title: Estimating the undetected infections in the Covid-19 outbreak by harnessing capture-recapture methods

text: A major open question, affecting the policy makers decisions, is the estimation of the true size of COVID-19 infections. Most of them are undetected, because of a large number of asymptomatic cases. We provide an efficient, easy to compute and robust lower bound estimator for the number of undetected cases. A "modified" version of the Chao estimator is proposed, based on the cumulative time-series distribution of cases and deaths. Heterogeneity has been accounted for by assuming a geometrical distribution underlying the data generation process. An (approximated) analytical variance formula has been properly derived to compute reliable confidence intervals at 95%. An application to Austrian situation is provided and results from other European Countries are mentioned in the discussion.


The Battle Against COVID-19: Where Do We Stand Now?


title: Using nucleocapsid proteins to investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses

text: An initial outbreak of coronavirus disease 2019 (COVID-19) in China has resulted in a massive global pandemic causing well over 10,000,000 cases and 500,000 deaths worldwide. The virus responsible, SARS-CoV-2, has been found to possess a very close association with Bat-CoV RaTG13 and Pangolin-CoV MP789. The nucleocapsid protein can serve as a decent model for determining phylogenetic, evolutionary, and structural relationships between coronaviruses. Therefore, this study uses the nucleocapsid gene and protein to further investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses. Sequence and phylogenetic analyses have revealed the nucleocapsid gene and protein in SARS-CoV-2 are both closely related to those found in Bat-CoV RaTG13 and Pangolin-CoV MP789. Evidence of recombination was detected within the N gene, along with the presence of a double amino acid insertion found in the N-terminal region. Homology modeling for the N-Terminal Domain revealed similar structures but distinct electrostatic surfaces and topological variations in the β-hairpin that likely reflect specific adaptive functions. In respect to SARS-CoV-2, two amino acids (37S and 267A) were found to exist only in its N protein, along with an extended β-hairpin in the N-Terminal Domain. Collectively, this study strengthens the relationship among SARS-CoV-2, Bat-CoV RaTG13, and Pangolin-CoV MP789, providing additional insights into the structure and adaptive nature of the nucleocapsid protein found in these coronaviruses. Furthermore, this data will help enhance our understanding of the complete history behind SARS-CoV-2 and help assist in antiviral and vaccine development.


title: Characterizing and Forecasting Emergency Department Visits Related to COVID-19 Using Chief Complaints and Discharge Diagnoses

text: In response to the unprecedented public health challenge posed by the SARS CoV-2 virus (COVID-19) in the United States, we and our colleagues at the Johns Hopkins University Applied Physics Laboratory (JHU/APL) have developed a model of COVID-19 progression using emergency department (ED) visit data from the National Capital Region (NCR). We obtained ED visits counts through targeted queries of the NCR Electronic Surveillance System for the Early Notification of Community-Based Epidemics (ESSENCE). To focus on ED visits by COVID-19 patients, we adjusted the query results for typical ED visit volumes and for reductions in ED volumes due to COVID-19 precautions. With these ED visit data, we fitted a logistic growth model to characterize and forecast the increase in cumulative COVID-19 ED visits. Our model achieves the best fit when we assume that the first NCR visit occurred in early January. We estimate that approximately 15,000 COVID-19 ED visits occurred prior to May 2020 and that approximately 17,000 more visits will occur in subsequent months. We plan to deploy an operational pilot of this model in the NCR ESSENCE environment, assisting local public health authorities as they brace for a second wave of COVID-19. Additionally, we will iteratively assess potential model refinements, aiming to maximize the relevance of our model for the situational awareness and decision-making of local public health authorities.


New security feature for patient management software


title: CORRELATION BETWEEN CHEST COMPUTED TOMOGRAPHY AND LUNG ULTRASONOGRAPHY IN PATIENTS WITH CORONAVIRUS DISEASE 2019 (COVID-19)

text: INTRODUCTION: There is growing evidence regarding the imaging findings of Coronavirus Disease 2019 (COVID-19), in chest X-ray and Computed Tomography scan (CT). At this moment, the role of Lung Ultrasonography (LUS) has yet to be explored. OBJECTIVES: The main purpose of this study is to evaluate the correlation between LUS findings and chest CT in confirmed (positive RT-PCR) or clinically highly suspicious (dyspnea, fever, myasthenia, gastrointestinal symptoms, dry cough, ageusia or anosmia) of COVID-19 patients. METHODS: Prospective study carried out in the emergency department (ED) of confirmed or clinically highly suspicious COVID-19 patients who were subjected to a chest CT and concurrent LUS exam. An experienced ED physician performed the LUS exam blind to the clinical history and results of the CT scan, which were reviewed by two radiologists in consensus for signs compatible with COVID-19 (bilateral ground-glass opacities in peripheral distribution). Compatible LUS exam was considered a bilateral pattern of B-lines, irregular pleural line and subpleural consolidations. RESULTS: Between March and April 2020, fifty-one patients were consecutively enrolled. The indication for CT was a negative or indeterminate RT-PCR test (49.0%) followed by suspicion of pulmonary embolism (41.2%). Radiological signs compatible with COVID-19 were present in thirty-seven patients (72.5%) on CT scan and forty patients (78.4%) on LUS exam. The presence of LUS findings was correlated with a positive CT scan suggestive of COVID-19 (OR: 13.3, 95%CI: 4.5-39.6, p<0.001) with a sensitivity of 100.0% and a specificity of 78.6%, positive predictive value of 92.5% and negative of 100.0%. There was no missed diagnosis of COVID-19 with LUS compared to CT in our cohort. The LUS Score had a good correlation with CT total severity score (ICC 0.803, 95% CI 0.60-0.90, p<0.001). CONCLUSION: LUS presents similar accuracy compared to chest CT to detect lung abnormalities in COVID-19 patients.


Gotcha! Coronavirus, Crises and the Politics of Blame Games


title: Mathematical Analysis of a COVID-19 Epidemic Model by using Data Driven Epidemiological Parameters of Diseases Spread in India

text: This paper attempts to describe the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or named as novel coronavirus (COVID-19) via an epidemic model. This dangerous virus has dissimilar effects in different countries in the world. It is observable that the number of new active coronavirus cases is increasing day by day across the globe. India is now in the second stage of COVID-19 spreading, and as a densely populated country, it will be an epidemic very quickly if proper protection / strategies are not under-taken based on the database of the transmission of the disease. This paper is using the current data of COVID-19 for the mathematical modeling and its dynamical analysis. As an alternative of the standard SEIR model, we bring in a new representation to appraise and manage the outbreak of infectious disease COVID-19 through SEQIR pandemic model, which is based on the supposition that the infected but undetected by testing individuals are send to quarantine during the incubation period. During the incubation period if any individual be infected by COVID-19, then that confirmed infected individuals are isolated and the necessary treatments are arranged in proper way so that they cannot taint the other residents in the community. Dynamics of the SEQIR model is presented by basic reproduction number R and the comprehensive stability analysis. Numerical results are depicted through apt graphical appearances using the data of five states and India.


title: Do Men and Women Lockdown Differently? An Examination of Panamas COVID-19 Sex-Segregated Social Distancing Policy

text: Mobility enables individuals to generate income and is a key input for empowerment and personal autonomy. Curtailment of aggregate social mobility - through policies such as: social distancing recommendations, shelter in place orders and state-enforced lockdowns - has become a primary strategy to address COVID-19 to limit social contact and reduce disease transmission. In this context, a small number of countries have instituted gender or sex-segregated mobility policies (Panama, Peru, and Bogota, Colombia). Through a retrospective analysis of global geographic positioning (GPS) data, this study presents an overview of aggregate mobility in Panama following the countrys implementation of a sex-segregated social distancing policy. Panama was selected as the nationwide sex-segregated policy was enforced throughout the lockdown period. The paper looks at mobility trends on female- and male-sex mobility days, examining differences by volume of movement and type of community locations visited as compared to pre-COVID trends. We find lower visits to all community location categories on female-mobility days. However, we found no significant difference in visits to workplace locations on male- v. female-mobility days. The paper discusses the implications of these findings in three areas: (1) Informal burden of labor and social reproduction, (2) Implications for womens autonomy and safety in the home, and (3) Womens economic empowerment. In addition, it raises open ethical questions regarding gender identity in COVID-19 policies.


title: A model to estimate demand for personal protective equipment for Ontario acute care hospitals during the COVID-19 pandemic

text: In addition to instituting public health measures for COVID-19, managing healthcare resources is important for outcomes. The experiences in Italy and New York have shown that personal protective equipment (PPE) shortages can cause increased morbidity and mortality. We demonstrate a method to predict PPE demand across a health care system.


title: A County-Level Susceptibility Index and Coronavirus Disease 2019 Mortality in the United States: A Socioecological Study

text: As of June 2020, the United States (US) has experienced the highest number of deaths related to coronavirus disease 2019 (Covid-19) in the world, but significant geographic heterogeneity exists at the county-level. Therefore, we sought to classify counties in the United States across multiple domains utilizing a socioecological framework and examine the association between these county-level groups and Covid-19 mortality. We harmonized and linked county-level sociodemographic, health, and environmental metrics associated with increased susceptibility for Covid-19 mortality. Latent class analysis defined a county-level susceptibility index (CSI) based on these metrics (n=2701 counties). Next, we used linear regression models to estimate the associations of the CSI and Covid-19 deaths per capita and initial mortality doubling time (as of 6/2/20), adjusted for days since first Covid-19 case. We identified 4 groups classified by the CSI with distinct sociodemographic, health, and environmental profiles and widespread geographic dispersion. Covid-19 deaths per capita were significantly higher in the group consisting of rural, vulnerable counties (55.8 [95% CI 50.3-61.2] deaths per 100,000) compared with the group with diverse, urban counties (32.2 [27.3-37.0]) at similar points in the outbreak (76 days since first case). Our findings can inform equitable resource allocation for Covid-19 to allow targeted public health preparedness and response in vulnerable counties.


title: Many brains are better than one: the importance of interdisciplinary studies on COVID-19 in and beyond tourism

text: As the COVID-19 outbreak expands across the globe, researchers in both the medical and health sciences and social sciences continue to share timely insight meant to enlighten all sectors of society. In this paper, a cross-disciplinary team of tourism and public health academics critically consider how these and other seemingly disparate research domains can cooperate on timely research endeavours, including but not limited to COVID-19. This article provides a brief overview of the intricacies of interdisciplinary work. We then discuss some of the diverse challenges and benefits of cross-disciplinary research. Future interdisciplinary research collaboration opportunities regarding COVID-19, within and outside tourism, are also proposed. Our conclusions should promote multidisciplinary research into global health problems as a way to enhance social welfare.


title: Self-amplifying RNA SARS-CoV-2 lipid nanoparticle vaccine induces equivalent preclinical antibody titers and viral neutralization to recovered COVID-19 patients

text: The spread of the SARS-CoV-2 into a global pandemic within a few months of onset motivates the development of a rapidly scalable vaccine. Here, we present a self-amplifying RNA encoding the SARS-CoV-2 spike protein encapsulated within a lipid nanoparticle as a vaccine and demonstrate induction of robust neutralization of a pseudo-virus, proportional to quantity of specific IgG and of higher quantities than recovered COVID-19 patients. These data provide insight into the vaccine design and evaluation of immunogenicity to enable rapid translation to the clinic.


title: COVID-19-associated ARDS treated with DEXamethasone (CoDEX): Study design and rationale for a randomized trial.

text: OBJECTIVES: The infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) spreads worldwide and is considered a pandemic. The most common manifestation of SARS-CoV2 infection (Coronavirus disease 2019 - COVID-19) is viral pneumonia with varying degrees of respiratory compromise and up to 40% of hospitalized patients might develop Acute Respiratory Distress Syndrome (ARDS). Several clinical trials evaluated the role of corticosteroids in non-COVID-19 ARDS with conflicting results. We designed a trial to evaluate the effectiveness of early intravenous dexamethasone administration on the number of days alive and free of mechanical ventilation within 28 days after randomization in adult patients with moderate or severe ARDS due to confirmed or probable COVID-19. METHODS: This is a pragmatic, prospective, randomized, stratified, multicenter, open-label, controlled trial including 350 patients with early-onset (less than 48h before randomization) moderate or severe ARDS, defined by the Berlin criteria, due to COVID-19. Eligible patients will be randomly allocated to either standard treatment plus dexamethasone (intervention group) or standard treatment without dexamethasone (control group). Patients in the intervention group will receive dexamethasone 20mg IV once daily for 5 days, followed by dexamethasone 10mg IV once daily for additional 5 days or until Intensive Care Unit (ICU) discharge, whichever occurs first. The primary outcome is ventilator-free days within 28 days after randomization, defined as days alive and free from invasive mechanical ventilation. Secondary outcomes are all-cause mortality rates at day 28, evaluation of the clinical status at day 15 assessed with a 6-level ordinal scale, mechanical ventilation duration from randomization to day 28, Sequential Organ Failure Assessment (SOFA) Score evaluation at 48h, 72h and 7 days and ICU-free days within 28. ETHICS AND DISSEMINATION: This trial was approved by the Brazilian National Committee of Ethics in Research (Comissao Nacional de Etica em Pesquisa - CONEP) and National Health Surveillance Agency (ANVISA). An independent data monitoring committee will perform interim analyses and evaluate adverse events throughout the trial. Results will be submitted for publication after enrolment and follow-up are complete.


title: Infodemiological Study Using Google Trends on Coronavirus Epidemic in Wuhan, China

text: The recent emergence of a new coronavirus (COVID-19) has gained a high cover in public media and worldwide news. The virus has caused a viral pneumonia in tens of thousands of people in Wuhan, a central city of China. This short paper gives a brief introduction on how the demand for information on this new epidemic is reported through Google Trends. The reported period is 31 December 2020 to 20 March 2020. The authors draw conclusions on current infodemiological data on COVID-19 using three main search keywords: coronavirus, SARS and MERS. Two approaches are set. First is the worldwide perspective, second - the Chinese one, which reveals that in China this disease in the first days was more often referred to SARS then to general coronaviruses, whereas worldwide, since the beginning, it is more often referred to coronaviruses.


title: Cancer immunotherapy does not increase the risk of death by COVID-19 in melanoma patients

text: Background: Covid-19 pandemic by the new coronavirus SARS-Cov-2 has produced devastating effects on the health care system, affecting also cancer patient care. Data about COVID-19 infection in cancer patients are scarce, and they point out a higher risk of complications due to the viral infection in this population. Moreover, cancer treatments could increase viral complications, specially those treatments based on the use of immunotherapy with checkpoints antibodies. There are no clinical data about the safety of immune check point antibodies in cancer patients when they become infected by SARS-CoV-2. As checkpoint inhibitors, mainly anti PD-1 and anti CTLA-4 antibodies, are an effective treatment for most melanoma patients, avoiding their use during the pandemic could lead to a decrease in the chances of curing melanoma. Methods: In Spain we have started a national registry of melanoma patients infected by SARS-Cov-2 since April 1st, 2020. A retrospective analysis of patients included in the Spanish registery has been performed weekly since the activation of the study. Interim analysis shows unexpected findings about cancer treatment safety in SARS-Cov-2 infected melanoma patients, so a rapid communication to the scientific community is mandatory Results: Fifty patients have been included as of May 17th, 2020. Median age is 69 years (range 6 to 94 years), 27 (54%) patients are males and 36 (70%) patients have stage IV melanoma. Twenty-two (44%) patients were on active anticancer treatment with anti PD-1 antibodies, 16 (32%) patients were on treatment with BRAF plus MEK inhibitors and 12 (24%) patients were not on active cancer treatment. COVID-19 episode has been resolved in 43 cases, including 30 (70%) patients cured, four (9%) patients that have died due to melanoma progression, and nine (21%) patients that have died from COVID-19. Mortality rates from COVID-19 according to melanoma treatment type were 16%, 15% and 36% for patients on immunotherapy, targeted drugs, and for those that were not undergoing active cancer treatment, respectively. Conclusion: These preliminary findings show that the risk of death in those patients undergoing treatment with anti PD-1 antibodies does not exceed the global risk of death in this population. These results could be relevant in order to select melanoma therapy during the COVID-19 pandemic


title: Meta-regression of COVID-19 prevalence/fatality on socioeconomic characteristics of data from top 50 U.S. large cities

text: To screen potential risk and protective socioeconomic factors for Coronavirus disease 2019 (COVID-19) prevalence and fatality, meta-regression of data from top 50 U.S. large-population cities was performed. The population estimate (in 2019) of each country to which the city belongs was abstracted from the "County Population Totals: 2010-2019." From the "Johns Hopkins Coronavirus Resource Center," the cumulative number of confirmed cases and deaths of COVID-19 in each country was obtained on May 22, 2020. Socioeconomic characteristics of each country were extracted from the "2014-2018 American Community Survey (ACS) 5-Year Data Profile" and "Small Area Income and Poverty Estimates (SAIPE) Program (for 2018)." Radom-effects meta-regression was performed using OpenMetaAnalyst (http://www.cebm.brown.edu/openmeta/index.html). A coefficient (slope of the meta-regression line) for COVID-19 prevalence was significantly negative for male sex, education attainment, computer and Internet use, and private health insurance. Whereas, the coefficient was significantly positive for black race, never matrimony, unemployment, and poverty. In the multivariable model, the coefficient was significantly negative for male sex (P = 0.036) and computer use (P = 0.024), and significantly positive for never matrimony (P < 0.001). A coefficient for COVID-19 fatality was significantly negative for no health insurance, and significantly positive for elderly, unemployment, and public coverage. In the multivariable model, the coefficient was significantly positive for only elderly (P = 0.002). In conclusion, a number of socioeconomic factors, e.g. male sex (negatively for prevalence), elderly (positively for fatality), never matrimony (positively for prevalence), and computer use (negatively for prevalence) may be associated with COVID-19.


title: Robust estimation of diagnostic rate and real incidence of COVID-19 for European policymakers

text: Policymakers need a clear and fast assessment of the real spread of the epidemic of COVID-19 in each of their respective countries. Standard measures of the situation provided by the governments include reported positive cases and total deaths. While total deaths immediately indicate that countries like Italy and Spain have the worst situation as of mid April 2020, on its own, reported cases do not provide a correct picture of the situation. The reason is that different countries diagnose diversely and present very distinctive reported case fatality rate (CFR). The same levels of reported incidence and mortality might hide a very different underlying picture. Here we present a straightforward and robust estimation of the diagnostic rate in each European country. From that estimation we obtain an uniform unbiased incidence of the epidemic. The method to obtain the diagnostic rate is transparent and empiric. The key assumption of the method is that the real CFR in Europe of COVID-19 is not strongly country-dependent. We show that this number is not expected to be biased due to demography nor the way total deaths are reported. The estimation protocol has a dynamic nature, and it has been giving converging numbers for diagnostic rates in all European countries as of mid April 2020. From this diagnostic rate, policy makers can obtain an Effective Potential Growth (EPG) updated everyday providing an unbiased assessment of the countries with more potential to have an uncontrolled situation. The method developed will be used to track possible improvements on the diagnostic rate in European countries as the epidemic evolves.


title: Kidney Allograft Recipients Diagnosed with Coronavirus Disease-2019: A Single Center Report

text: Background: Organ graft recipients receiving immunosuppressive therapy are likely to be at heighted risk for the Coronavirus Disease 2019 (Covid-19) and adverse outcomes including death. It is therefore important to characterize the clinical course and outcome of Covid-19 in this vulnerable population and identify therapeutic strategies that are safe. Methods: We performed a retrospective chart review of 54 adult kidney transplant patients diagnosed with Covid-19 and managed in New York State, the epicenter of Covid-19 pandemic. The patients were evaluated by video visits, phone interviews, or in the Emergency Room for respiratory illness symptoms consistent with Covid-19 from March 13, 2020 to April 20, 2020. Characteristics of the patients were stratified by hospitalization status and disease severity. Clinical course including alterations in immunosuppressive therapy were retrieved from their electronic medical records. Primary outcomes included recovery from Covid-19 symptoms, acute kidney injury, graft failure, and case fatality rate. Results: Of the 54 SARS-Cov-2 positive kidney transplant recipients, 39 with moderate to severe symptoms were admitted and 15 with mild symptoms were managed at home. Hospitalized patients compared to non-hospitalized patients were more likely to be male, of Hispanic ethnicity, and to have cardiovascular disease. At baseline, all but 2 were receiving tacrolimus, mycophenolate mofetil (MMF) and 32 were on a steroid free immunosuppression regimen. Tacrolimus dosage was reduced in 46% of hospitalized patients and maintained at baseline level in the non-hospitalized cohort. Mycophenolate mofetil (MMF) dosage was maintained at the baseline dosage in 11% of hospitalized patients and 64% of non-hospitalized patients, and was stopped in 61% hospitalized patients and 0% in the non-hospitalized cohort. Azithromycin or doxycycline were prescribed at a similar rate among hospitalized and non-hospitalized patients (38% vs. 40%). Hydroxychloroquine was prescribed in 79% of hospitalized patients and only one of 15 non-hospitalized patients. Acute kidney injury occurred in 51% of hospitalized patients. Patients with severe disease were more likely to have elevations in inflammatory biomarkers at presentation. At a median of 21 days follow up, 67% of patients have had their symptoms resolved or improved and 33% have persistent symptoms. Graft failure requiring hemodialysis occurred in 3 of 39 hospitalized patients (8%). Three of 39 (8%) hospitalized patients expired and none of the 15 non-hospitalized patients expired. Conclusions: Clinical presentation of Covid-19 in kidney transplant recipients was similar to what has been described in the general population. The case fatality rate in our entire cohort of 54 kidney transplant recipients was reassuringly low and patients with mild symptomology could be successfully managed at home. Data from the pilot study suggest that a strategy of systematic screening and triage to inpatient or outpatient care, close monitoring, and judicious use of immunosuppressive drugs rather than cessation is beneficial.


title: Modeling COVID19 mortality in the US: Community context and mobility matter

text: The United States has become an epicenter for the coronavirus disease 2019 (COVID-19) pandemic. However, communities have been unequally affected and evidence is growing that social determinants of health may be exacerbating the pandemic. Furthermore, the impact and timing of social distancing at the community level have yet to be fully explored. We investigated the relative associations between COVID-19 mortality and social distancing, sociodemographic makeup, economic vulnerabilities, and comorbidities in 24 counties surrounding 7 major metropolitan areas in the US using a flexible and robust time series modeling approach. We found that counties with poorer health and less wealth were associated with higher daily mortality rates compared to counties with fewer economic vulnerabilities and fewer pre-existing health conditions. Declines in mobility were associated with up to 15% lower mortality rates relative to pre-social distancing levels of mobility, but effects were lagged between 25-30 days. While we cannot estimate causal impact, this study provides insight into the association of social distancing on community mortality while accounting for key community factors. For full transparency and reproducibility, we provide all data and code used in this study.


title: Study on active compounds of Yupingfeng San for prevention of coronavirus disease 2019 (COVID-19) based on network pharmacology and molecular docking/ 基于网络药理学和分子对接的玉屏风散预防新型冠状病毒肺炎（COVID-19）活性化合物的研究

text: Objective: To find out the active compounds of Yupingfeng San for the prevention and treatment of the coronavirus pneumoniadisease 2019 (COVID-19) using network pharmacology and molecular docking, with a purpose to find a better clinical use of Yupingfeng San. Methods: The effective ingredients and targets of Astragali Radix, Atractylodis Macrocephalae Rhizoma and Saposhnikoviae Radix were searched from the traditional Chinese medicine system pharmacology analysis platform (TCMSP) website, and the protein and protein interactive network of Yupingfeng San was established using the String database (PPI). Cytoscape 3.6.1 software was used for data analysis to extract the Hub network from the PPI network. The KEGG pathway analysis was performed using the String database and the molecular docking was performed using ChemOffice, PyMOL, and Auto Dock software. Results: A total of 45 effective ingredients were obtained with limited screening conditions [oral bioavailability (OB) ≥ 30%; drug-like (DL) ≥ 0.18], and 345 potential targets and 15 key targets of Yupingfeng San were screened. A total of 50 pathways were obtained by KEGG pathway analysis, among which 25 main pathways were selected, including PIK3R1 target regulation PI3K-Akt signaling pathway, Ras signaling pathway, HIF-1 signaling pathway, and MAPK signaling pathways and T cell receptor signaling pathways. Conclusion: The active compounds in Yupingfeng San can inhibit the combination between SARS-CoV-2 protein and angiotensin-converting enzyme II (ACE2), thus regulating multiple signal pathways (PIK3R1, IGF1R, etc), which plays a role in the prevention of COVID-19.


title: Serial interval of novel coronavirus (2019-nCoV) infections

text: Objective: To estimate the serial interval of novel coronavirus (COVID-19) from information on 28 infector-infectee pairs. Methods: We collected dates of illness onset for primary cases (infectors) and secondary cases (infectees) from published research articles and case investigation reports. We subjectively ranked the credibility of the data and performed analyses on both the full dataset (n=28) and a subset of pairs with highest certainty in reporting (n=18). In addition, we adjusting for right truncation of the data as the epidemic is still in its growth phase. Results: Accounting for right truncation and analyzing all pairs, we estimated the median serial interval at 4.0 days (95% credible interval [CrI]: 3.1, 4.9). Limiting our data to only the most certain pairs, the median serial interval was estimated at 4.6 days (95% CrI: 3.5, 5.9). Conclusions: The serial interval of COVID-19 is shorter than its median incubation period. This suggests that a substantial proportion of secondary transmission may occur prior to illness onset. The COVID-19 serial interval is also shorter than the serial interval of severe acute respiratory syndrome (SARS), indicating that calculations made using the SARS serial interval may introduce bias.


title: Early Hemoglobin kinetics in response to ribavirin: Safety lesson learned from Hepatitis C to CoVID-19 therapy

text: Background: Ribavirin (RBV) is been used for SARS-CoV-2 infection. This drug is associated with a wide range of side effects, mainly anemia, so its use in patients with potential respiratory affectation could not be appropriate. The evidences of adverse events associated with RBV-use has mainly been derived in the context of hepatitis C (HCV) treatment, however the possible use of RBV in CoVID-19 patients could be limited to 14 days. Methods: Longitudinal study including HIV/HCV coinfected patients. We evaluate the hemoglobin dynamics and reductions as well as evaluate the development rate of anemia during the first 2 weeks of therapy in HCV infected patients. Results: 189 patients were included in the study. The median hemoglobin levels were 14.6 g/dL (IQR: 13.2-15.6 g/dL) and 13.5 g/dL (IQR: 12.3-14.5 g/dL) at weeks 1 and 2 of therapy, respectively. A cumulative number of 27 (14.2%) patients developed anemia (23 grade 1 [12.1%] and 4 grade 2 [2.1%]). We identify a baseline hemoglobin levels of 14 g/dL as the better cut-off to identify those patients with a high chance to develop anemia. Of the 132 patients with baseline hemoglobin level >14 g/dL, 8 developed anemia (6.1%) compared with 19 of 57 (33.3%) with hemoglobin levels lower than 14 g/dL (p < 0.001). Conclusions: Our study shows valuable information about the early hemoglobin kinetic timing in patients on RBV-therapy, that could be useful to tailor CoVID-19 treatment if RBV use is considered.


title: Evaluation of COVID-19 RT-qPCR test in multi-sample pools

text: The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented levels. Though diagnostic tests are fundamental to the ability to detect and respond, many health systems are already experiencing shortages of reagents associated with this test. Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts.


title: Advance in research of beta coronavirus receptors on ocular surface/ 眼表β属冠状病毒受体的研究进展

text: 2019-Novel coronavirus (2019-nCoV) caused an outbreak of corona virus disease 2019 (COVID-19) from December 2019 in China.2019-nCoV which was identified as a kind of beta coronavirus belongs to one of four coronavirus genera.Except 2019-nCoV, two other beta coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are also quite harmful to human beings.2019-nCoV uses the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), as SARS-CoV.And dipeptidyl peptidase 4 (DPP4) or CD26 is the cell receptor for MERS-CoV.The expression of ACE2 was found to have obvious positive expression in human corneal and conjunctival epithelium, and corneal endothelium.DPP4 activity was presented in normal animal conjunctival epithelium and fibroblasts of the subjacent connective tissue.It was also presented in the whole corneal epithelium and tear fluid of animal with severe injured corneas.The two receptors, ACE2 and DPP4, are involved in many cellular signaling pathways and pathophysiological processes.Their expression in the cells of ocular surface may be an access route of corona virus in eye, which provides clues to elucidating the pathogenesis of corona virus in the eyeballs.


title: Comprehensive variant and haplotype landscapes of 50,500 global SARS-CoV-2 isolates and accelerating accumulation of country-private variant profiles

text: Understanding the genetic etiology of COVID-19 requires a comprehensive understanding of the variant and haplotype landscape of all reported genomes of SARS-COV-2, the causative virus of the disease. Country-, state/region- and possibly even city-private variant profiles may contribute to varied disease exemplifications and fatality rates observed across the globe along with host factors such as age, ethnicity and comorbidity. The Children’s Hospital of Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) captures up-to-date fulllength SARS-CoV-2 sequences of ~50,500 isolates from GISAID, GenBank, CHLA Center for Personalized Medicine, and other sources (as of June 18, 2020). Among which, 49,637 isolates carry at least one variation from the reference genome NC_045512, a total of 6,070 variants and 2,513 haplotypes were detected in at least three isolates independently. Together, they constituted the most likely SARS-CoV-2 variant and haplotype landscapes world-wide currently. Evidence supporting positive (orf3a, orf8, S genes) and purifying (M gene) selections were detected, which warrants further investigation. Most interestingly, we identified 1,583 countryprivate variants from 10,238 isolates (20.6% overall) reported in 48 countries. 807 countryprivate haplotypes, defined as a haplotype shared by at least 5 isolates all of which came from the same country, were identified in in 8,656 isolates from 39 countries. United Kingdom, USA, and Australia had 464, 166 and 32 private haplotypes respectively, comprising 22.4%, 16.6% and 16.4% of the isolates from each country. Together with their descendent and private haplotypes with fewer members, 22,171 (45.8%) isolates carried country-private haplotypes globally. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions. The localization of the variant profiles appeared to be similarly accelerating from 14.2% in March and 28.4% in April to over 40% isolates carrying the country-private variants around May. In summary, a common pattern is seen world-wide in COVID-19 in which at the onset of disease there appeared to be a significant number of SARS-CoV-2 variants that accumulate quickly and then begin to rapidly coalesce into distinct haplotypes. This may be the result of localized outbreaks due to factors such as multiple points viral introduction, geographic separation and the introduction of policies such as travel restriction, social distancing and quarantine, resulting in the emergence of country-private haplotypes.


La fisioterapia española en tiempos de pandemia del covid19


title: Estimates of the Undetected Rate among the SARS-CoV-2 Infected using Testing Data from Iceland

text: Testing for SARS-CoV-2 in the United States is currently targeted to individuals whose symptoms and/or jobs place them at a high presumed risk of infection. An open question is, what is the share of infections that are undetected under current testing guidelines? To answer this question, we turn to COVID-19 testing data from Iceland. The criteria for testing within the Icelandic medical system, processed by the National University Hospital of Iceland (NUHI), have also been targeted at high-risk individuals, but additionally most Icelanders qualify for voluntary testing through the biopharmaceutical company deCODE genetics. We use results from Iceland's two testing programs to estimate the share of infections that are undetected under standard (NUHI) testing guidelines. Because of complications in the deCODE testing regime, it is not possible to estimate a single value for this this undetected rate; however, a range can be estimated. Our primary estimates for the fraction of infections that are undetected range from 88.7% to 93.6%.


title: UK begins to open up

text: Parts of the UK are set to further lift lockdown restrictions, but a political scandal could put public health at risk, says Penny Sarchet


title: Expected impact of reopening schools after lockdown on COVID-19 epidemic in Ile-de-France

text: As several countries around the world are planning exit strategies to progressively lift the rigid social restrictions implemented with lockdown, different options are being chosen regarding the closure or reopening of schools. We evaluate the expected impact of reopening schools in lIe-de-France region after the withdrawal of lockdown currently scheduled for May 11, 2020. We explore several scenarios of partial, progressive, or full school reopening, coupled with moderate social distancing interventions and large-scale tracing, testing, and isolation. Accounting for current uncertainty on the role of children in COVID-19 epidemic, we test different hypotheses on children's transmissibility distinguishing between younger children (pre-school and primary school age) and adolescents (middle and high school age). Reopening schools after lifting lockdown will likely lead to an increase in the number of COVID-19 cases in the following 2 months, even with lower transmissibility of children, yet protocols exist that would allow maintaining the epidemic under control without saturating the healthcare system. With pre-schools and primary schools in session starting May 11, ICU occupation would reach at most 72% [55,83]% (95% probability ranges) of a 1,500-bed capacity (here foreseen as the routine capacity restored in the region post-first wave) if no other school level reopens before summer or if middle and high schools reopen one month later through a progressive protocol (increasing attendance week by week). Full attendance of adolescents at school starting in June would overwhelm the ICU system (138% [118,159]% occupation). Reopening all schools on May 11 would likely lead to a second wave similar to the one recently experienced, except if maximum attendance is limited to 50% for both younger children and adolescents. Based on the estimated situation on May 11, no substantial difference in the epidemic risk is predicted between progressive and prompt reopening of pre-schools and primary schools, thus allowing full attendance of younger children mostly in need of resuming learning and development. Reopening would require however large-scale trace and testing to promptly isolate cases, in addition to moderate social distancing interventions. Full attendance in middle and high schools is instead not recommended. Findings are consistent across different assumptions on the relative transmissibility of younger children and for small increase of the reproductive number possibly due to decreasing compliance to lockdown.


title: Mitogen-activated protein kinases are carbon dioxide receptors in plants

text: The amount of CO2 in the atmosphere is increasing continuously in the industrial era, posing a threat to the ecological balance on Earth. There are two ways to reduce elevated CO2 concentrations ([CO2]high): reducing human emissions or increasing their absorption by oceans and plants. However, in response to [CO2]high, plants diminish gas exchange and CO2 uptake by closing stomata. Surprisingly, we do not know how plants sense CO2 in their environment, and the basic mechanisms of the plant response to [CO2]high are very poorly understood. Here, we show that mitogen-activated protein kinases (MAPKs) are plant CO2 receptors. We demonstrate that MPK4, a prominent MAPK that is known to be involved in the stomatal response to [CO2]high1–3, is capable of binding CO2 and is directly activated by a very low increase in [CO2] in vivo and in vitro. Unlike MPK4 activation by infections4, stress and hormones within known MAPK signalling cascades, [CO2]high-induced MPK4 activation is independent of the upstream regulators MKK1 and MKK2. Moreover, once activated, MPK4 is prone to inactivation by bicarbonate. The identification of stress-responsive MPK4 as a CO2 receptor sheds new light on the integration of various environmental signals in guard cells, setting up MPK4 as the main hub regulating CO2 availability for photosynthesis. This result could help to find new ways to increase CO2 uptake by plants.


title: Tracking and Predicting COVID-19 Epidemic in China Mainland

text: By proposing a varying coefficient Susceptible-Infected-Removal model (vSIR), we track the epidemic of COVID-19 in 30 provinces in China and 15 cities in Hubei province, the epicenter of the outbreak. It is found that the spread of COVID-19 has been significantly slowing down within the two weeks from January 27 to February 10th with 87.0% and 84.3% reductions in the reproduction number R0 among the 30 provinces and 15 Hubei cities, respectively. This suggests the extreme control measures implemented since January 23, which include cutting off Wuhan and many other cities and towns, a great public awareness and high level of self isolation at home, have contributed to a substantial decline in the reproductivity of the COVID-19 in China. We predict that Hubei province will reach its peak between February 20 and 22, 2020, and if the removal rate can be increased to 0.1, the epidemic outside Hubei province will end in May 2020, and inside Hubei in early June.


title: Sensitivity analysis of the effects of non-pharmaceutical interventions on COVID-19 in Europe

text: The role of non-pharmaceutical interventions (NPIs) on the spread of SARS-CoV-2 has drawn significant attention, both scientific and political. Particularly, an article by the Imperial College COVID-19 Response Team (ICCRT), published online in Nature on June 8, 2020, evaluates the efficiency of 5 NPIs. Based on mortality data up to early May, it concludes that only one of the interventions, lockdown, has been efficient in 10 out of 11 studied European countries. We show, via simulations using the ICCRT model code, that conclusions regarding the effectiveness of individual NPIs are not justified. Our analysis focuses on the 11th country, Sweden, an outlier in that no lockdown was effectuated. The new simulations show that estimated NPI efficiencies across all 11 countries change drastically unless the model is adapted to give the Swedish data special treatment. While stated otherwise in the Nature article, such adaptation has been done in the model code reproducing its results: An ungrounded country-specific parameter said to have been introduced in all 11 countries, is in the code only activated for Sweden. This parameter de facto provides a new NPI category, only present in Sweden, and with an impact comparable to that of a lockdown. While the considered NPIs have unarguably contributed to reduce virus spread, our analysis reveals that their individual efficiency cannot be reliably quantified by the ICCRT model, provided mortality data up to early May.


The scandals of covid-19


title: Key to successful treatment of COVID-19: accurate identification of severe risks and early intervention of disease progression

text: Abstract Background COVID-19 is a new and highly contagious respiratory disease that has caused global spread, high case fatality rate in severe patients, and a huge medical burden due to invasive mechanical ventilation. The current diagnosis and treatment guidelines are still need to be improved, and more excellent clinical experience is needed to provide reference. Methods We analyzed and summarized clinical data of 97 confirmed COVID-19 adult patients (including 26 severe cases) admitted to the Fifth Affiliated Hospital of Sun Yat-sen University from January 17, 2020 to March 10, 2020,included laboratory examination results, imaging findings, treatment effect, prognosis , etc, in order to put forward prediction index of severe COVID-19 patients, principles of early intervention and methylprednisolone usages in COVID-19 patients. Results 1.Hypoxemia, hyperlactic acid, hypoproteinemia, and hypokalemia were prevalent in COVID-19 patients.The significant low lymphocyte count, hypoproteinemia, hypokalemia, the persistent or worsen high CRP, high D-dimer, and high BNP, and the occurrence of hemoptysis and novel coronavirus (SARS-CoV-2) viremia were important indicators for early diagnosis and prediction of severe disease progression. 2.Characteristic images of lung CT had a clear change in COVID - 19, Ground-glass opacity (GGO) and high-density linear combinations may indicate different pathological changes. Rapid lobular progression of GGO suggests the possibility of severe disease. 3.Basic principles of early intervention treatment of COVID-19: on the premise of no effective antiviral drugs, treatment is based on supportive and symptomatic therapy (albumin supplementation, supplement of potassium, supplement blood plasma, etc.) in order to maintain the stability of the intracellular environment and adequately reactivate body immunity to clean up SARS-CoV-2 . 4. According to severity, oxygenation index, body weight, age, underlying diseases, appropriate amount methylprednisolone application on severe/critical COVID-19 patients on demand, improved blood oxygen and reduced the utilization rate of invasive mechanical ventilation, case fatality rate and medical burden significantly. The most common indications for invasive mechanical ventilation should be strictly control in critical COVID-19 patients. Conclusions: 1.Accurate and timely identification of clinical features in severe risks, and early and appropriate intervention can block disease progression. 2.Appropriate dose of methylprednisolone can effectively avoid invasive mechanical ventilation and reduce case fatality rate in critical COVID-19 patients.


title: Predicting mortality attributable to SARS-CoV-2: A mechanistic score relating obesity and diabetes to COVID-19 outcomes in Mexico

text: BACKGROUND AND AIMS: The SARS-CoV-2 outbreak has posed a challenge to the healthcare systems due to high complications rates observed in patients with cardiometabolic diseases, such as diabetes and obesity. Despite the high prevalence of these conditions, a mechanistic association of its interactions in COVID-19 remain unclear. Here, we identify risk factors and propose a clinical score to predict 30-day lethality in COVID-19 cases, including specific factors for diabetes and obesity and its role in improving risk prediction. METHODS: We obtained data of suspected, confirmed and negative COVID-19 cases and their demographic and health characteristics from the General Directorate of Epidemiology of Mexican Ministry of Health. We investigated specific risk factors associated to SARS-CoV-2 positivity and mortality due to COVID-19. Additionally, we explored the impact of diabetes and obesity on COVID-19 related outcomes and their interaction with other comorbidities in modifying COVID-19 related lethality. Finally, we built our clinical score to predict 30-day lethality using the previously identified risk factors. RESULTS: Among 49,570 evaluated subjects (at April 19th, 2020), we observed an increased risk of SARS-CoV-2 positivity (n=8,261) in those with diabetes, obesity, male subjects and in patients with diabetes and age <40 years (early-onset). Risk factors for increased lethality in COVID-19 includes early-onset diabetes obesity, chronic obstructive pulmonary disease, advanced age, immunosuppression, and chronic kidney disease; we also found that obesity mediates 47.8% of the effect of diabetes on COVID-19 lethality. Early-onset diabetes conferred an increased risk of hospitalization and obesity conferred an increased risk for ICU admission and intubation. Our predictive score for COVID-19 lethality included age [≥]65 years, diabetes, diabetes & age <40 years, obesity, age <40 years, CKD, pregnancy and immunosuppression and a categorization of low-risk, mild-risk, moderate-risk, high-risk and very high-risk significantly discriminates lethal from non-lethal COVID-19 cases (c-statistic=0.837). CONCLUSIONS: Here, we propose a mechanistic approach to evaluate risk for complication and lethality attributable to COVID-19 in patients with obesity and diabetes patients in a country with high susceptibility. Furthermore, our novel score offers a clinical tool for quick determination of high-risk susceptibility patients in a first contact scenario.


title: Reduction in stroke patients' referral to the ED in the COVID-19 era: A four-year comparative study

text: Abstract Introduction. Current reports indicate that the increased use of social distancing for preventive COID-19 distribution may have a negative effect on patients who suffering from acute medical conditions. Aim. We examined the effect of social distancing on acute ischemic stroke (AIS) patients' referral to the emergency department (ED) Method. A retrospective archive study was conducted between January 2017 and April 2020 in a comprehensive stroke center. We compare the number of neurologic consultations, time from symptoms onset to ED arrival, patients diagnosis with AIS, number of patients receiving treatment (tPA, endovascular thrombectomy (EVT) or combine) and in-hospital death. Results. The analysis included a total of 14,626 neurological consultations from the years 2017 to 2020. A significant decrease of 58.6% was noted during the months of January-April of the year 2020 compared to the parallel period of 2017. Percent of final AIS diagnosis for the year of 2020 represent 24.8% of suspected cases, with the highest diagnosis rate demarcated for the year of 2019 with 25.6% of confirmed patients. The most remarkable increase was noted in EVT performance through the examined years (2017, n=21; 2018, n=32; 2019, n=42; 2020, n=47). Conclusion. COVID-19 pandemic resulted in routing constraints on health care system resources that were dedicated for treating COVID-19 patients. The healthcare system must develop and offer complementary solutions that will enable access to health services even during these difficult times.


title: Ectopic hepatocyte transplantation cures the pig model of tyrosinemia

text: The effectiveness of cell-based therapies to treat liver failure is limited by the diseased liver environment. Herein we provide preclinical proof-of-concept for the treatment of liver failure through hepatocyte transplantation into lymph nodes in a large-animal model of hereditary tyrosinemia type 1 (HT1), a metabolic liver disease caused by deficiency of fumarylacetoacetate hydrolase (FAH) enzyme. FAH-deficient pigs received autologous hepatocyte transplantation into mesenteric lymph nodes after ex vivo transduction with a lentiviral vector carrying the pig Fah gene. Hepatocytes showed early (6 hour) and durable (8 month) engraftment in lymph nodes, with reproduction of vascular and hepatic microarchitecture. Subsequently, hepatocytes migrated to and repopulated the native diseased liver. The corrected cells generated enough liver mass to clinically ameliorate disease as early as 97 days post-transplantation, with complete normalization of tyrosine levels and liver function tests. Integration site analysis defined the corrected hepatocytes in the liver as a subpopulation of hepatocytes in the lymph nodes, indicating that the lymph nodes served as a source for healthy hepatocytes to repopulate a diseased liver. Ectopic transplantation of hepatocytes cures the pig model of HT1 and presents a promising approach to the treatment of liver disease in patients with pre-existing liver damage and fibrosis. One Sentence Summary Transplantation of corrected hepatocytes in mesenteric lymph nodes can cure fatal metabolic liver disease by providing organized liver tissue and by repopulating the diseased liver in the pig tyrosinemia model.


title: Clinical Characteristics of 34 Children with Coronavirus Disease-2019 in the West of China: a Multiple-center Case Series

text: BACKGROUND Up to 9 March, 2020, 109577 patients were diagnosed with coronavirus disease-2019 (COVID-19) globally. The clinical and epidemiological characteristics of adult patients have been revealed recently. However, the information of paediatric patients remains unclear. We describe the clinical and epidemiological characteristics of paediatric patients to provide valuable insight into early diagnosis of COVID-19 in children, as well as epidemic control policy making. METHODS and FINDINGS This retrospective, observational study was a case series performed at 4 hospitals in the west of China. Thirty-four paediatric patients with COVID-19 were included from January 1 to February 25, 2020. And the final follow-up visit was completed by February 28, 2020. Clinical and epidemiological characteristics were analyzed on the basis of demographic data, medical history, laboratory tests, radiological findings, and treatment information. Data analysis was performed on 34 paediatrics patients with COVID-19 aged from 1 to 144 months (median 33.00, IQR 10.00 - 94.25), among whom 14 males (41.18%) were included. 47.60% of patients were noticed without any exposure history. The median incubation period was 10.50 (7.75 - 25.25) days. Infections of other respiratory pathogens were reported in 16 patients (47.06%). The most common initial symptoms were fever (76.47%), cough (58.82%), and expectoration (20.59%). Vomiting (11.76%) and diarrhea (11.76%) were also reported in a considerable portion of cases. A remarkable increase was detected in serum amyloid A for 17 patients (85.00%) and high-sensitivity C-reactive protein for 17 patients (58.62%), while a decrease of prealbumin was noticed in 25 patients (78.13%). In addition, the levels of lactate dehydrogenase was increased significantly in 28 patients (82.35%), as well as α-hydroxybutyrate dehydrogenase in 25 patients (73.53%). Patchy lesions in lobules were detected by chest computed tomographic scans in 28 patients (82.36%). The typical feature of ground-glass opacity for adults was rare in paediatric patients (2.94%). A late-onset pattern of lesions in lobules were also noticed. Stratified analysis of the clinical features were not performed due to relatively limited samples. CONCLUSIONS Our data presented the clinical and epidemiological features of paediatric patients systemically. The findings offer new insight into the early identification and intervention of paediatric patients with COVID-19.


title: COVID-19: Forecasting short term hospital needs in France

text: Europe is now considered as the epicenter of the SARS-CoV-2 pandemic, France being among the most impacted country. In France, there is an increasing concern regarding the capacity of the healthcare system to sustain the outbreak, especially regarding intensive care units (ICU). The aim of this study was to estimate the dynamics of the epidemic in France, and to assess its impact on healthcare resources for each French metropolitan Region. We developed a deterministic, age-structured, Susceptible-Exposed-Infectious-Removed (SEIR) model based on catchment areas of each COVID-19 referral hospitals. We performed one month ahead predictions (up to April 14, 2020) for three different scenarios (R0=1.5, R0=2.25, R0=3), where we estimated the daily number of COVID-19 cases, hospitalizations and deaths, the needs in ICU beds per Region and the reaching date of ICU capacity limits. At the national level, the total number of infected cases is expected to range from 22,872 in the best case (R0=1.5) to 161,832 in the worst case (R0=3), while the total number of deaths would vary from 1,021 to 11,032, respectively. At the regional level, all ICU capacities may be overrun in the worst scenario. Only seven Regions may lack ICU beds in the mild scenario (R0=2.25) and only one in the best case. In the three scenarios, Corse may be the first Region to see its ICU capacities overrun. The two other Regions, whose capacity will be overrun shortly after are Grand-Est and Bourgogne-Franche-Comté. Our analysis shows that, even in the best case scenario, the French healthcare system will very soon be overwhelmed. While drastic social distancing measures may temper our results, a massive reorganization leading to an expansion of French ICU capacities seems to be necessary to manage the coming wave of critically affected COVID-19 patients.


title: Quality & safety in the literature: July 2020

text: Retrospective analysis of electronic health records, combined with institutional telecommunication logs, showed incoming telephone call interruptions for paediatric intensive care unit nurses were significantly and temporally associated with medication administration errors Effect of cognitive aids on adherence to best practice in the treatment of deteriorating surgical patients: a randomised clinical trial in a simulation setting JAMA Surgery 27 November 2019 Failure to rescue from a state of clinical deterioration while admitted is a major source of morbidity and mortality in surgical and medical patients Contributors to failure to rescue that have been targets for intervention include uncertainty in who is leading the treatment plan (eg, team leader for a ‘code’ event such as cardiac arrest), too many people with unclear roles attending code events and inability to quickly recall and execute appropriate steps of resuscitation due to infrequent practice of such skills and/or stressful environments 5 Prior studies have found benefit in providing training including ‘mock’ codes Team members are often not used to working together, clinicians are redeployed outside of their usual area of practice and clinical expertise (eg, outpatient physicians now leading inpatient teams) and healthcare providers must quickly learn and anticipate complications arising from COVID-19 infection such as rapidly progressive respiratory failure, acute cardiovascular conditions and venous thromboembolic disease [ ]in the development of expanding clinical teams to function together in a crisis like the COVID-19 pandemic, it is also important to thoughtfully design the emergency response teams and resources available to manage the inevitable emergencies that will arise


title: Gene Expression Network Analysis Provides Potential Targets Against SARS-CoV-2

text: BACKGROUND Cell entry of SARS-CoV-2, the novel coronavirus causing COVID-19, is facilitated by host cell angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We aimed to identify and characterize genes that are co-expressed with ACE2 and TMPRSS2, and to further explore their biological functions and potential as druggable targets. METHODS Using the gene expression profiles of 1,038 lung tissue samples, we performed a weighted gene correlation network analysis (WGCNA) to identify modules of co-expressed genes. We explored the biology of co-expressed genes using bioinformatics databases, and identified known drug-gene interactions. RESULTS ACE2 was in a module of 681 co-expressed genes; 12 genes with moderate-high correlation with ACE2 (r>0.3, FDR<0.05) had known interactions with existing drug compounds. TMPRSS2 was in a module of 1,086 co-expressed genes; 15 of these genes were enriched in the gene ontology biologic process ‘Entry into host cell’, and 53 TMPRSS2-correlated genes had known interactions with drug compounds. CONCLUSION Dozens of genes are co-expressed with ACE2 and TMPRSS2, many of which have plausible links to COVID-19 pathophysiology. Many of the co-expressed genes are potentially targetable with existing drugs, which may help to fast-track the development of COVID-19 therapeutics.


title: Prevalence of Low-Credibility Information on Twitter During the COVID-19 Outbreak

text: As the novel coronavirus spreads across the world, concerns regarding the spreading of misinformation about it are also growing. Here we estimate the prevalence of links to low-credibility information on Twitter during the outbreak, and the role of bots in spreading these links. We find that the combined volume of tweets linking to low-credibility information is comparable to the volume of New York Times articles and CDC links. Content analysis reveals a politicization of the pandemic. The majority of this content spreads via retweets. Social bots are involved in both posting and amplifying low-credibility information, although the majority of volume is generated by likely humans. Some of these accounts appear to amplify low-credibility sources in a coordinated fashion.


title: Real-time time-series modelling for prediction of COVID-19 spread and intervention assessment

text: Substantial amount of data about the COVID-19 pandemic is generated every day. Yet, data streaming, while considerably visualized, is not accompanied with advanced modelling techniques to provide real-time insights. This study introduces a unified platform which integrates visualization capabilities with advanced statistical methods for predicting the virus spread in the short run, using real-time data. The platform is backed up by advanced time series models to capture any possible non-linearity in the data which is enhanced by the capability of measuring the expected impact of preventive interventions such as social distancing and lockdowns. The platform enables lay users, and experts, to examine the data and develop several customized models with different restriction such as models developed for specific time window of the data. Our policy assessment of the case of Australia, shows that social distancing and travel ban restriction significantly affect the reduction of number of cases, as an effective policy.


title: Estimating the global spread of COVID-19

text: Limited and inconsistent testing and differences in age distribution, health care resources, social distancing, and policies have caused large variations in the extent and dynamics of the COVID-19 pandemic across nations, complicating the estimation of prevalence, the infection fatality rate (IFR), and other factors important to care providers and policymakers. Using data for all 84 countries with reliable testing data (spanning 4.75 billion people) we develop a dynamic epidemiological model integrating data on cases, deaths, excess mortality and other factors to estimate how asymptomatic transmission, disease acuity, hospitalization, and behavioral and policy responses to risk condition prevalence and IFR across nations and over time. For these nations we estimate IFR averages 0.68% (0.64%-0.7%). Cases and deaths through June 18, 2020 are estimated to be 11.8 and 1.48 times official reports, respectively, at 88.5 (85-95.3) million and 600 (586-622) thousand. Prevalence and IFR vary substantially, e.g., Ecuador (18%; 0.61%), Chile (15.5%; 0.57%), Mexico (8.8%; 0.69%), Iran (7.9%; 0.44%), USA (5.3%; 0.99%), UK (5.2%; 1.59%), Iceland (1.65%, 0.56%), New Zealand (0.1%, 0.64%), but all nations remain well below the level needed for herd immunity. By alerting the public earlier and reducing contacts, extensive testing when the pandemic was declared could have averted 35.3 (32.7-42.7) million cases and 197 (171-232) thousand deaths. However, future outcomes are less dependent on testing and more contingent on the willingness of communities and governments to reduce transmission. Absent breakthroughs in treatment or vaccination and with mildly improved responses we project 249 (186-586) million cases and 1.75 (1.40-3.67) million deaths in the 84 countries by Spring 2021.


title: SARS-CoV-2/COVID-19: el virus, la enfermedad y la pandemia/ SARS-CoV-2/COVID-19: The virus, the disease and the pandemic

text: El brote de la enfermedad por coronavirus 2019 (COVID-19), causado por el virus del síndrome respiratorio agudo severo tipo-2 (SARS-CoV-2), fue declarado como una pandemia en marzo de 2020. Las tasas de letalidad se estiman entre 1% y 3%, afectando principalmente a los adultos mayores y a aquellos con comorbilidades, como hipertensión, diabetes, enfermedad cardiovascular y cáncer. El periodo de incubación promedio es de 5 días, pero puede ser hasta de 14 días. Muchos pacientes infectados son asintomáticos; sin embargo, debido a que liberan grandes cantidades de virus, son un desafío permanente para contener la propagación de la infección, causando el colapso de los sistemas de salud en las áreas más afectadas. La vigilancia intensa es vital para controlar la mayor propagación del virus, y el aislamiento sigue siendo el medio más efectivo para bloquear la transmisión. Este artículo tiene como objetivo revisar el virus causante de esta nueva pandemia COVID-19 que afecta al mundo, mayor aún que la de influenza A H1N1 en 2009, la cual significó la muerte de cientos de miles de personas en todo el mundo. Se abordan temas como el patógeno, la epidemiología, las manifestaciones clínicas, el diagnóstico y el tratamiento.


title: Coronavirus in pregnancy. What we know so far?

text: Coronaviruses are a group of viruses which, even if they are affecting mainly mammals and birds, could be transmitted to humans, generating common cold The new virus strain is named SARS-CoV-2 and has 85% sequence similarity to SARS-CoV Until now, it has caused more than 100 000 confirmed cases of infection and almost 5000 deaths, having a mortality rate of 4% All information (symptoms, signs, management, complications) are taken from the other pandemic infections (SARS, MERS) Information about viral infection concerning pregnant women are limited and are common to other SARS infections There are very few cases of pregnant patients infected with SARS-CoV-2 and studies are ongoing


title: Estimation of protection for COVID-19 in children from epidemiological information and estimate effect of policy in Japan

text: Background: Incidence in children was much less than in adults during the COVID−19 outbreak. Sports and entertainment events were canceled (VEC) in Japan for two weeks during 26 February − 13 March. Most schools were closed (SC). Object: We construct a susceptible−infected −recovered model using three age classes and estimate the basic reproduction number (R0) and protection level among children simultaneously. Then we simulate SC and VEC effects. Method: We used data of patients with symptoms in Japan during 14 January to assess SC and VEC introduction. Effects of SC and VEC were incorporated into the model through change in the contact pattern or frequencies among age classes. Results: Results suggest R0 as 2.86 [95%CI of 2.73, 2.97]. The protection level was estimated as 0.4 [0.2, 0.7]. SC and VEC can reduce the total number of patients significantly, by 6−7%. Discussion and Conclusion: The estimated R0 was similar to that found from other studies in China and Japan. We found a significant protection level among children, and by effects of SC and VEC. Introduction


title: Current status of treatment for 2019 novel coronavirus pneumonia/ 2019新型冠状病毒肺炎治疗研究现状

text: 2019 novel coronavirus (2019-nCoV) is a new member of coronavirus family that can cause serious respiratory diseases after the emergence of severe acute respiratory syndrome-coronavirus (SARS-CoV) and middle east respiratory syndrome-coronavirus (MERS-CoV). At present, there is no specific antiviral drug targeting 2019-nCoV. In facing of the increasingly serious epidemic of 2019-nCoV pneumonia and the urgent needs in drug treatment strategies, this paper reviewed the current research situation and progress in antiviral treatment for the newly identified disease.


title: Applying Lexical Link Analysis to Discover Insights from Public Information on COVID-19

text: SARS-Cov-2, the deadly and novel virus, which has caused a worldwide pandemic and drastic loss of human lives and economic activities. An open data set called the COVID-19 Open Research Dataset or CORD-19 contains large set full text scientific literature on SARS-CoV-2. The Next Strain consists of a database of SARS-CoV-2 viral genomes from since 12/3/2019. We applied an unique information mining method named lexical link analysis (LLA) to answer the call to action and help the science community answer high-priority scientific questions related to SARS-CoV-2. We first text-mined the CORD-19. We also data-mined the next strain database. Finally, we linked two databases. The linked databases and information can be used to discover the insights and help the research community to address high-priority questions related to the SARS-CoV-2’s genetics, tests, and prevention. Significance Statement In this paper, we show how to apply an unique information mining method lexical link analysis (LLA) to link unstructured (CORD-19) and structured (Next Strain) data sets to relevant publications, integrate text and data mining into a single platform to discover the insights that can be visualized, and validated to answer the high-priority questions of genetics, incubation, treatment, symptoms, and prevention of COVID-19.


title: Coarse-grained molecular simulations of the binding of the SARS-CoV 2 spike protein RBD to the ACE2 cell receptor

text: Since it was first observed in late 2019, the COVID-19 pandemic has created a global emergency for national health systems due to millions of confirmed cases and hundreds of thousands of deaths. At a molecular level, the bottleneck for the infection is the binding of the receptor binding domain (RBD) of the viral spike protein to ACE2, an enzyme exposed on human cell membranes. Several experimental structures of the ACE2:RBD complex have been made available, however they offer only a static description of the arrangements of the molecules in either the free or bound states. In order to gain a dynamic description of the binding process that is key to infection, we use molecular simulations with a coarse grained model of the RBD and ACE2. We find that binding occurs in an all-or-none way, without intermediates, and that even in the bound state, the RBD exhibits a highly dynamic behaviour. From short equilibrium simulations started in the unbound state we provide snapshots that result in a tentative mechanism of binding. Our findings may be important for the development of drug discovery strategies that target the RBD.


title: A Computational Model for Estimating the Progression of COVID-19 Cases in the US West and East Coasts

text: The ongoing coronavirus disease 2019 (COVID-19) pandemic is of global concern and has recently emerged in the US. In this paper, we construct a stochastic variant of the SEIR model to make a quasi-worst-case scenario prediction of the COVID-19 outbreak in the US West and East Coasts. The model is then fitted to current data and implemented using Runge-Kutta methods. Our computation results predict that the number of new cases would peak around mid-April and begin to abate by July, and that the number of cases of COVID-19 might be significantly mitigated by having greater numbers of functional testing kits available for screening. The model also showed how small changes in variables can make large differences in outcomes and highlights the importance of healthcare preparedness during pandemics.


title: Assessment of Inactivation Procedures for SARS-CoV-2

text: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease 2019 (COVID-19), presents a challenge to laboratorians and healthcare workers around the world. Handling of biological samples from individuals infected with the SARS-CoV-2 virus requires strict biosafety and biosecurity measures. Within the laboratory, non-propagative work with samples containing the virus requires, at minimum, Biosafety Level-2 (BSL-2) techniques and facilities. Therefore, handling of SARS-CoV-2 samples remains a major concern in areas and conditions where biosafety and biosecurity for specimen handling is difficult to maintain, such as in rural laboratories or austere field testing sites. Inactivation through physical or chemical means can reduce the risk of handling live virus and increase testing ability worldwide. Herein we assess several chemical and physical inactivation techniques employed against SARS-CoV-2 isolates from Cambodian COVID-19 patients. This data demonstrates that all chemical (AVL, inactivating sample buffer and formaldehyde) and heat treatment (56°C and 98°C) methods tested completely inactivated viral loads of up to 5 log10.


title: Short distance non-autonomy and intercellular transfer of chitin synthase in Drosophila

text: The complex structure of insect exoskeleton has inspired material scientists and engineers. Chitin is a major component of the cuticle and it is synthesized by the enzyme chitin synthase. There is a single chitin synthase gene (kkv) in Drosophila facilitating research on the function of chitin. Previous editing of kkv lead to the recovery of a viable hypomorphic allele. Experiments described in this paper argue that a reduction in chitin synthase leads to the shafts of sensory bristles becoming fragile and frequently breaking off as the animals age. This is likely due to reduced chitin levels and further suggests that chitin plays a role in resilience of insect cuticle. The different layers in cuticle are continuous across the many epidermal cells that secrete the cuticle that covers the body. Little is known about the mechanisms responsible for this continuity. Using genetic mosaics and scanning electron microscopy this paper establishes that kkv shows short range cell non-autonomy. It also provides evidence for 2 possible mechanisms. One is the intercellular transfer of Kkv protein from one cell to its neighbors and the second is the deposition of cuticular material across the boundaries of neighboring cells.


title: Mechanistic modeling of the SARS-CoV-2 disease map

text: Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map in which the detailed activity of the human signaling circuits related to the viral infection and the different antiviral responses, including immune and inflammatory activities, can be inferred from gene expression experiments. Moreover, given to the mechanistic properties of the model, the effect of potential interventions, such as knock-downs, over-expression or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied in specific conditions. By providing a holistic, systems biology approach to the understanding of the complexities of the viral infection process, this tool will become an important asset in the search for efficient antiviral treatments. The tool is freely available at: http://hipathia.babelomics.org/covid19/


title: Risk factors for mortality in pregnant women with SARS-CoV-2 infection

text: Since the first case of pneumonia was described, SARS-CoV-2 infection (coronavirus disease [COVID]-19) rapidly spread worldwide With 94,288 infections and more than 10,000 deaths, Mexico is the third Latin-American country in number of confirmed cases and second in mortality1. A major risk factor for adverse outcome in COVID-19 infection is the presence of advance age, co-morbidities including diabetes, hypertension and obesity among other non-communicable diseases2. Epidemiological data from high-prevalence countries reveal that compared to men, women are less likely to die or to require hospital admission to intensive care. This may suggest that pregnant women are not more susceptible to infection or to experience serious complications. However, whether the presence of co-morbidities or advanced maternal age confers a higher risk of adverse outcome in pregnant women with COVID-19 is unknown3. In this research letter, we aimed at evaluating the risk factor associated with maternal mortality secondary to COVID-19 infection in a middle-income country. Advanced maternal age is linked to an increased risk of mortality, while diabetes is the most important risk factor for maternal death. This is partly explained by an increasing incidence of non-communicable diseases in women of advanced age which is a common feature in most countries4. In the last decades, low- and middle-income countries have experienced accelerated socio-cultural changes associated with its incorporation into the international economic community, which have increased the number of obese and diabetic population, including pregnant women5. This has caused an increased risk for complications and fatality among COVID-19 positive population2,3. Thus, policies for reducing obesity and diabetes in low- and middle-income countries are most needed to reduce the mortality of COVID-19 in pregnant women.


After the toolkit: anticipatory logics and the future of government


title: Robust and sensitive detection of SARS-CoV-2 using PCR based methods

text: The World Health Organization (WHO) has declared the Coronavirus disease 2019 (COVID-19) as an international health emergency. Current diagnostic tests are based on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method, the gold standard test that involves the amplification of viral RNA. However, the RT-qPCR assay has limitations in terms of sensitivity and quantification. In this study, we tested both qPCR and droplet digital PCR (ddPCR) to detect low amounts of viral RNA. The cycle threshold (CT) of viral RNA by RT-PCR significantly varied according to the sequence of primer and probe sets with in vitro transcript (IVT) RNA or viral RNA as templates, whereas the copy number of viral RNA by ddPCR was effectively quantified with IVT RNA, cultured viral RNA, and RNA from clinical samples. Furthermore, the clinical samples were assayed via both methods, and the sensitivity of the ddPCR was determined to be significantly higher than RT-qPCR. These findings suggest that ddPCR could be used as a highly sensitive and compatible diagnostic method for viral RNA detection.


title: Municipality- level predictors of COVID-19 mortality in Mexico: a cautionary tale

text: Background. Inequalities and burden of comorbidities of the Coronavirus disease 2019 (COVID-19) vary importantly inside the countries. We aimed to analyze the Municipality-level factors associated with a high COVID-19 mortality rate of in Mexico. Methods. We retrieved information from 142,643 cumulative confirmed symptomatic cases and 18,886 deaths of COVID-19 as of June 20th, 2020 from the publicly available database of the Ministry of Health of Mexico. Public official data of the most recent census and surveys of the country were used to adjust a negative binomial regression model with the quintiles (Q) of the distribution of sociodemographic and health outcomes among 2,457 Municipality-level. Expected Mortality Rates (EMR), Incidence Rate Ratios (IRR) and 95% Confidence Intervals are reported. Results. Factors associated with high MR of COVID-19, relative to Quintile 1 (Q1), were; diabetes prevalence (Q4, IRR=2.60), obesity prevalence (Q5, IRR=1.93), diabetes mortality rate (Q5, IRR=1.58), proportion of indigenous population (Q2, IRR=1.68), proportion of economically active population (Q5, IRR=1.50), density of economic units that operate essential activities (Q4, IRR=1.54) and population density (Q5, IRR=2.12). We identified 1,351 Municipality-level without confirmed COVID-19 deaths, of which, 202 had nevertheless high (Q4, Mean EMR= 8.0 deaths per 100,000) and 82 very high expected COVID-19 mortality (Q5, Mean EMR= 13.8 deaths per 100,000). Conclusion. This study identified 1,351 Municipality-level of Mexico that, in spite of not having confirmed COVID-19 deaths yet, share characteristics that could eventually lead to a high mortality scenario later in the epidemic and warn against premature easing of mobility restrictions. Local information should be used to reinforce strategies of prevention and control of outbreaks in communities vulnerable to COVID-19. Keywords: COVID-19; risk factors; social determinants; health determinants; Municipality-level; counties.


title: China’s diplomacy and changing the COVID-19 narrative

text: The world has declared COVID-19 (a disease caused by the SARS-CoV-2 virus or novel coronavirus) to be a pandemic. China has been chastised by various countries, especially the United States, for suppressing information and not taking necessary measures which could have helped in controlling the spread of and/or eradicating the disease in the earlier stages. Consequently, China has undertaken numerous measures to change the COVID-19 narrative and disassociate itself from COVID-19. It launched a campaign to question the origins of SARS-CoV-2, blamed the United States for spreading COVID-19, claimed victory in combating COVID-19 domestically, and provided aid (“mask diplomacy”) to countries. These actions betray China’s concern about its image. The country wants to portray itself as a Good Samaritan, a responsible and reliable partner, and an essential global power. Additionally, China has grave concerns about regime stability and survival. President Xi’s legitimacy is built on technocratic competence. The outbreak has the potential to seriously dent his personal legacy.


title: Novel Coronavirus: How Atmospheric Particulate Affects Our Environment and Health

text: It is well-known that atmospheric pollution, first and foremost the particulate matter (PM), causes serious diseases in humans China’s metropolises and Italy’s Po Valley have in fact achieved a concerning degree of notoriety thanks to runaway air pollution problems The spread of viral respiratory diseases is facilitated in polluted environments, an example of which is the respiratory syncytial virus bronchiolitis In this opinion paper, we consider the possible relationship between air pollution, primarily airborne PM10–2 5, and the spread of the novel coronavirus in Northern Italy If it is true that the novel coronavirus remains active from some hours to several days on various surfaces, it is logical to postulate that the same can occur when it is adsorbed or absorbed by the atmospheric particulate matter, which may also help carry the virus into the human respiratory system As the Earth presents us with a very high bill to pay, governments and other authorities need to take prompt action to counter excessive pollution levels, both in Italy and in other countries


title: High-Frequency and High-Quality Survey Data Collection: The Mannheim Corona Study

text: The outbreak of the COVID-19 pandemic has a massive impact on society. To curb the spread of the SARS-CoV-2 virus, unprecedented containment measures are being taken by governments around the world. These measures and the fear of the disease itself are likely affecting the economy, social inequality, mental and physical health, and even people’s perception of good democratic governance. Equally unprecedented is the speed at which these massive changes take place and the lack of statistical evidence that accompanies them. Within days of the first containment measures in Germany, the German Internet Panel (GIP) launched the Mannheim Corona Study (MCS), a daily rotating panel study of the general adult population of approximately 3,600 respondents. Its data and reports now inform the crisis cabinet of the German government and are the basis for groundbreaking social and economic research. This paper gives insights into the MCS methodology and data quality.


title: Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

text: Main protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.


title: How to Teach Pedagogy Courses Online at University in COVID-19 Pandemic: Search for Answers

text: The worldwide spread of COVID-19 pandemic poses new challenges to higher education, in general, and to pedagogical education in particular The transition to distance education can minimize the impact of the pandemic on the teacher training system The purpose of the article is defining approaches to teaching online pedagogy courses at the university Didactic effect was determined of the complex use of Moodle and Prometheus online platforms, Zoom webinar software, mobile learning technologies and various web servers for teachers in the course of online teaching of pedagogical disciplines to future teachers The results of the study indicate their flexibility, multidimensionality and ability to provide interactive learning It has been found that an important condition for the effectiveness of distance learning in quarantine is the provision of educational and information support for teachers and students Most of the students positively accepted the proposed methodology, and the teachers noted an increase in students' motivation for learning and their cognitive activity The results of the study indicate the appropriateness of using the selected platforms and tools in teaching online pedagogy courses at university


title: Epidemiological and Clinical Characteristics of 17 Hospitalized Patients with 2019 Novel Coronavirus Infections Outside Wuhan, China

text: An increasing number of cases of novel coronavirus pneumonia (NCP) infected with 2019-nCoV have been identified in Wuhan and other cities in China, since December 2019. We analyzed data on the 17 confirmed cases in Dazhou to provide the epidemiologic characteristics of NCP outside Wuhan. Among them, 12 patients were still quarantined in the hospital, 5 patients were discharged NCP patients according to the national standards. Compared with non-discharged NCP patients, the discharged NCP patients had younger ages. Moreover, discharged NCP patients had higher heart rate, lymphocytes levels and monocytes levels than non-discharged NCP patients on admission to the hospital. Notably, all of 17 patients had abnormal increased C-reactive protein levels, and 16 patients had abnormal computed tomography images. This study provided some information that younger age, higher lymphocytes levels and monocytes levels at the diagnoses of 2019-nCoV may contributed to faster recovery and better therapeutic outcome.


title: Predicted success of prophylactic antiviral therapy to block or delay SARS-CoV-2 infection depends on the targeted mechanism

text: Repurposed drugs that are immediately available and have a good safety profile constitute a first line of defense against new viral infections. Despite a limited antiviral activity against SARS-CoV-2, several drugs serve as candidates for application, not only in infected individuals but also as prophylaxis to prevent infection establishment. Here we use a stochastic model to describe the early phase of a viral infection. We find that the critical efficacy needed to block viral establishment is typically above 80%. This value can be improved by combination therapy. Below the critical efficacy, establishment can still sometimes be prevented; for that purpose, drugs blocking viral entry into target cells (or equivalently enhancing viral clearance) are more effective than drugs reducing viral production or enhancing infected cell death. When a viral infection cannot be prevented because of high exposure or low drug efficacy, antivirals can still delay the time to reach detectable viral loads from 4 days when untreated to up to 30 days. This delay flattens the within-host epidemic curve, and possibly reduces transmission and symptom severity. These results suggest that antiviral prophylaxis, even with reduced efficacy, could be efficiently used to prevent or alleviate infection in people at high risk. It could thus be an important component of the strategy to combat the SARS-CoV-2 pandemic in the months or years to come.


title: The spatiotemporal estimation of the dynamic risk and the international transmission of 2019 Novel Coronavirus (COVID-19) outbreak: A global perspective

text: An ongoing novel coronavirus SARS-CoV-2 pneumonia infection outbreak called COVID-19 started in Wuhan, Hubei Province, China, in December 2019. It both spread rapidly to all provinces in China and started spreading around the world quickly through international human movement from January 2020. Currently, the spatiotemporal epidemic transmission patterns, prediction models, and possible risk analysis for the future are insufficient for COVID-19 but we urgently need relevant information, particularly from the global perspective. We have developed a novel two-stage simulation model to simulate the spatiotemporal changes in the number of COVID-19 cases and estimate the future worldwide risk. Based on the connectivity of countries to China and the country's medical and epidemic prevention capabilities, different scenarios are generated to analyze the possible transmission throughout the world and use this information to evaluate each country's vulnerability to and the dynamic risk of COVID-19. Countries' vulnerability to the COVID-19 outbreak from China is calculated for 63 countries around the world. Taiwan, South Korea, Hong Kong, and Japan are the most vulnerable areas. The relationship between each country's vulnerability and days before the first imported case occurred shows a very high exponential decrease. The cumulative number of cases in each country also has a linear relationship with vulnerability, which can compare and quantify the initial epidemic prevention capabilities to various countries' management strategies. In total, 1,000 simulation results of future cases around the world are generated for the spatiotemporal risk assessment. According to the simulation results of this study, if there is no specific medicine for it, it will likely form a global pandemic. This method can be used as a preliminary risk assessment of the spatiotemporal spread for a new global epidemic. * Note: This study was completed on February 15, 2020.


Psychological interventions for covid-19 outbreak in mazandaran province, iran


title: Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19

text: Background. Real-time reverse transcription polymerase chain reaction (RT-PCR) targeting select genes of the SARS-CoV-2 RNA has been the main diagnostic tool in the global response to the COVID-19 pandemic. However, the diagnostic accuracy of the test has not been studied systematically outside of the laboratory setting. The aim of this study is to provide estimates of the diagnostic sensitivity and specificity of the RT-PCR test developed by China CDC. Methods. The study design is a secondary analysis of published findings on 1014 patients in Wuhan, China, of whom 601 tested positive and 413 were negative for COVID-19. Sensitivity and specificity were reconstructed using a Bayesian approach from probabilistic knowledge of the diagnostic errors. Predictive values of the test were calculated, resulting in estimates for the number of confirmatory tests that are needed for establishing the presence or absence of COVID-19, depending on the prior probability of a patient having the disease. Results. The sensitivity of the RT-PCR diagnostic test was estimated to be 0.777 (95% CI: 0.715, 0.849), while the specificity was 0.988 (95% CI: 0.933, 1.000). The confidence intervals include sampling error in addition to the error due to probabilistic knowledge of the data. Discussion. The Chinese version of the RT-PCR test had a conspicuous rate of false negative results, likely missing between 15% and 29% of patients with COVID-19. For a patient with a prior probability of COVID-19 greater than 18%, at least two negative test results would be needed to lower the chances of COVID-19 below 5%. Caution is advised in generalizing these findings to other versions of the RT-PCR test that are being used in diverse geographic regions.


title: Interaction rituals and ‘social distancing’: New haptic trajectories and touching from a distance in the time of COVID-19

text: Previous research in the social sciences has shown that haptic interaction rituals are critical for maintaining social relationships. However, during the coronavirus (COVID-19) pandemic, ‘social distancing’ was encouraged in order to avoid the spread of disease. Drawing on data from self-ethnography as well as publicly available resources, in this study we explore some new, locally negotiated haptic trajectories to accomplish interaction rituals in the time of coronavirus. First, we present self-ethnographic observations of distancing in face-to-face encounters from our everyday lives. Second, utilizing methods of microanalysis of naturally occurring interaction, we investigate video recordings of the embodied negotiation of space and touch among politicians. We analyze three different ways in which politicians negotiate transitional moves in this haptic ritual when one party initiates a handshake: repairing, declining and apologizing. Our analysis shows that politicians adapt their entire bodies in conjunction with talk, gestures and laughter not only to accomplish the greeting but also to remedy the potentially face-threatening situation of not getting the greeting right. This research has implications for better understanding the spontaneous ability of human beings to invent new ways of engaging with each other. Moreover, it adds to our knowledge of how the materiality of human bodies can impact forms of sociality.


title: Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

text: In December 2019 rising pneumonia cases caused by a novel β-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern therefore several scientists are dedicated to the study of the new virus. Since human viruses have codon usage biases that match highly expressed proteins in the tissues they infect and depend on host cell machinery for replication and co-evolution, we selected the genes that are highly expressed in the tissue of human lungs to perform computational studies that permit to compare their molecular features with SARS, SARS-CoV-2 and MERS genes. In our studies, we analysed 91 molecular features for 339 viral genes and 463 human genes that consisted of 677873 codon positions. Hereby, we found that A/T bias in viral genes could propitiate the viral infection favoured by a host dependant specialization using the host cell machinery of only some genes. The envelope protein E, the membrane glycoprotein M and ORF7 could have been further benefited by a high rate of A/T in the third codon position. Thereby, the mistranslation or de-regulation of protein synthesis could produce collateral effects, as a consequence of viral occupancy of the host translation machinery due tomolecular similarities with viral genes. Furthermore, we provided a list of candidate human genes whose molecular features match those of SARS-CoV-2, SARSand MERS genes, which should be considered to be incorporated into genetic population studies to evaluate thesusceptibility to respiratory viral infections caused by these viruses. The results presented here, settle the basis for further research in the field of human genetics associated with the new viral infection, COVID-19, caused by SARS-CoV-2 and for the development of antiviral preventive methods.


Oncolytic Viral Therapy: Harnessing the Potential of Viruses