bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized qRT-PCR approach for the detection of intra- and extra-cellular SARS-CoV-2 RNAs
Authors: Toptan Tuna , Hoehl Sebastian , Westhaus Sandra , Bojkova Denisa , Berger Annemarie , Rotter Björn , Hoffmeier Klaus , Ciesek Sandra , Widera Marek 
Published: April 2020

AbstractThe novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19 which has become a global concern due to its rapid spread. Meanwhile, increased demand in testing has led to shortage of reagents, supplies, and compromised the performance of diagnostic laboratories in many countries. Both the world health organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate interpretation of the test results especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in the diagnostics as well as in research labs using a low cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infection and performed RT-PCR assays along with successive dilutions of RNA standards to determine the limit of detection. We identified an M-gene binding primer and probe pair highly suitable for quantitative detection of SARS-CoV-2 RNA for diagnostic and research purposes.
A statistical forecast of LOW mortality and morbidity due to COVID-19, in ARGENTINA and other Southern Hemisphere countries
Authors: Barbero Cesar A. 
Published: April 2020

AbstractA set of open source programs in Python is devised to fit a parametric integrated Gaussian equation to cumulative deaths due to COVID-19 in Southern Hemisphere countries. The programs were successfully tested using data from advanced outbreak trajectories (Italy and Spain). The procedure was applied to data reported by Argentina. The projected total death toll will be 182 (277-182) with a peak of deaths (6(+/-2)) the 14 of April. The outbreak begins the 9thof March and end completely the 20thof May. However, already on 1stof May, 2 s (95.45%) of the deaths have occurred. The death toll arises from a number of infected individuals between 36412 and 2275. Then, they were to use to process data from several Southern Hemisphere countries: Argentina, Brazil, Mexico, Peru, Colombia, Ecuador, Cuba, Chile, Panama, Australia, Bolivia, Honduras, New Zealand, Paraguay, Guatemala, Venezuela, Uruguay, El Salvador, Jamaica, Haiti, Costa Rica and Nicaragua. The trend is to show low number of total deaths compared with other disease outbreaks. A total projected number of deaths between 15148 and 9939 deaths for a total population of ca. 664 M inhabitants. The projected death toll is much lower (5-10 times) than those forecasted by the Imperial College Group (ICG) even considering the best scenario of total suppression of virus transmission. Using actual mortality rates it is possible to back calculate which number of infected individuals would produce such mortality. The calculated number of infected individuals (worst case scenario) is below 2.5 million. This is significantly lower than that calculated by ICG (> 45 millions). In most countries the outbreak will end in May or early June. The dynamics of the outbreaks seems to do not saturate the health services (hospital beds) but only Peru, Ecuador and Panama should have not enough ICU beds for grave COVID-19 patients.
Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes
Authors: Littlefair Joanne E. , Hrenchuk Lee E. , Blanchfield Paul J. , Rennie Michael D. , Cristescu Melania E. 
Published: April 2020

AbstractSignificant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the “ecology” of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm- and cool-water fishes as well as the cold-water stenotherm, lake trout (Salvelinus namaycush). Habitat use by lake trout was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became “stratified” into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, lake trout, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm-water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the “ecology” of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localised spatial scales influences our ability to detect species.
Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands
Authors: Oude Munnink Bas B. , Nieuwenhuijse David F. , Stein Mart , O’Toole Áine , Haverkate Manon , Mollers Madelief , Kamga Sandra K. , Schapendonk Claudia , Pronk Mark , Lexmond Pascal , van der Linden Anne , Bestebroer Theo , Chestakova Irina , Overmars Ronald J. , van Nieuwkoop Stefan , Molenkamp Richard , van der Eijk Annemiek , GeurtsvanKessel Corine , Vennema Harry , Meijer Adam , Rambaut Andrew , van Dissel Jaap , Sikkema Reina S. , Timen Aura , Koopmans Marion ,   on behalf of the Dutch-Covid-19 response team
Published: April 2020

AbstractSARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also, outside the South of the Netherlands. The timely generation of whole genome sequences combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.
The Approved Dose of Ivermectin Alone is not the Ideal Dose for the Treatment of COVID-19
Authors: Schmith Virginia D. , Zhou Jie (Jessie) , Lohmer Lauren RL 
Published: April 2020

AbstractIntroductionCaly, Druce (1) reported that ivermectin inhibited SARS-CoV-2 in vitro for up to 48 h using ivermectin at 5μM. The concentration resulting in 50% inhibition (IC50, 2 µM) was >35x higher than the maximum plasma concentration (Cmax) after oral administration of the approved dose of ivermectin when given fasted.MethodSimulations were conducted using an available population pharmacokinetic model to predict total (bound and unbound) and unbound plasma concentration-time profiles after a single and repeat fasted administration of the approved dose of ivermectin (200 μg/kg), 60 mg, and 120 mg. Plasma total Cmax was determined and then multiplied by the lung:plasma ratio reported in cattle to predict the lung Cmax after administration of each single dose.ResultsPlasma ivermectin concentrations of total (bound and unbound) and unbound concentrations do not reach the IC50, even for a dose level 10x higher than the approved dose. Even with higher exposure in lungs than plasma, ivermectin is unlikely to reach the IC50 in lungs after single oral administration of the approved dose (predicted lung: 0.0857 µM) or at doses 10x higher that the approved dose administered orally (predicted lung: 0.817 µM).ConclusionsThe likelihood of a successful clinical trial using the approved dose of ivermectin is low. Combination therapy should be evaluated in vitro. Re-purposing drugs for use in COVID-19 treatment is an ideal strategy but is only feasible when product safety has been established and experiments of re-purposed drugs are conducted at clinically relevant concentrations.
Understanding the asymmetric spread and case fatality rate (CFR) for COVID-19 among countries
Authors: Iype Eldhose , Gulati Sadhya 
Published: April 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are rising rapidly every day in the world, causing the disease COVID-19 with around 2 million people infected and more than 100,000 people died so far, in more than 200 countries. One of the baffling aspects of this pandemic is the asymmetric increase in cases and case fatality rate (CFR) among countries. We analyze the time series of the infection and fatality numbers and found two interesting aspects. Firstly, the rate of spread in a region is directly connected to the population density of the region where the virus is spreading. For example, the high rate of increase in cases in the United States of America (USA) is related to the high population density of New York City. This is shown by scaling the cumulative number of cases with a measure of the population density of the affected region in countries such as Italy, Spain, Germany, and the USA and we see that the curves are coinciding. Secondly, we analyzed the CFR number as a function of the number of days, since the first death, and we found that there are two clear categories among countries: one category with high CFR numbers (around 10%) and the other category with low CFR numbers (2% to 4%). When we analyzed the results, we see that countries with lower CFR numbers more or less tend to have implemented active control measures such as aggressive testing, tracking down possible infections, effective quarantine measures, etc. Moreover, we did not see any convincing correlation between mortality rates and the median age of the population.
Analysis of Effectiveness of Quarantine Measures in Controlling COVID-19
Authors: Kaushik Garima , Mantri Shaney , Kaushik Shrishti , Kalbande Dhananjay , Chaudhari B. N. 
Published: April 2020

AbstractCOVID-19 has created an interesting discourse among the people of the world particularly regarding preventive measures of infectious diseases. In this paper, the authors forecast the spread of the Coronavirus outbreak and study how the reduction of transmission rates influences its decline. The paper makes use of the SIR (Susceptible Infected Recovered) Model which is a deterministic model used in the field of epidemiology-based on differential equations derived from sections of the population. The Basic Reproduction Number (Ro) represents the criticality of the epidemic in numeric terms. Forecasting an epidemic provides insights about the geographic spreading of the disease and the case incidences required to better inform intervention strategists about situations that may occur during the outbreak. Through this research paper, the authors wish to provide an insight into the impact of control measures on the pandemic. By drawing a comparison of three countries and their quarantine measures, observations on the decline of the outbreak are made. Authors intend to guide the intervention strategies of under-resourced countries like India and aid in the overall containment of the outbreak.
The spatio-temporal epidemic dynamics of COVID-19 outbreak in Africa
Authors: Gayawan Ezra , Awe Olawale , Oseni Bamidele M , Uzochukwu Ikemefuna C. , Adekunle Adeshina , Samuel Gbemisola , Eisen Damon P , Adegboye Oyelola A 
Published: April 2020

AbstractThe novel coronavirus (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the city of Wuhan, China in December 2019. Although, the disease appears on the African continent late, it has spread to virtually all the countries. We provide early spatio-temporal dynamics of COVID-19 within the first 62 days of the disease’s appearance on the African continent. We used a two-parameter hurdle Poisson model to simultaneously analyze the zero counts and the frequency of occurrence. We investigate the effects of important healthcare capacities including hospital beds and number of medical doctors in the different countries. The results show that cases of the pandemic vary geographically across Africa with notable high incidence in neighboring countries particularly in West and North Africa. The burden of the disease (per 100,000) was most felt in Djibouti Tunisia, Morocco and Algeria. Temporally, during the first 4 weeks, the burden was highest in Senegal, Egypt and Mauritania, but by mid-April it shifted to Somalia, Chad, Guinea, Tanzania, Gabon, Sudan, and Zimbabwe. Currently, Namibia, Angola, South Sudan, Burundi and Uganda have the least burden. The findings could be useful in implementing epidemiological intervention and allocation of scarce resources based on heterogeneity of the disease patterns.
COVID-19 Epidemic in Algeria: Assessment of the implemented preventive strategy
Authors: Hamidouche Mohamed 
Published: April 2020

AbstractSince the spread of the COVID-19 epidemic in China, several preventive strategies have been implemented worldwide to fight against the spread of SARS-CoV-2, in Algeria the control actions have been mainly social distancing, movement’s restriction, quarantine and lockdown.In order to assess the preventive strategy adopted in Algeria, we studied three zones (whole country, the main outbreak at Blida, and whole country except Blida), we used as a indicator the basic reproduction number R0, we compared the mean R0-before and R0-after the implementation of the mitigation measures using bivariate analysis, then we used the results we found to estimate the number of COVID-19 cases avoided by these measures, then after, we predicted the peak of the epidemic’s first wave.We note that the decrease in R0 after the preventive measures implementation was statistically significant (p value<10−4) in the three areas, thus, the preventive strategy in Algeria has been effective in its entirety. Our projection revealed that 15613 cases of COVID-19 were avoided in 14 days (from April 6, to April 19, 2020) in the whole country, and 1747 cases were prevented in Blida during the same period. We estimate that the peak of the first wave of the epidemic in Algeria will be reached with herd immunity of 15.93% as of November 2020, however, at least 56% of people with protective immunity would be needed to be sufficient to avoid a second wave. The used method to carry out the evaluation has given us a good overview, but, R0 is not the only factor to consider when estimating the burden of the epidemic, to do that, the number of daily admissions to intensive care units and hospitalizations remain good indicators.In order to better the epidemic control in Algeria, it is possible to act on contact efficacy rate by adding an instruction to wear medical mask by ordinary population outside, this measure has been reported to be effective in some countries.To conclude, it is good to keep in mind that a new way of life based on good hygiene habits and social distancing must therefore be in place and adopted by the population for at least several months, otherwise the demand for health care will exceed the availability.
Covid-19 and Inequity: A comparative spatial analysis of New York City and Chicago hot spots
Authors: Maroko Andrew , Nash Denis , Pavilonis Brian 
Published: April 2020

AbstractThere have been numerous reports that the impact of the ongoing COVID-19 epidemic has disproportionately impacted traditionally vulnerable communities, including well-researched social determinants of health, such as racial and ethnic minorities, migrants, and the economically challenged. The goal of this ecological cross-sectional study is to examine the demographic and economic nature of spatial hot and cold spots of SARS-CoV-2 rates in New York City and Chicago as of April 13, 2020.In both cities, cold spots (clusters of low SARS-CoV-2 rate ZIP code tabulation areas) demonstrated typical protective factors associated with the social determinants of health and the ability to social distance. These neighborhoods tended to be wealthier, have higher educational attainment, higher proportions of non-Hispanic white residents, and more workers in managerial occupations. Hot spots (clusters of high SARS-CoV-2 rate ZIP code tabulation areas) also had similarities, such as lower rates of college graduates and higher proportions of people of color. It also appears to be larger households (more people per household), rather than overall population density, that may to be a more strongly associated with hot spots.Findings suggest important differences between the cities’ hot spots as well. They can be generalized by describing the NYC hot spots as working-class and middle-income communities, perhaps indicative of service workers and other occupations (including those classified as “essential services” during the pandemic) that may not require a college degree but pay wages above poverty levels. Chicago’s hot spot neighborhoods, on the other hand, are among the city’s most vulnerable, low-income neighborhoods with extremely high rates of poverty, unemployment, and non-Hispanic Black residents.
Modelling the potential impact of social distancing on the COVID-19 epidemic in South Africa
Authors: Nyabadza F. , Chirove F. , Chukwu W. , Visaya M.V. 
Published: April 2020

AbstractThe novel coronavirus (COVID-19) pandemic continues to be a global health problem whose impact has been significantly felt in South Africa. Social distancing has been touted as the best form of response in managing a rapid increase in the number of infected cases. In this paper, we present a deterministic model to model the impact of social distancing on the transmission dynamics of COVID-19 in South Africa. The model is fitted to the currently available data on the cumulative number of infected cases and a scenario analysis on different levels of social distancing are presented. The results show a continued rise in the number of cases in the lock down period with the current levels of social distancing albeit at a lower rate. The model shows that the number of cases will rise to above 4000 cases by the end of the lockdown. The model also looks at the impact of relaxing the social distancing measures after the initial announcement of the lock down measures. A relaxation of the social distancing by 2% can result in a 23% rise in the number of cumulative cases while on the other hand increasing the levels of social distancing by 2% would reduce the number of cumulative cases by about 18%. These results have implications on the management and policy direction in the early phases of the epidemic.
COVID-19 Fatality and Comorbidity Risk Factors among Diagnosed Patients in Mexico
Authors: Solís Patricio , Carreño Hiram 
Published: April 2020

AbstractAs of April 18, 2020, 2.16 million patients in the world had been tested positive with Coronavirus (COVID-19) and 146,088 had died, which accounts for a case fatality rate of 6.76%. In Mexico, according to official statistics (April 18), 7,497 cases have been confirmed with 650 deaths, for a case fatality rate of 8.67%. These estimates, however, may not reflect the final fatality risk among COVID-19 confirmed patients, because they are based on cross-sectional counts of diagnosed and deceased patients, and therefore are not adjusted by time of exposure and right-censorship. In this paper we estimate fatality risks based on survival analysis methods, calculated from individual-level data on symptomatic patients confirmed with COVID-19 recently released by the Mexican Ministry of Health. The estimated fatality risk after 35 days of onset of symptoms is 12.38% (95% CI: 11.37-13.47). Fatality risks sharply rise with age, and significantly increase for males (59%) and individuals with comorbidities (38%-168%, depending on the disease). Two reasons may explain the high COVID-19 related fatality risk observed in Mexico, despite its younger age structure: the high selectivity and self-selectivity in testing and the high prevalence of chronic-degenerative diseases.
The role of comorbidities and clinical predictors of severe disease in COVID-19: a systematic review and meta-analysis
Authors: Tabrizi Reza , Lankarani Kamran B , Nowrouzi-sohrabi Peyman , Shabani-Borujeni Mojtaba , Rezaei Shahla , Hosseini-bensenjan Mahnaz , vakili Sina , Heydari Seyed Taghi , Ashraf Mohammad Ali 
Published: April 2020

AbstractBackgroundCOVID_19 is unpredictable due to non-specific symptoms and clinical course diversity in different individuals. We analyzed studies regarding the factors associated with severe status of the disease to identify unique findings in severely affected patients.MethodsWe systematically searched the electronic databases, including PubMed, Scopus, EMBASE, Web of Science, and Google Scholar from inception to 12thof March 2020. Cochrane’s Q and I-square statistics were used to assess the existence of heterogeneity between the included studies. We used the random-effects model to pool the odds ratios (ORs) at 95% confidence intervals (CIs).ResultsSeventeen articles out of 3009 citations were included. These contained 3189 patients, of whom 732 were severely affected (severe group) and 3189 were in non-severe group. Using the random-effects model, our meta-analyses showed that the odds of comorbidities, including COPD, DM, HTN, CVD, CKD, and symptoms, including dyspnea, dizziness, anorexia, and cough, were significantly higher among the severe group compared with the non-severe group. There were no significant changes in odds of CVA, liver disease, immunodeficiency/immunosuppression, fever, fatigue, myalgia, headache, diarrhea, sore throat, nasal congestion, sputum, nausea, vomiting, chest pain between the two groups.ConclusionsEarly recognition and intervention can be critical in management, and might stop progression to severe disease. Predictive symptoms and comorbidities can be used as a predictor in patients who are at risk of severe disease.