Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (10)

Cough (9)

Hypertension (5)

Fatigue (4)

Pneumonia (3)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 86
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    SARS-CoV-2 antigens expressed in plants detect antibody SERO responses in COVID-19 patients

    Authors: Mohau S Makatsa; Marius B Tincho; Jerome M Wendoh; Sherazaan D Ismail; Rofhiwa Nesamari; Francisco Pera; Scott de Beer; Anura David; Sarika Jugwanth; Maemu P Gededzha; Nakampe Mampeule; Ian Sanne; Wendy Stevens; Lesley Scott; Jonathan Blackburn; Elizabeth S Mayne; Roanne S Keeton; Wendy A Burgers

    doi:10.1101/2020.08.04.20167940 Date: 2020-08-04 Source: medRxiv

    Background: The SARS-CoV-2 pandemic has swept the world and poses a significant global threat to lives and livelihoods, with over 16 million confirmed cases TRANS and at least 650 000 deaths MESHD from COVID-19 in the first 7 months of the pandemic. Developing tools to measure seroprevalence SERO and understand protective immunity to SARS-CoV-2 is a priority. We aimed to develop a serological assay SERO using plant-derived recombinant viral proteins, which represent important tools in less-resourced settings. Methods: We established an indirect enzyme-linked immunosorbent assay SERO ( ELISA SERO) using the S1 and receptor-binding domain (RBD) portions of the spike protein from SARS-CoV-2, expressed in Nicotiana benthamiana. We measured antibody SERO responses in sera from South African patients (n=77) who had tested positive by PCR for SARS-CoV-2. Samples were taken a median of six weeks after the diagnosis, and the majority of participants had mild and moderate COVID-19 disease MESHD. In addition, we tested the reactivity of pre-pandemic plasma SERO (n=58) and compared the performance SERO of our in-house ELISA SERO with a commercial assay. We also determined whether our assay could detect SARS-CoV-2-specific IgG and IgA in saliva. Results: We demonstrate that SARS-CoV-2-specific immunoglobulins are readily detectable using recombinant plant-derived viral proteins, in patients who tested positive for SARS-CoV-2 by PCR. Reactivity to S1 and RBD was detected in 51 (66%) and 48 (62%) of participants, respectively. Notably, we detected 100% of samples identified as having S1-specific antibodies SERO by a validated, high sensitivity SERO commercial ELISA SERO, and OD values were strongly and significantly correlated between the two assays. For the pre-pandemic plasma SERO, 1/58 (1.7%) of samples were positive, indicating a high specificity for SARS-CoV-2 in our ELISA SERO. SARS-CoV-2-specific IgG correlated significantly with IgA and IgM responses. Endpoint titers of S1- and RBD-specific immunoglobulins ranged from 1:50 to 1:3200. S1-specific IgG and IgA were found in saliva samples from convalescent volunteers. Conclusions: We demonstrate that recombinant SARS-CoV-2 proteins produced in plants enable robust detection of SARS-CoV-2 humoral responses. This assay can be used for seroepidemiological studies and to measure the strength and durability of antibody SERO responses to SARS-CoV-2 in infected patients in our setting.

    Altitude as a protective factor from COVID-19

    Authors: Timothy M Thomson; Fresia Casas; Harold Andre Guerrero; Rómulo Figueroa-Mujica; Francisco C Villafuerte; Claudia Machicado

    doi:10.1101/2020.08.03.20167262 Date: 2020-08-04 Source: medRxiv

    The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August, 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases TRANS and deaths MESHD per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence SERO in the population of risk factors associated with severe COVID-19, including hypertension MESHD hypertension HP and hypercholesterolemia MESHD hypercholesterolemia HP. We discuss long-term multisystemic adaptations to hypobaric hypoxia MESHD as possible mechanisms that may explain the observed protective effect of high altitude from death MESHD from COVID-19.

    Children TRANS with COVID-19 like symptoms in Italian Pediatric Surgeries: the dark side of the coin

    Authors: Gianfranco Trapani; Vassilios Fanos; Enrico Bertino; Giulia Maiocco; Osama Al Jamal; Michele Fiore; VIncenzo Bembo; Domenico Careddu; Lando Barberio; Luisella Zanino; Giuseppe Verlato

    doi:10.1101/2020.07.27.20149757 Date: 2020-07-29 Source: medRxiv

    BACKGROUND: Symptoms of SARS-CoV-2 infection MESHD in children TRANS are nonspecific and shared with other common acute viral illnesses ( fever MESHD fever HP, respiratory or gastrointestinal symptoms, and cutaneous signs), thus making clinical differential diagnosis tricky. In Italy, first line management of pediatric care is handed over to Primary Care Pediatricians (PCPs), who were not allowed to directly perform diagnostic tests during the recent COVID-19 outbreak. Without a confirmatory diagnosis, PCPs could only collect information on ''COVID-19 like symptoms'' rather than identify typical COVID-19 symptoms. AIM: To evaluate the prevalence SERO of COVID-19 like symptoms in outpatient children TRANS, during Italian lockdown. To provide PCPs a risk score to be used in clinical practice during the differential diagnosis process. METHODS: A survey was submitted to 50 PCPs (assisting 47,500 children TRANS) from 7 different Italian regions between the 4th of March and the 23rd of May 2020 (total and partial lockdown period). COVID-19 like symptoms in the assisted children TRANS were recorded, as well as presence of confirmed/suspected cases in children TRANS's families, which was taken as proxy of COVID-19. Multivariable logistic regression was accomplished to estimate the risk of having suspected/ confirmed cases TRANS in families, considering symptoms as potential determinants. RESULTS: 2,300 children TRANS (4.8% of overall survey population) fell HP ill with COVID-19 like symptoms, 3.1% and 1.7% during total and partial lockdown period respectively. The concurrent presence of fatigue MESHD fatigue HP, cough MESHD cough HP, and diarrhea MESHD diarrhea HP in children TRANS, in absence of sore throat/ earache MESHD and abnormal skin signs, represents the maximum risk level of having a suspected/ confirmed case TRANS of COVID-19 at home. CONCLUSIONS: The percentage of children TRANS presenting COVID-19 like symptoms at home has been remarkable also during the total lockdown period. The present study identified a pattern of symptoms which could help, in a cost-effective perspective, PCPs in daily clinical practice to define priorities in addressing children TRANS to the proper diagnostic procedure.

    Seroprevalence SERO of SARS-CoV-2 IgG Antibodies SERO in Utsunomiya City, Greater Tokyo, after first pandemic in 2020 (U-CORONA): a household- and population-based study

    Authors: Nobutoshi Nawa; Jin Kuramochi; Shiro Sonoda; Yui Yamaoka; Yoko Nukui; Yasunari Miyazaki; Takeo Fujiwara

    doi:10.1101/2020.07.20.20155945 Date: 2020-07-26 Source: medRxiv

    Background: The number of confirmed cases TRANS of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infections MESHD in Japan are substantially lower in comparison to the US and UK, potentially due to the under-implementation of polymerase chain reaction (PCR) tests. Studies reported that more than half of the SARS-CoV-2 infections are asymptomatic MESHD asymptomatic TRANS, confirming the importance for conducting seroepidemiological studies. Although the seroepidemiological studies in Japan observed a reported prevalence SERO of 0.10% in Tokyo, 0.17% in Osaka, and 0.03% in Miyagi, sampling bias was not considered. The study objective was to assess the seroprevalence SERO of SARS-CoV-2 in a random sample of households in Utsunomiya City in Tochigi Prefecture, Greater Tokyo, Japan. Methods: We launched the Utsunomiya COVID-19 seROprevalence SERO Neighborhood Association (U-CORONA) Study to assess the seroprevalence SERO of COVID-19 in Utsunomiya City. The survey was conducted between 14 June 2020 and 5 July 2020, in between the first and second wave of the pandemic. Invitations enclosed with a questionnaire were sent to 2,290 people in 1,000 households randomly selected from Utsunomiya basic resident registry. Written informed consent was obtained from all participants. The level of IgG antibodies SERO to SARS-CoV-2 was assessed by chemiluminescence immunoassay SERO analysis. Results: Among 2,290 candidates, 753 returned the questionnaire and 742 received IgG tests (32.4 % participation rate). Of the 742 participants, 86.8% were 18 years or older, 52.6% were women, 71.1% were residing within 10 km from the test clinic, and 89.2% were living with another person. The age TRANS and sex distribution, distance to clinic and police district were similar with those of non-participants, while the proportion of single-person households was higher among non-participants than participants (16.2% vs. 10.8%). We confirmed three positive cases through quantitative antibody testing SERO. No positive cases were found among the people who live in the same household as someone with positive. All cases were afebrile. The estimated unweighted and weighted prevalence SERO of SARS-CoV-2 infection MESHD were 0.40% (95% confidence interval: 0.08-1.18%) and 1.23% (95% confidence interval: 0.17-2.28%), respectively. Conclusion: This study suggests the importance of detecting all cases using PCR or antigen testing, not only at a hospital, but also in areas where people assemble. Further prospective studies using this cohort are needed to monitor SARS-CoV-2 antibody SERO levels.

    Population Risk Factors for COVID-19 Deaths MESHD in Nigeria at Subnational Level

    Authors: Zubaida Hassan; Muhammad Jawad Hashim; Gulfaraz Khan

    id:10.20944/preprints202007.0621.v1 Date: 2020-07-25 Source: Preprints.org

    Nigeria is the most populous country in the African continent. The aim of this study was to analyze risk factors for COVID-19 prevalence SERO and deaths MESHD in all 6 geopolitical regions and 37 states in Nigeria. We analyzed the data retrieved from various sources, including Nigeria CDC, Nigeria National Bureau of Statistics, Unicef-Nigeria multiple indicator cluster survey and the Institute of Health Metrics and Evaluation, University of Washington. We examined 4 clinical risk factors ( prevalence SERO of TB, HIV, smoking and BCG vaccination coverage) and 5 sociodemographic factors ( age TRANS ≥65, population density, literacy rate, unemployment and GDP per capita). Multivariate modeling was conducted using generalized linear model. Our analysis showed that the incidence of confirmed COVID-19 cases differed widely across the 37 states, from 0.09 per 100,000 in Kogi to 83.7 in Lagos. However, more than 70% of confirmed cases TRANS were concentrated in just 7 states: Lagos, Abuja, Oyo, Kano, Edo, Rivers and Delta. Case mortality rate (CMR) per million population also varied considerably, with Lagos, Abuja and Edo having CMR above 9. On bivariate analysis, higher CMR correlated positively with GDP and to a lesser extent with TB and population density. On multivariate analysis, which is more definitive, states with higher HIV prevalence SERO and BCG coverage had lower CMR, while high GDP states had a greater CMR. This study indicates that COVID-19 has disproportionately affected certain states in Nigeria. Population susceptibility factors include higher economic development but not literacy or unemployment. Death MESHD rates were mildly lower in states with higher HIV prevalence SERO and BCG vaccination coverage.

    SARS-CoV-2 serosurvey in Health Care Workers of the Veneto Region

    Authors: Mario Plebani; Andrea Padoan; Ugo Fedeli; Elena Schievano; Elena Vecchiato; Giuseppe Lippi; Giuliana Lo Cascio; Stefano Porru; Giorgio Palu

    doi:10.1101/2020.07.23.20160457 Date: 2020-07-24 Source: medRxiv

    Background: The ongoing outbreak of coronavirus disease MESHD (COVID-19) caused by the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) poses formidable challenges to all health care systems. Serological assays SERO may improve disease MESHD management when appropriately used, for better understanding the antibody SERO responses mounted upon SARS-CoV-2 infection MESHD and for assessing its real prevalence SERO. Although testing the whole population is impratical, well-designed serosurveys in selected subpopulations in specific risk groups may provide valuable information. Aim: we evaluated the prevalence SERO of SARS-CoV-2 infection MESHD in health care workers who underwent molecular testing with reverse transcription real-time polymerase chain reaction (rRT-PCR) in the main hospitals of the Veneto Region by measuring specific antibodies SERO (Abs). Methods: both IgM and IgG antibodies SERO against SARS-Cov-2 S-antigen and N-protein were measured using a validated chemiluminescent analytical system (CLIA) called Maglumi 2000 Plus (New Industries Biomedical EngineeringCo., Ltd [Snibe], Shenzhen, China) Results: A total of 8285 health care workers were tested. SARS-CoV-2 specific antibodies SERO (IgM, IgG or both) were detectable in 378 cases (4.6%, 95% CI 4.1-5.0%). Seroconversion was observed in 4.4% women and 5% men, but the difference was not significant. Although detectable antibodies SERO were found in all severe COVID-19 patients (100%), lower seropositivity was found in mild disease MESHD (83%) and the lowest prevalence SERO (58%) was observed in asymptomatic TRANS subjects. Conclusion: Seroprevalence SERO surveys are of utmost importance for understanding the rate of population that has already developed antibodies SERO against SARS-CoV-2. The present study has the statistical power to define precisely the circulation of SARS-CoV-2 in a cohort of health workers in our region, with its prevalence SERO (4.6%) reflecting a relatively low circulation. Symptomatic individuals or those hospitalized for medical care were 100% antibody SERO positive, whilst Abs were only detectable in 58% of asymptomatic TRANS carriers TRANS.

    Community-level SARS-CoV-2 Seroprevalence SERO Survey in urban slum dwellers of Buenos Aires City, Argentina: a participatory research.

    Authors: Silvana Figar; Vanina Pagotto; Lorena Luna; Julieta Salto; Magdalena Wagner Manslau; Alicia Mistchenko; ANDREA GAMARNIK; Ana Maria Gomez Saldano; Fernan Quiros

    doi:10.1101/2020.07.14.20153858 Date: 2020-07-16 Source: medRxiv

    Background By July 1st, the incidence rate of RT-qPCR SARS-CoV-2 infection MESHD was 5.9% in Barrio Padre Mugica, one of the largest slums in Buenos Aires City. This study aimed to establish the seroprevalence SERO of SARS-CoV-2 three months after the first case was reported. Methods Between June 10th and July 1st, a cross-sectional design was carried out on people over 14 years old, selected from a probabilistic sample of households. A finger prick sample was tested by ELISA SERO to detect IgG-class antibodies SERO against SARS-CoV-2. Multilevel model was applied to understand sector, household and individual conditions associated with seroconvert. Results Prevalence SERO based on IgG was 53.4% (95%IC 52.8% to 54.1%). Among the IgG positive cases, 15% reported having compatible symptoms at some point in the past two months. There is evidence of within-household clustering effect (rho=0.52; 95% IC 0.36-0.67); living with a PCR- confirmed case TRANS doubled the chance of being SARS-CoV2 IgG positive (OR 2.13; 95% IC 1.17-3.85). The highest risk of infection TRANS risk of infection TRANS infection MESHD was found in one of the most deprived areas of the slum, the Bajo autopista sector. Discussion High seroprevalence SERO is shown, for each symptomatic RT-qPCR-confirmed diagnosis, 9 people were IgG positive, indicating a high rate of undetected (probable asymptomatic) infections MESHD asymptomatic TRANS. Given that transmission TRANS among family members TRANS is a leading driver of the disease MESHD`s spread, it is unsurprising that crowded housing situations in slums are directly associated with higher risk of infection TRANS risk of infection TRANS infection MESHD and consequently high seroprevalence SERO levels. This study contributes to the understanding of population immunity against SARS-CoV2, its relation to living conditions and viral spread, for future decision making.

    Smart Pooling: AI-powered COVID-19 testing

    Authors: María Escobar; Guillaume Jeanneret; Laura Bravo-Sánchez; Angela Castillo; Catalina Gómez; Diego Valderrama; Maria F. Roa; Julián Martínez; Jorge Madrid-Wolff; Martha Cepeda; Marcela Guevara-Suarez; Olga L. Sarmiento; Andrés L. Medaglia; Manu Forero-Shelton; Mauricio Velasco; Juan Manuel Pedraza-Leal; Silvia Restrepo; Pablo Arbelaez

    doi:10.1101/2020.07.13.20152983 Date: 2020-07-15 Source: medRxiv

    Background: COVID-19 is an acute respiratory illness caused by the novel coronavirusSARS-CoV-2. The disease MESHD has rapidly spread to most countries and territories and hascaused 14.2 million confirmed infections TRANS infections MESHD and 602,037 deaths MESHD as of July 19th 2020. Massive molecular testing for COVID-19 has been pointed as fundamental to moderate the spread of the disease TRANS disease MESHD. Pooling methods can enhance the efficiency of testing, but they are viable only at very low incidences of the disease MESHD. We propose Smart Pooling, a machine learning method that uses clinical and sociodemographic data from patients to increase the efficiency of pooled molecular testing for COVID-19 by arranging samples into all-negative pools. Methods: We developed machine learning methods that estimate the probability that a sample will test positive for SARS-Cov-2 based on complementary information from the sample. We use these predictions to exclude samples predicted as positive from pools. We trained our machine learning methods on a dataset of 2000 patients tested for SARS-Cov-2 from April to July in Bogota, Colombia. Findings: Our method, Smart Pooling, shows efficiency of 306% at a disease MESHD prevalence SERO of 5% and efficiency of 107% at disease MESHD a prevalence SERO of up to 50%, a regime in which two-stage pooling offers marginal efficiency gains compared to individual testing. Additionally, we calculate the possible efficiency gains of one- and two-dimensional two-stage pooling strategies, and present the optimal strategies for disease MESHD prevalences SERO up to 25%. We discuss practical limitations to conduct pooling in the laboratory. Interpretation: Pooled testing has been a theoretically alluring option to increase the coverage of diagnostics since its proposition by Dorfmann during World War II. Although there are examples of successfully using pooled testing to reduce the cost of diagnostics, its applicability has remained limited because efficiency drops rapidly as prevalence SERO increases. Not only does our method provide a cost-effective solution to increase the coverage of testing amid the COVID-19 pandemic, but it also demonstrates that artificial intelligence can be used complementary with well-established techniques in the medical praxis.

    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 Source: medRxiv

    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 Source: medRxiv

    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.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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