Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (55)

Fever (49)

Cough (38)

Fatigue (14)

Hypertension (13)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 631
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    Clinical and epidemiological characteristics of children TRANS with SARS-CoV-2 infection MESHD: case series in Sinaloa

    Authors: Giordano Perez Gaxiola; Rosalino Flores Rocha; Julio Cesar Valadez Vidarte; Melissa Hernandez Alcaraz; Gilberto Herrera Mendoza; Miguel Alejandro Del Real Lugo

    doi:10.1101/2020.07.07.20146332 Date: 2020-07-11

    Background: The SARS-CoV-2 virus may affect both adults TRANS and children TRANS. Although the disease MESHD, named COVID-19, has a lower prevalence SERO in infancy and has been described as mild, the clinical characteristics may vary and there is a possibility of complications. Objectives: To describe the clinical and epidemiological characteristics of pediatric cases confirmed TRANS in the state of Sinaloa, Mexico, during the first three months of the pandemic, and of children TRANS admitted with COVID-19 to a secondary hospital. Methods: This case series includes all patients with SARS-CoV-2 infection MESHD infection confirmed TRANS confirmed by PCR testing, identified in the state epidemiological surveillance system between March 1 and May 31, 2020. Confirmed patients admitted to the Sinaloa Pediatric Hospital (HPS) during the same dates are also described. Results: Fifty one children TRANS with SARS-CoV-2 were included, 10 of the admitted to HPS. The median age TRANS was 10 years. The more frequent symptoms were fever MESHD fever HP (78%), cough MESHD cough HP (67%) and headache MESHD headache HP (57%). Most cases were mild or asymptomatic TRANS. Three patients with comorbidities died. Only 4 of 10 patients identified in HPS had been admitted with the diagnosis of possible COVID-19. Conclusions: SARS-CoV-2 infection MESHD in children TRANS was mostly mild or asymptomatic TRANS, but with a wide range of clinical presentations.

    Wastewater SARS-CoV-2 Concentration and Loading Variability from Grab and 24-Hour Composite Samples

    Authors: Kyle Curtis; David Keeling; Kathleen Yetka; Allison Larson; Raul Gonzalez

    doi:10.1101/2020.07.10.20150607 Date: 2020-07-11

    The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) requires a significant, coordinated public health response. Assessing case density and spread of infection MESHD is critical and relies largely on clinical testing data. However, clinical testing suffers from known limitations, including test availability and a bias towards enumerating only symptomatic individuals. Wastewater-based epidemiology (WBE) has gained widespread support as a potential complement to clinical testing for assessing COVID-19 infections MESHD at the community scale. The efficacy of WBE hinges on the ability to accurately characterize SARS-CoV-2 concentrations in wastewater. To date, a variety of sampling schemes have been used without consensus around the appropriateness of grab or composite sampling. Here we address a key WBE knowledge gap by examining the variability of SARS-CoV-2 concentrations in wastewater grab samples collected every 2 hours for 72 hours compared with corresponding 24-hour flow-weighted composite samples. Results show relatively low variability (mean for all assays = 741 copies 100 mL-1, standard deviation = 508 copies 100 mL-1) for grab sample concentrations, and good agreement between most grab samples and their respective composite (mean deviation from composite = 159 copies 100 mL-1). When SARS-CoV-2 concentrations are used to calculate viral load, the discrepancy between grabs (log10 difference = 12.0) or a grab and its associated composite (log10 difference = 11.8) are amplified. A similar effect is seen when estimating carrier TRANS prevalence SERO in a catchment population with median estimates based on grabs ranging 62-1853 carriers TRANS. Findings suggest that grab samples may be sufficient to characterize SARS-CoV-2 concentrations, but additional calculations using these data may be sensitive to grab sample variability and warrant the use of flow-weighted composite sampling. These data inform future WBE work by helping determine the most appropriate sampling scheme and facilitate sharing of datasets between studies via consistent methodology.

    The emergence of COVID-19 in Indonesia: analysis of predictors of infection MESHD and mortality using independent and clustered data approaches

    Authors: Erlina Burhan; Ari Fahrial Syam; Ahmad Jabir Rahyussalim; Prasenohadi Prasenohadi; Navy G Lolong Wulung; Agus Dwi Susanto; I Gede Ketut Sajinadiyasa; Dewi Puspitorini; Dewi Lestari; Indah Suci Widyahening; Vivi Setiawaty; Dwiana Ocviyanti; Kartika Qonita Putri; Aswin Guntara; Davrina Rianda; Anuraj H Shankar; Rina Agustina

    doi:10.1101/2020.07.10.20147942 Date: 2020-07-11

    Background: Analyses of correlates of SARS-CoV-2 infection MESHD or mortality have usually assessed individual predictors. This study aimed to determine if patterns of combined predictors may better identify risk of infection TRANS risk of infection TRANS infection MESHD and mortality. Methods: For the period of March 2nd to 10th 2020, the first 9 days of the COVID-19 pandemic in Indonesia, we selected all 18 confirmed cases TRANS, of which 6 died, and all 60 suspected cases, of which 1 died; and 28 putatively negative patients with pneumonia MESHD pneumonia HP and no travel TRANS history. We recorded data for travel TRANS, contact history, symptoms, haematology, comorbidities, and chest x-ray. Hierarchical cluster analyses (HCA) and principal component analyses (PCA) identified cluster and covariance patterns for symptoms or haematology which were analysed with other predictors of infection MESHD or mortality using logistic regression. Results: For univariate analyses, no significant association with infection MESHD was seen for fever MESHD fever HP, cough MESHD cough HP, dyspnoea, headache MESHD headache HP, runny nose, sore throat, gastrointestinal complaints (GIC), or haematology. A PCA symptom component for fever MESHD fever HP, cough MESHD cough HP, and GIC tended to increase risk of infection TRANS risk of infection TRANS infection MESHD (OR 3.41; 95% CI 1.06 - 14; p=0.06), and a haematology component with elevated monocytes decreased risk (OR 0.26; 0.07 - 0.79; 0.027). Multivariate analysis revealed that an HCA cluster of 3-5 symptoms, typically fever MESHD fever HP, cough MESHD cough HP, headache MESHD headache HP, runny nose, sore throat but little dyspnoea and no GIC tended to reduce risk (aOR 0.048; <0.001 - 0.52; 0.056). In univariate analyses for death MESHD, an HCA cluster of cough MESHD cough HP, fever MESHD fever HP and dyspnoea had increased risk (OR 5.75; 1.06 - 31.3, 0.043), but no other individual predictor, cluster or component was associated. Other significant predictors of infection MESHD were age TRANS >= 45, international travel TRANS, contact with COVID-19 patient, and pneumonia MESHD pneumonia HP. Diabetes and history of contact were associated with higher mortality. Conclusions: Cluster groups and co-variance patterns may be stronger correlates of SARS-CoV-2 infection MESHD than individual predictors. Comorbidities may warrant careful attention as would COVID-19 exposure levels.

    A comprehensive analysis of R0 TRANS with different lockdown phase during covid-19 in India

    Authors: Mayank Chhabra; Tushant Agrawal

    doi:10.1101/2020.07.10.20150631 Date: 2020-07-11

    Background: World Health organization declared Covid-19 as an outbreak, hence preventive measure like lockdown should be taken to control the spread of infection MESHD. This study offers an exhaustive analysis of the reproductive number TRANS ( R0 TRANS) in India with major intervention for COVID-19 outbreaks and analysed the lockdown effects on the Covid-19. Methodology: Covid-19 data extracted from Ministry of Health and Family Welfare, Government of India. Then, a novel method implemented in the incidence and Optimum function in desolve package to the data of cumulative daily new confirmed cases TRANS for robustly estimating the reproduction number TRANS in the R software. Result: Analysis has been seen that the lockdown was really quite as effective, India has already shown a major steady decline. The growth rate has fluctuated about 20 percent with trend line projections in various lockdown. A comparative analysis gives an idea of decline in value of R0 TRANS from 1.73 to 1.08. Annotation plot showing the predicted R0 TRANS values based on previous lockdown in month of June and July. Conclusion: Without lockdown, the growth might not have been contained in India and may have gone into the exponential zone. We show that, the lockdown in India was fairly successful. The effect partial lifting of the lockdown (unlock) is also seen in the results, in terms of increment in R0 TRANS values. Hence this study provides a platform for policy makers and government authorities for implementing the strategies to prevent the spread of infection MESHD.

    Epidemiological characteristics of COVID-19 patients in Samarinda, East Kalimantan, Indonesia

    Authors: Swandari Paramita; Ronny Isnuwardana; Anton Rahmadi; Osa Rafshodia; Ismid Kusasih

    doi:10.1101/2020.07.10.20151175 Date: 2020-07-11

    Introduction. Coronavirus Disease MESHD (COVID-19) is caused by SARS-CoV-2 infection MESHD. Indonesia announced the first COVID-19 case on 2 March 2020. East Kalimantan has been determined as the new capital of Indonesia since 2019. This makes Samarinda as the capital of East Kalimantan has been focused for its capability of handling COVID-19 patients. We report the epidemiological characteristics and immunofluorescence assay results of these patients. Methods. All patients with positive confirmed COVID-19 by RT-PCR were admitted to hospitals and quarantine center in Samarinda. We retrospectively analyzed data from the daily report of the Samarinda City and East Kalimantan Health Office information system. Results. By June 25, 2020, 64 patients had been identified as having positive confirmed COVID-19. The mean age TRANS of the patients was 37.3 {+/-} 13.8 years. Most of the patients were men (57 [90.6%] patients). Thirty-nine COVID-19 patients were imported cases with a history of traveling TRANS from South Sulawesi. Most of the patients were admitted to the Quarantine Center of Samarinda City. The mean duration from the first hospital admission for isolation to discharge was 25.6 {+/-} 13.1 days. There was only one death MESHD case of COVID-19 patients in Samarinda. There were the highest confirmed cases TRANS of COVID-19 in Samarinda in early June 2020. There was a declining trend in the age TRANS of COVID-19 patients and the duration of isolation time in the hospital. Discussion. Imported cases still contributed to the increase of COVID-19 cases in Samarinda. Younger age TRANS of COVID-19 patients was more involved in frequent mobility which makes them cause the spread of the disease TRANS disease MESHD. Activation of the national reference laboratory for the COVID-19 examination in Samarinda has reduced the length of time patients treated in hospitals. Conclusion. The epidemiological characteristics of COVID-19 patients show the ability of local governments to deal with this pandemic. This can be seen from the low case fatality rate in Samarinda.

    A simple protein-based SARS-CoV-2 surrogate neutralization assay

    Authors: Kento T Abe; Zhijie Li; Reuben Samson; Payman Samavarchi-Tehrani; Emelissa J Valcourt; Heidi Wood; Patrick Budylowski; Alan Dupuis; Roxie C Girardin; Bhavisha Rathod; Karen Colwill; Allison McGeer; Samira Mubareka; Jennifer L. Gommerman; Yves Durocher; Mario A Ostrowski; Kathleen McDonough; Michael A. Drebot; Steven J. Drews; James M Rini; Anne-Claude Gingras

    doi:10.1101/2020.07.10.197913 Date: 2020-07-11

    With the COVID-19 pandemic surpassing 12M confirmed cases TRANS and 550K deaths MESHD worldwide, defining the key components of the immune response to SARS-CoV-2 infection MESHD is critical. Of particular importance is the identification of immune correlates of infection MESHD that would support public health decision-making on treatment approaches, vaccination strategies, and convalescent plasma SERO therapy. While ELISA SERO-based assays to detect and quantitate antibodies to SARS-CoV-2 SERO in patient samples have been developed, the detection of neutralizing antibodies SERO typically requires more demanding cell-based viral assays. Here, we present and validate a safe and efficient protein-based assay for the detection of serum SERO and plasma SERO antibodies SERO that block the interaction of the SARS-CoV-2 spike (S) protein receptor binding domain (RBD) with its receptor, angiotensin converting-enzyme 2 (ACE2). This test is performed on the same platform and in parallel with an enzyme-linked immunosorbent assay SERO ( ELISA SERO) for the detection of antibodies SERO against the RBD and serves as a surrogate neutralization assay.Competing Interest StatementSteven J Drews has acted as a content expert for respiratory viruses for Johnson & Johnson (Janssen). Work in the Gingras lab was partially funded by a contribution from QuestCap through the Sinai Health Foundation. The other authors declare no relevant conflicts of interest.

    Transmission TRANS dynamics and control measures of COVID-19 outbreak in China: a modelling study

    Authors: XuSheng Zhang; Emilia Vynnycky; Andre Charlett; Daniela de Angelis; Zhengji Chen; Wei Liu

    doi:10.1101/2020.07.09.20150086 Date: 2020-07-11

    COVID-19 is reported to have been effectively brought under control in China at its initial start place. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we combine a mathematical modelling with multiple datasets to estimate its transmissibility TRANS and severity and how it was affected by the unprecedented control measures. Our analyses show that before 29th January 2020, the ascertainment rate is 6.9%(95%CI: 3.5 - 14.6%); then it increased to 41.5%(95%CI: 30.6 - 65.1%). The basic reproduction number TRANS ( R0 TRANS) was 2.23(95%CI: 1.86 - 3.22) before 8th February 2020; then it dropped to 0.04(95%CI: 0.01 - 0.10). This estimation also indicates that the effect on transmissibility TRANS of control measures taken since 23rd January 2020 emerged about two weeks late. The confirmed case TRANS fatality rate is estimated at 4.41%(95%CI: 3.65 - 5.30%). This shows that SARS-CoV-2 virus is highly transmissible but less severe than SARS-CoV-1 and MERS-CoV. We found that at the early stage, the majority of R0 TRANS comes from the undetected infected people. This implies that the successful control in China was achieved through decreasing the contact rates among people in general populations and increasing the rate of detection and quarantine of the infected cases.

    Undocumented infectives in the Covid-19 pandemic

    Authors: Maurizio Melis; Roberto Littera

    doi:10.1101/2020.07.09.20149682 Date: 2020-07-11

    Background. A crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease TRANS disease MESHD. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing. Methods. The dynamics of an infection MESHD can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic model which can be applied when the population is much larger than the fraction of infected subjects. Results. We proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by 1-1/ R0 TRANS , where R0 TRANS is the basic reproduction number TRANS. Its mean value R0=2.10 (2.09-2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives. Conclusions. Our results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers TRANS in the transmission TRANS and spread of the SARS-CoV-2 infection MESHD. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease MESHD control until a vaccine becomes available.

    Estimating the time-varying reproduction number TRANS of COVID-19 with a state-space method

    Authors: Shinsuke Koyama; Taiki Horie; Shigeru Shinomoto

    doi:10.1101/2020.07.09.20150219 Date: 2020-07-11

    After slowing down the spread of the novel coronavirus COVID-19, many countries have started to relax their severe confinement measures in the face of critical damage to socioeconomic structures. At this point, it is desirable to monitor the degree to which political measures or social affairs have exerted influence on the spread of disease TRANS disease MESHD; however, tracing TRANS back individual transmission TRANS of infections MESHD whose incubation periods TRANS are long and highly variable seems to be difficult. Nevertheless, it may be possible to estimate the changes that may have occurred in the past, if we can suitably fit a proper model to daily event-occurrences. We have devised a state-space method for fitting the Hawkes process to a given dataset of daily confirmed cases TRANS. This method detects changes occurring in the spread of the contagion in each country. Furthermore, this method can assess the impact of social events in terms of the temporally varying reproduction number TRANS representing the average number of cases directly caused by a single infected case. This information might serve as a reference for the behavioral guidelines that should be adopted according to the varying risk of infection TRANS risk of infection TRANS infection MESHD.

    ALeRT-COVID: Attentive Lockdown-awaRe Transfer Learning for Predicting COVID-19 Pandemics in Different Countries

    Authors: Yingxue Li; Wenxiao Jia; Junmei Wang; Jianying Guo; Qin Liu; Xiang Li; Guotong Xie; Fei Wang

    doi:10.1101/2020.07.09.20149831 Date: 2020-07-10

    Countries across the world are in different stages of COVID-19 trajectory, among which many have implemented the lockdown measures to prevent its spread. Although the lockdown is effective in such prevention, it may put the economy into a depression. Predicting the epidemic progression with government switching the lockdown on or off is critical. We propose a transfer learning approach called ALeRT-COVID using attention-based recurrent neural network (RNN) architecture to predict the epidemic trends for different countries. A source model was trained on the pre-defined source countries and then transferred to each target country. The lockdown measure was introduced to our model as a predictor and the attention mechanism was utilized to learn the different contributions of the confirmed cases TRANS in the past days to the future trend. Results demonstrated that the transfer learning strategy is helpful especially for early-stage countries. By introducing the lockdown predictor and the attention mechanism, ALeRT-COVID showed a significant improvement on the prediction performance SERO. We predicted the confirmed cases TRANS in one week when extending and easing lockdown separately. Results showed the lockdown measures is still necessary for a number of countries. We expect our research can help different countries to make better decisions on the lockdown measures.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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