.44% of patients with Crohn's disease (CD) were in remission. There was not a statistically significant difference in the proportion of the active disease stage between the two types of disease (p=0.103). The majority of patients (85.29%) had a good health-related quality of life (HRQoL) (SIBDQ[≥]50). The reduction in physical exercise is a risk factor for worsening in conditions (OR=17.593, 95%CI 2.035 to 152.097, p=0.009). Conclusions: The outbreak of COVID-19 might not have a significant impact on most Hubei IBD patients within one month after the traffic control. The patient's disease condition could be assessed by our questionnaires. Doctors utilized the information and advised for IBD patients about self-management during the period of COVID-19.


title: Male gender and kidney illness associated with an increased risk of severe laboratory-confirmed coronavirus disease

text: Objective: To identify factors predicting severe coronavirus disease 2019 (COVID-19) in adolescent and adult patients with laboratory-positive (quantitative reverse-transcription polymerase chain reaction) infection. Methods: A retrospective cohort study took place, and data from 740 subjects, from all 32 states of Mexico, were analyzed. The association between the studied factors and severe (dyspnea requiring hospital admission) COVID-19 was evaluated through risk ratios (RRs) and 95% confidence intervals (CIs). Results: Severe illness was documented in 28% of participants. In multiple analysis, male gender (RR = 1.13, 95% CI 1.06 - 1.20), advanced age ([reference: 15 - 29 years old] 30 - 44, RR = 1.02, 95% CI 0.94 - 1.11; 45 - 59, RR = 1.26, 95% CI 1.15 - 1.38; 60 years or older, RR = 1.44, 95% CI 1.29 - 1.60), chronic kidney disease (RR = 1.31, 95% CI 1.04 - 1.64) and thoracic pain (RR = 1.16, 95% CI 1.10 - 1.24) were associated with an increased risk of severe disease. Conclusions: To the best of our knowledge, this is the first study evaluating predictors of COVID-19 severity in a large subset of the Latin-American population. It is also the first in documenting gender-related differences regarding the severity of the illness. These results may be useful for health care protocols for the early detection and management of COVID-19 patients that may benefit from opportune and specialized supportive medical treatment.


title: Preface of Special Issue “Cares in the Age of Communication: Health Education and Healthy Lifestyles”: Social Media and Health Communication in a Pandemic?

text: In the midst and the mist of the Covid-19 outbreak, weare living in the age of global communication in a hyperconnected society in which the transmissions channels between people have been changed very clearly due to both the internet itself in general and social networks in particular [ ]


title: 3D Variability Analysis: Directly resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images

text: Proteins are dynamic molecules that constitute the molecular machinery of living cells. Single particle cryo-EM excels as an imaging technique to solve static structures of proteins, but existing computational 3D reconstruction methods for cryo-EM data have not been effective in practice for solving structures or modelling motion of flexible proteins. We introduce 3D variability analysis (3DVA), an algorithm that models the conformational landscape of a molecule as a linear subspace, and is able to fit the model to experimental cryo-EM data at high resolution. 3DVA makes it possible, for the first time, to resolve and visualize detailed molecular motions of both large and small proteins. Through extensive experimental results on cryo-EM data, we demonstrate the ability of 3DVA to resolve multiple flexible motions of α-helices in the sub-50 kDa transmembrane domain of a GPCR complex, bending modes of a sodium ion channel, five types of symmetric and symmetry-breaking flexibility in a proteasome, and large motions in a spliceosome complex. We also show that 3DVA can uncover discrete conformational states of heterogenous mixtures of ribosome particles from a single sample. The results demonstrate that 3DVA enables new biological insight to be extracted from single particle cryo-EM data. 3DVA is implemented in the cryoSPARC software package, and has already been used successfully in several notable structural studies.


Offline: COVID-19—what we can expect to come


title: Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series

text: Background Recent studies have focused initial clinical and Epidemiologic characteristics on the COVID-19, mainly revealing situation in Wuhan, Hubei. Aim To reveal more data on the epidemiologic and clinical characteristics of COVID-19 patients outside of Wuhan, in Zhejiang, China. Design Retrospective case series. Methods 88 cases of laboratory-confirmed and 3 cases of clinical-confirmed COVID-19 were admitted to five hospitals in Zhejiang province, China. Data were collected from 20 January 2020 to 11 February 2020. Results Of all 91 patients, 88 (96.70%) were laboratory-confirmed COVID-19 with throat swab samples that tested positive for SARS-Cov-2 while 3 (3.30%) were clinical-diagnosed COVID-19 cases. The median age of the patients was 50 (36.5-57) years, and female accounted for 59.34%. In this sample 40 (43.96%) patients had contracted the diseases from local cases, 31 (34.07%) patients had been to Wuhan/Hubei, 8 (8.79%) cases had contacted with people from Wuhan, 11 (12.09%) cases were confirmed aircraft transmission. In particular within the city of Ningbo, 60.52% cases can be traced back to an event held in a temple. The most common symptoms were fever (71.43%), cough (60.44%) and fatigue (43.96%). The median of incubation period was 6 (IQR, 3-8) days and the median time from first visit to a doctor to confirmed diagnosis was 1 (1-2) days. According to the Chest computed tomography scans, 67.03% cases had bilateral pneumonia. Conclusions Social activity cluster, family cluster and travel by airplane were how COVID-19 patients get transmitted and could be rapidly diagnosed COVID-19 in Zhejiang.


title: “Identification and enrichment of SECReTE cis-acting RNA elements in the Coronaviridae and other (+) single-strand RNA viruses”

text: cis-acting RNA motifs play a major role in regulating many aspects of RNA biology including posttranscriptional processing, nuclear export, RNA localization, translation and degradation. Here we analyzed the genomes of SARS-CoV-2 and other single-strand RNA (ssRNA) viruses for the presence of a unique cis RNA element called SECReTE. This motif consists of 10 or more consecutive triplet nucleotide repeats where a pyrimidine nucleotide (C or U) in present every third base, and which we identified in mRNAs encoding secreted proteins in bacteria, yeast, and humans. This motif facilitates mRNA localization to the endoplasmic reticulum (ER), along with the enhanced translation and secretion of translated protein. We now examined for SECReTE presence in Group IV and V RNA viruses, the former including the Coronaviridae, like SARS-CoV-2 and other positive (+)ssRNA viruses, and the latter consisting of negative (-) ssRNA viruses. Interestingly, the SARS-CoV-2 genome contains 40 SECReTE motifs at an abundance of ~1.3 SECReTEs/kilobase (kb). Moreover, all ssRNA viruses we examined contain multiple copies of this motif and appears in (+)ssRNA viruses as non-random in occurrence and independent of genome length. Importantly, (+)ssRNA viruses (e.g. Coronaviruses and Hepaciviruses), which utilize ER membranes to create double membrane vesicles to serve as viral replication centers (VRCs), contain more SECReTE motifs per kb as compared to (−)ssRNA viruses (e.g. Rabies, Mumps, and Influenza), that replicate in the nucleus or the cytoplasm, or other (+)ssRNA viruses (e.g. Enteroviruses and Flaviviruses) which employ different organellar membranes. As predicted by our earlier work, SECReTE sequences are mostly found in membranal or ER-associated/secreted proteins. Thus, we propose that SECReTE motifs could be important for the efficient translation and secretion of secreted viral proteins, as well as for VRC formation. Future studies of SECReTE function and identification of SECReTE-binding proteins could provide new drug targets to treat COVID-19 and other (+)ssRNA related diseases.


title: Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study

text: Background Novel coronavirus (SARS-CoV-2) infects human lung tissue cells through angiotensin-converting enzyme-2 (ACE2), and the body sodium is an important factor for regulating the expression of ACE2. Through a systematic review, meta-analysis and retrospective cohort study, we found that the low blood sodium population may significantly increase the risk and severity of SARS-CoV-2 infection. Methods We extracted the data of serum sodium concentrations of patients with COVID-19 on admission from the articles published between Jan 1 and April 28, 2020, and analyzed the relationship between the serum sodium concentrations and the illness severity of patients. Then we used a cohort of 244 patients with COVID-19 for a retrospective analysis. Results We identified 36 studies, one of which comprised 2736 patients.The mean serum sodium concentration in patients with COVID-19 was 138.6 mmol/L, which was much lower than the median level in population (142.0). The mean serum sodium concentration in severe/critical patients (137.0) was significantly lower than those in mild and moderate patients (140.8 and 138.7, respectively). Such findings were confirmed in a retrospective cohort study, of which the mean serum sodium concentration in all patients was 137.5 mmol/L, and the significant differences were found between the mild (139.2) and moderate (137.2) patients, and the mild and severe/critical (136.6) patients. Interestingly, such changes were not obvious in the serum chlorine and potassium concentrations. Conclusions The low sodium state of patients with COVID-19 may not be the consequence of virus infection, but could be a physiological state possibly caused by living habits such as low salt diet and during aging process, which may result in ACE2 overexpression, and increase the risk and severity of COVID-19. These findings may provide a new idea for the prevention and treatment of COVID-19.


title: Acetylcholine regulates pulmonary inflammation and facilitates the transition from active immunity to tissue repair during respiratory viral infection

text: Inflammatory control is critical to recovery from respiratory viral infection. Acetylcholine (ACh) secreted from non-neuronal sources, including lymphocytes, plays an important, albeit underappreciated, role in regulating immune-mediated inflammation. This study was designed to explore the role of ACh in acute viral infection and recovery. Using the murine model of influenza A, cholinergic status in the lungs and airway was examined over the course of infection and recovery. The results showed that airway ACh remained constant through the early stage of infection and increased during the peak of the acquired immune response. As the concentration of ACh increased, cholinergic lymphocytes appeared in the airway and lungs. Cholinergic capacity was found primarily in CD4 T cells, but also in B cells and CD8 T cells. The cholinergic CD4+ T cells bound to influenza-specific tetramers at the same frequency as their conventional (i.e., non-cholinergic) counterparts. In addition, they were retained in the lungs throughout the recovery phase and could still be detected in the resident memory regions of the lung up to two months after infection. Histologically, cholinergic lymphocytes were found in direct physical contact with activated macrophages throughout the lung. When ACh production was inhibited, mice exhibited increased tissue inflammation, altered lung architecture, and delayed recovery. Together, these findings point to a previously unrecognized role for ACh in the transition from active immunity to recovery and pulmonary repair following respiratory viral infection.


title: Global health security capacity against COVID-19 outbreak and its association with the case fatality rate: an analysis of annual data from 210 countries and territories

text: Background: Because infectious diseases, such as COVID-19, do not have specific boundaries, all countries must prioritize and use the necessary capabilities to prevent, detect, and respond quickly to public health emergencies. In this context, we aimed to review most recent GHS index annual report to observe the regional and global level of health security against COVID-19 outbreak, as well as their relationship with case fatality rate, among 210 countries and territories worldwide. Methods: We reviewed and analyzed October 2019 GHS index co-leaders joint report, to review health security capacities on the basis of the GHS index in the context of six categories. we prioritized not only the capacities of 210 countries and territories around the world using the GHS Index, but also the existence of functional, tested, proven capabilities for stopping outbreaks at the source. Data were collected from global databases including Worldometer, WHO, and Disease Control and Prevention Center (CDC). Findings: This study recruited data on 210 countries and territories, of which up to 14 April 2020, 72 countries (34.28%) with more than 1000 total COVID-19 cases were presents. In most prepared group, number of total COVID-19 diagnostic tests had a significant positive relation with GHS index (r=0.713; p=0.006). Case fatality rate was directly associated with the detection index (r=0.304; p=0.023) in more prepared group. In Lower-middle-income economies group, case fatality rate positively related to detection, response and risk environment indices. Implementation: With the exception of a very small number, countries that were ranked as most prepared countries, they were more likely to be affected by the COVID-19 outbreak of the virus and its health consequences, and needed to seriously reconsider their capabilities and health security in the context of detection, prevention, rapid response, health system facilities, and risk environment against disease outbreak


title: Population based estimates of comorbidities affecting risk for complications from COVID-19 in the US

text: We used 2017 Behavioral Risk Factor Surveillance System (BRFSS) data (N=444,649) to estimate the proportion of US adults who report comorbidities that suggest heightened risk of complications from COVID-19. Co-morbidities included cardiovascular disease, chronic obstructive pulmonary disease (COPD), diabetes, asthma, hypertension, and/or cancer other than skin, based on data from China. Overall 45.4% (95% CI 45.1-45.7) of adults reported any of the 6 comorbidities, increasing from 19.8% (19.1-20.4) for ages 18-29 years to 80.7% (79.5-81.8) for ages 80+ years. State rates ranged from 37.3% (36.2-38.5) in Utah to 58.7% (57.0-60.4) in West Virginia. Rates also varied by race/ethnicity, health insurance status, and employment. Excluded were residents of nursing homes or assisted living facilities. Although almost certainly an underestimate of all adults at risk due to these exclusions, these results should help in estimating healthcare needs for adults with COVID-19 complications living in the community.


title: Generalized logistic growth modeling of the COVID-19 outbreak in 29 provinces in China and in the rest of the world

text: Background: the COVID-19 has been successfully contained in China but is spreading all over the world. We use phenomenological models to dissect the development of the epidemics in China and the impact of the drastic control measures both at the aggregate level and within each province. We use the experience from China to analyze the calibration results on Japan, South Korea, Iran, Italy and Europe, and make future scenario projections. Methods: we calibrate the logistic growth model, the generalized logistic growth model, the generalized growth model and the generalized Richards model to the reported number of infected cases from Jan. 19 to March 10 for the whole of China, 29 provinces in China, four severely affected countries and Europe as a whole. The different models provide upper and lower bounds of our scenario predictions. Results: We quantitatively document four phases of the outbreak in China with a detailed analysis on the heterogenous situations across provinces. Based on Chinese experience, we identify a high risk in Japan with estimated total confirmed cases as of March 25 being 1574 (95% CI: [880, 2372]), and 5669 (95% CI: [988, 11340]) by June. For South Korea, we expect the number of infected cases to approach the ceiling, 7928 (95% CI: [6341, 9754]), in 20 days. We estimate 0.15% (95% CI: [0.03%, 0.30%]) of Italian population to be infected in a positive scenario. We would expect 114867 people infected in Europe in 10 days, in a negative but probable scenario, corresponding to 0.015% European population. Conclusions: The extreme containment measures implemented by China were very effective with some instructive variations across provinces. For other countries, it is almost inevitable to see the continuation of the outbreak in the coming months. Japan and Italy are in serious situations with no short-term end to the outbreak to be expected. There is a significant risk concerning the upcoming July 2020 Summer Olympics in Tokyo. Iran's situation is highly uncertain with unclear and negative future scenarios, while South Korea is approaching the end of the outbreak. Both Europe and the USA are at early stages of the outbreak, posing significant health and economic risks to the world in absence of serious measures.


title: Influence of conflicts of interest on public positions in the COVID-19 era, the case of Gilead Sciences

text: Fundings and gifts from the pharmaceutical industry have an influence on the decisions made by physicians and medical experts In the context of the COVID-19 epidemic, several treatments are available to treat patients infected with the virus Some are protected by patents, such as remdesivir, others are not, such as hydroxychloroquine We wanted to observe the possible correlation between the fact, for an academic doctor in infectious diseases, of having benefited from funding by Gilead Sciences, producer of remdesivir, and the public positions taken by this doctor towards hydroxychloroquine Our results show a correlation (correlation coefficient = 1) between the amount received from the Gilead Sciences company and public opposition to the use of hydroxychloroquine in France This should open up the debate on the role of the interest links of doctors with pharmaceutical companies in the medical and scientific public debate


title: Combined mobile-phone and social-media sampling for web survey on social effects of COVID-19 in spain

text: To minimize coverage and participation biases, this web survey adopted two complementary sampling strategies: (a) SMS invitations to random-number mobile phones, and (b) Internet advertisements targeting specific sociodemographic groups. This combination of aleatory selection from a rather comprehensive sampling frame, on one hand, and responsive definition of target profiles, on the other, largely succeeded in adjusting the sample to relevant population parameters, albeit with the noteworthy exception of education level.


From the EditorCommentary: Addressing Inequities in the Era of COVID-19: The Pandemic and the Urgent Need for Critical Race Theory


docid: udxvhano

title: Turkish medical oncology society covid-19 pandemic advisory board recommendations for cancer patients and medical oncologist


title: COVID-19: How to Relax Social Distancing If You Must

text: Following the April 16, 2020 release of the Opening Up America Again guidelines for relaxing COVID-19 social distancing policies, local leaders are concerned about future pandemic waves and lack robust strategies for tracking and suppressing transmission. Here, we present a framework for monitoring COVID-19 hospitalization data to project risks and trigger shelter-in-place orders to prevent overwhelming healthcare surges while minimizing the duration of costly lockdowns. Assuming the relaxation of social distancing increases the risk of infection ten-fold, the optimal strategy for Austin, Texas--the fastest-growing large city in the US--will trigger a total of 135 [90% prediction interval: 126-141] days of sheltering, allow schools to open in the fall, and result in an expected 2929 deaths [90% prediction interval: 2837-3026] by September 2021, which is 29% the annual mortality rate. In the months ahead, policy makers are likely to face difficult choices and the extent of public restraint and cocooning of vulnerable populations may save or cost thousands of lives.


title: IgA dominates the early neutralizing antibody response to SARS-CoV-2

text: A major dogma in immunology has it that the IgM antibody response precedes secondary memory responses built on the production of IgG, IgA and, occasionaly, IgE. Here, we measured acute humoral responses to SARS-CoV-2, including the frequency of antibody-secreting cells and the presence of specific, neutralizing, antibodies in serum and broncho-alveolar fluid of 145 patients with COVID-19. Surprisingly, early SARS-CoV-2-specific humoral responses were found to be typically dominated by antibodies of the IgA isotype. Peripheral expansion of IgA-plasmablasts with mucosal-homing potential was detected shortly after the onset of symptoms and peaked during the third week of the disease. While the specific antibody response included IgG, IgM and IgA, the latter contributed to a much larger extent to virus neutralization, as compared to IgG. However, specific IgA serum levels notably decrease after one month of evolution. These results represent a challenging observation given the present uncertainty as to which kind of humoral response would optimally protect against re-infection, and whether vaccine regimens should consider boosting a potent, although, at least in blood, fading IgA response.


title: Prevalence of SARS-CoV-2 infection in the Luxembourgish population: the CON-VINCE study.

text: BACKGROUND: After the World Health Organization declared the outbreak of coronavirus disease to be a public health emergency of international concern on January 30, 2020, the first SARS-CoV-2 infection was detected in Luxembourg on February 29, 2020. Representative population-based data, including asymptomatic individuals for assessing the viral spread and immune response were, however, lacking worldwide. METHODS: Using a panel-based method, we implemented a representative sample of the Luxembourgish population based on age, gender and residency for testing for SARS-CoV-2 infection and antibody status in order to define prevalence irrespective of clinical symptoms. Participants were contacted via email to fill an online questionnaire before biosampling at local laboratories. All participants provided information related to clinical symptoms, epidemiology, socioeconomic and psychological assessments and underwent biosampling, rRT-PCR testing and serology for SARS-CoV-2. RESULTS: We included a total of 1862 individuals in our representative sample of the general Luxembourgish population. Of these, 5 individuals had a current positive result for infection with SARS-CoV-2 based on rRT-PCR. Four of these individuals were oligosymptomatic and one was asymptomatic. Overall we found a positive IgG antibody status in 35 individuals (1.97%), of which 11 reported to be tested positive by rRT-PCR for SARS-CoV-2 previously and showed in addition their IgG positive status also a positive status for IgA. Our data indicate a prevalence of 0.3% for active SARS-CoV-2 infection and an infection rate of 2.15% in the Luxembourgish population between 18 and 79 years of age. CONCLUSIONS: Luxembourgish residents show a low rate of acute infections after 7 weeks of confinement and present with an antibody profile indicative of a more recent immune response to SARS-CoV-2. All infected individuals were oligo- or asymptomatic. Bi-weekly follow-up visits over the next 2 months will inform about the viral spread by a- and oligosymptomatic carriers and the individual changes in the immune profile.


title: Chloroquine, but not hydroxychlorquine, prolongs the QT interval in a primary care population

text: Background: Chloroquine (CQ) and Hydroxychloroquine (HCQ) have recently been suggested as treatment for the current Corona Virus Disease 2019 (COVID-19) pandemic. However, despite their long-term use and only few case reports on adverse effects, CQ and HCQ are listed as a known risk of the lethal ventricular arrhythmia Torsade de Pointes and their cardiac safety profile is being questioned. Thus, we aimed to investigate the electrocardiographic and mortality effects of CQ and HCQ in a primary care population. Methods: We used Danish health care registers and electrocardiograms (ECGs) from primary care to define three studies. 1) A paired study of subjects with ECGs before and during use of CQ/HCQ, 2) a matched ECG study of subjects taking CQ/HCQ compared to controls, and 3) a mortality study on people taking HCQ matched to control. In both matched studies, we adjusted for connective tissue diseases, use of QT-prolonging drugs, and cardiac disease. We used the QTc interval as the marker for electrocardiographic safety. In the mortality study, cases were followed from first claimed prescription until 300 days after estimated completion of the last prescription. 95% confidence intervals follow estimates in parenthesis. Results: Use of CQ was associated with a 5.5 (0.7;10) ms increase in QTc in the paired study (n=10). In the matched study (n=28, controls=280), QTc was insignificantly increased in subjects taking CQ by 4.7 (-3.4;13) ms. With a {Delta}QTc of 1.0 (-5.6;7.5), use of HCQ was not associated with an increased QTc in the paired study (n=32). In the matched study (n=172, controls=1,720), QTc also was not different between groups (p=0.5). In the mortality study (n=3,368), use of HCQ was associated with a hazard ratio of 0.67 (0.43;1.05). Conclusions: In subjects free of COVID-19, we found a small increase in QTc associated with use of chloroquine, but not hydroxychloroquine. We found no increased mortality associated with use of hydroxychloroquine.


title: Physical activity levels and related energy expenditure during COVID-19 quarantine among the sicilian active population: A cross-sectional online survey study

text: Background: During the coronavirus disease 2019 (COVID-19) pandemic, the Italian government has adopted containment measures to control the virus's spread, including limitations to the practice of physical activity (PA). The aim of this study was to estimate the levels of PA, expressed as energy expenditure (MET-minute/week), among the physically active Sicilian population before and during the last seven days of the COVID-19 quarantine. Furthermore, the relation between this parameter and specific demographic and anthropometric variables was analyzed. Methods: 802 Sicilian physically active participants (mean age: 32.27 ± 12.81 years; BMI: 23.44 ± 3.33 kg/m2) were included in the study and grouped based on gender, age and BMI. An adapted version of the International Physical Activity Questionnaire-short form (IPAQ-SF) was administered to the participants through an online survey. The Wilcoxon signed-rank test and the Kruskal-Wallis rank-sum test were used for statistical analyses. Results: As expected, we observed a significant decrease of the total weekly energy expenditure during the COVID-19 quarantine (p < 0.001). A significant variation in the MET-min/wk in the before quarantine condition (p = 0.046) and in the difference between before and during quarantine (p = 0.009) was found for males and females. The male group decreased the PA level more than the female one. Moreover, a significant difference in the MET-min/wk was found among groups distributions of BMI (p < 0.001, during quarantine) and of age (p < 0.001, both before and during quarantine). In particular, the highest and the lowest levels of PA were reported by the young and the elderly, respectively, both before and during quarantine. Finally, the overweight group showed the lowest level of PA during quarantine. Conclusion: Based on our outcomes, we can determine that the current quarantine has negatively affected the practice of PA, with greater impacts among males and overweight subjects. In regards to different age groups, the young, young adults and adults were more affected than senior adults and the elderly.


title: In Vitro Inhibition of SARS-CoV-2 Infection by Bovine Lactoferrin

text: Since its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing a serious threat to public health worldwide as the causative agent of coronavirus disease 2019 (COVID-19). Now distributed in a pandemic pattern, this disease still lacks an effective drug treatment with low toxicity, leading pharmaceutical companies and research labs to work against time to find a candidate molecule to efficiently treat the affected patients. Due to the well-known broad-spectrum antimicrobial activity of the lactoferrin protein, we sought to verify whether its bovine form (bLf) would also be effective in vitro against SARS-CoV-2. Using an antiviral assay based on quantitative reverse transcription-polymerase chain reaction (qRT-PCR), we found that bLf reduced progeny virus yield by up to ∼84,6% in African green monkey kidney epithelial cells (Vero E6) and ∼68,6% in adenocarcinomic human alveolar basal epithelial cells (A549) at 1 mg/mL, a concentration previously shown to have low cytotoxicity. Therefore, our preliminary data suggest that bLf has the potential to constitute a biochemical approach to fight the new coronavirus pandemic.


title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals

text: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a wide range of systemic manifestations. Several observations support a role for vascular endothelial dysfunction in the pathogenesis including an increased incidence of thrombotic events and coagulopathy and the presence of vascular risk factors as an independent predictor of poor prognosis. It has recently been reported that endothelitis is associated with viral inclusion bodies suggesting a direct role for SARS-CoV-2 in the pathogenesis. The ACE2 receptor has been shown to mediate SARS-CoV-2 uptake and it has been proposed that CD147 (BSG) can function as an alternative cell surface receptor. To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). We found that CD147 (BSG) but not ACE2 is detectable in vascular endothelial cells within single cell sequencing datasets derived from multiple tissues in healthy individuals. This implies that either ACE2 is not expressed in healthy tissue but is instead induced in response to SARS-Cov2 or that SARS-Cov2 enters endothelial cells via an alternative receptor such as CD147.


title: Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis

text: To reveal the detailed spread dynamics of SARS-CoV-2 epidemic in China, a phylogenetic analysis was performed by the Bayesian inference framework tool. 233 strains were retrieved from confirmed cases in China until March 31, 2020. The tMRCA of SARS-CoV-2 strains in China could be traced back to December 9, 2019. According to the effective population size curve reconstructed by Skyline model, this research revealed the influence of travel ban measures on the effective population size in China. Furthermore, we divided the epidemic process of SARS-CoV-2 in China into 4 stages according to the effective population size curve. With the Bayesian stochastic search variable selection method, phylogeographical reconstruction detailedly described the geographic spread behavior of SARS-CoV-2 in each stage and confirmed the importance of travel ban in blocking SARS-CoV-2 cross-regional spread. This article summarizes the influence of prevention and control measures in China, which has a positive impact on the world.


Introducing special cutaneous “sign” tribute to healthcare workers managing new coronavirus disease (Covid −19)


Coronavirus hält Weltkonjunktur in Atem


title: Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data

text: The surfaces of proteins are generally hydrophilic but there have been reports of sites that exhibit an exceptionally high affinity for individual water molecules. Not only do such molecules often fulfil critical biological functions, but also, they may alter the binding of newly designed drugs. In crystal structures, sites consistently occupied in each unit cell yield electron density clouds that represent water molecule presence. These are recorded in virtually all high-resolution structures obtained through X-ray diffraction. In this work, we utilized the wealth of data from the RCSB Protein Data Bank to train a residual deep learning model named ‘hotWater’ to identify sites on the surface of proteins that are most likely to bind water, the so-called water hot spots. The model can be used to score existing water molecules from a PDB file to provide their ranking according to the predicted binding strength or to scan the surface of a protein to determine the most likely water hot-spots de novo. This is computationally much more efficient than currently used molecular dynamics simulations. Based on testing the model on three example proteins, which have been resolved using both high-resolution X-ray crystallography (providing accurate positions of trapped waters) as well as low-resolution X-ray diffraction, NMR or CryoEM (where structure refinement does not yield water positions), we were able to show that the hotWater method is able to recover in the “water-free” structures many water binding sites known from the high-resolution structures. A blind test on a newly solved protein structure with waters removed from the PDB also showed good prediction of the crystal water positions. This was compared to two known algorithms that use electron density and was shown to have higher recall at resolutions >2.6 Å. We also show that the algorithm can be applied to novel proteins such as the RNA polymerase complex from SARS-CoV-2, which could be of use in drug discovery. The hotWater model is freely available at (https://pypi.org/project/hotWater/).


title: Correction to: The Perfect Moral Storm: Diverse Ethical Considerations in the COVID-19 Pandemic

text: Regrettably, in the original version of this article the name of one of the authors was spelt incorrectly. “Li Yan Hsu” should be “Li Yang Hsu”. Li Yang Hsu is affiliated with the Saw Swee Hock School of Public Health, National University of Singapore, Singapore AND the Yong Loo Lin School of Medicine, National University of Singapore, Singapore.


Respiratory mucus and persistence of virus on surfaces