Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
    displaying 1 - 10 records in total 13
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    Evaluating ten commercially-available SARS-CoV-2 rapid serological tests SERO using the STARD (Standards for Reporting of Diagnostic Accuracy Studies) method.

    Authors: Laurent Dortet; Jean-Baptiste Ronat; Christelle Vauloup-Fellous; Céline Langendorf; David-Alexis Mendels; Cécile Emeraud; Saoussen Oueslati; Delphine Girlich; Anthony Chauvin; Ali Afdjei; Sandrine Bernabeu; Samuel Le Pape; Rim Kallala; Alice Rochard; Celine Verstuyft; Nicolas Fortineau; Anne-Marie Roque-Afonso; Thierry Naas; Duncan Kimmel; James H Lee; Margarette Mariano; Antonio Nakouzi; Jose Quiroz; Johanna Rivera; Wendy A Szymczak; Karen Tong; Jason Barnhill; Mattias NE Forsell; Clas Ahlm; Daniel T. Stein; Liise-anne Pirofski; Doctor Y Goldstein; Scott J. Garforth; Steven C. Almo; Johanna P. Daily; Michael B. Prystowsky; James D. Faix; Amy S. Fox; Louis M. Weiss; Jonathan R. Lai; Kartik Chandran

    doi:10.1101/2020.09.10.20192260 Date: 2020-09-11 Source: medRxiv

    Numerous SARS-CoV-2 rapid serological tests SERO have been developed, but their accuracy has usually been assessed using very few samples, and rigorous comparisons between these tests are scarce. In this study, we evaluated and compared 10 commercially-available SARS-CoV-2 rapid serological tests SERO using the STARD methodology (Standards for Reporting of Diagnostic Accuracy Studies). 250 sera from 159 PCR-confirmed SARS-CoV-2 patients (collected from 0 to 32 days after onset of symptoms TRANS) were tested with rapid SERO serological tests SERO. Control sera (N=254) were retrieved from pre-COVID periods from patients with other coronavirus infections MESHD (N=11), positive rheumatoid factors HP rheumatoid MESHD factors (N=3), IgG/ IgM hyperglobulinemia MESHD (N=9), malaria MESHD (n=5), or no documented viral infection MESHD (N=226). All samples were tested using rapid SERO lateral flow immunoassays SERO (LFIA) from ten manufacturers. Only four tests achieved [≥]98% specificity, with other tests ranging from 75.7%-99.2%. Sensitivities SERO varied by the day of sample collection, from 31.7%-55.4% (Days 0-9), 65.9%-92.9% (Days 10-14), and 81.0%-95.2% (>14 days) after the onset of symptoms TRANS, respectively. Only three tests evaluated met French Health Authorities' thresholds for SARS-CoV-2 serological tests SERO ([≥]90% sensitivity SERO + [≥]98% specificity). Overall, the performances SERO between tests varied greatly, with only a third meeting acceptable specificity and sensitivity SERO thresholds. Knowing the analytical performance SERO of these tests will allow clinicians to use them with more confidence, could help determine the general population's immunological status, and may diagnose some patients with false-negative RT-PCR results.

    Comprehensive analysis of the key epidemiological parameters to evaluate the impact of BCG vaccination on COVID-19 pandemic

    Authors: Niloy R Datta; Sneha Datta; Syed Hussain Baqar Abidi; Wajiha Farooq; Mabel Aylwin; Gigia Roizen; Mirentxu Iruretagoyena; Vivianne Agar; Javiera Donoso; Margarita Fierro; Jose Montes; Graham Cooke; Steven Riley; Paul Elliott; Rachel Vreeman; Joseph Masci; Nick A Maskell; Shaney Barratt

    doi:10.1101/2020.08.12.20173617 Date: 2020-08-14 Source: medRxiv

    Globally, the heterogenous coronavirus disease MESHD 2019 (COVID-19) case fatality rate (CFR) could be influenced by various epidemiological parameters. Identifying these could help formulate effective public health strategies. Incidence and mortality of COVID-19 for each of the 220 countries as on July 30, 2020 were evaluated against key epidemiological variables, namely - BCG vaccination (ongoing vs. discontinued/never undertaken), %population aged TRANS [≥]65 years, incidences of ischemic heart disease MESHD ( IHD MESHD), hypertensive heart disease MESHD ( HHD MESHD), cancer MESHD, malaria MESHD, and diabetes MESHD; human development index (HDI) and population density. These were retrieved from the public domains of WHO, UN, World Bank and published reports. The COVID-19 CFRs ranged between 0.0% and 28.3% (mean {+/-} SD: 3.05% {+/-} 3.48). The influence of the individual epidemiological parameters on CFR were evaluated through the event rate estimations. A significantly lower event rate was observed in countries with ongoing BCG vaccination program (ER: with vs without ongoing BCG vaccination: 0.020 vs 0.034, p<0.001). The type of BCG strains used also influenced the ER; this being 0.018, 0.031 and 0.019 for early, late and mixed strains respectively (p=0.008). The epidemiological variables significantly associated with higher COVID-19 event rate were countries with higher %population aged TRANS [≥]65 years (p<0.001), greater incidence of IHD MESHD (p<0.001) and cancer MESHD (p=0.003) and better HDI (p=0.003). Incidences of malaria MESHD, HHD MESHD and diabetes MESHD along with population density had no significant impact on COVID-19 CFR. Further, BCG vaccination significantly lowered the COVID-19 ER in each of the high-risk population subgroups - countries with >7.1% population aged TRANS [≥]65 years (p=0.008), >0.737 HDI (p=0.001), IHD MESHD >1171/105 population (p=0.004) and cancer MESHD incidence >15726 (p<0.001). The results supports BCG induced trained immunity leading to heterologous immunoprotection against COVID-19. Thus BCG vaccination with early strains could provide a cost-effective prophylaxis, especially in high-risk individuals and bridge the gap till an effective vaccine against SARS-CoV-2 is freely available globally.

    Diagnostics and spread of SARS-CoV-2 in Western Africa: An observational laboratory-based study from Benin

    Authors: Anges Yadouleton; Anna-Lena Sander; Andres Moreira-Soto; Carine Tchibozo; Gildas Hounkanrin; Yvette Badou; Carlo Fischer; Nina Krause; Petas Akogbeto; Edmilson F. de Oliveira Filho; Anges Dossou; Sebastian Bruenink; Melchior AIssi; Mamoudou Harouna Djingarey; Benjamin Hounkpatin; Michael Nagel; Jan felix Drexler

    doi:10.1101/2020.06.29.20140749 Date: 2020-07-08 Source: medRxiv

    Information on severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) spread in Africa is limited by fragile 2 surveillance systems and insufficient diagnostic capacity. 3 We assessed the coronavirus disease-19 (COVID-19)-related diagnostic workload in Benin, Western Africa, 4 characterized SARS-CoV-2 genomes from 12 acute cases of COVID-19, used those together with public data to 5 estimate SARS-CoV-2 transmission TRANS dynamics in a Bayesian framework, validated a widely used diagnostic dual target 6 RT-PCR kit donated to African countries, and conducted serological analyses in 68 sera from confirmed COVID-19 7 cases and from febrile patients sampled before the predicted SARS-CoV-2 introduction. 8 We found a 15-fold increase in the monthly laboratory workload due to COVID-19. Genomic surveillance showed 9 introductions of three distinct SARS-CoV-2 lineages. SARS-CoV-2 genome-based analyses yielded an R0 TRANS estimate of 10 4.4 (95% confidence interval: 2.0-7.7), suggesting intense spread of SARS-CoV-2 in Africa. RT-PCR-based tests 11 were highly sensitive but showed variation of internal controls and between diagnostic targets. Commercially available 12 SARS-CoV-2 ELISAs SERO showed up to 25% false-positive results depending on antigen and antibody SERO types, likely due 13 to unspecific antibody SERO responses elicited by acute malaria MESHD according to lack of SARS-CoV-2-specific neutralizing 14 antibody SERO responses and relatively higher parasitemia MESHD in those sera. 15 We confirm an overload of the diagnostic capacity in Benin and provide baseline information on the usability of 16 genome-based surveillance in resource-limited settings. Sero-epidemiological studies SERO Sero-epidemiological studies SERO needed to assess SARS-CoV-2 17 spread may be put at stake by low specificity of tests in tropical settings globally. The increasing diagnostic challenges 18 demand continuous support of national and supranational African stakeholders.

    Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

    Authors: Cleidy Osorio-Mogollon; Gustavo E. Olivos-Ramirez; Kewin Otazu; Manuel E. Chenet-Zuta; Georcki Ropon-Palacios; Ihosvany Camps; Gabriel M. Jimenez-Avalo; Eduardo Apari-Cossio; Natalia E. Torres-Moreira; Reyna G. Cardenas-Cardenas

    doi:10.26434/chemrxiv.12501791.v1 Date: 2020-06-19 Source: ChemRxiv

    The world is currently facing a pandemic caused by the new 2019 coronavirus disease MESHD (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesisof genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNApolymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drugsearch, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning isconsidered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria MESHD, which were filtered under the criteria of selecting those that do not present any violation of Lipinski'sRule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can beconsidered as drugs for the development of effective treatments against this new pandemic.

    Comparative analyses revealed reduced spread of COVID-19 in malaria MESHD endemic countries

    Authors: Azhar Muneer; Kiran Kumari; Manish Tripathi; Rupesh Srivastava; Asif Mohmmed; Sumit Rathore

    doi:10.1101/2020.05.11.20097923 Date: 2020-05-14 Source: medRxiv

    In late 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection MESHD started in Hubei province of China and now it has spread like a wildfire in almost all parts of the world except some. WHO named the disease caused by SARS-CoV-2 as COVID-19 ( CoronaVirus Disease MESHD-2019). It is very intriguing to see a mild trend of infection MESHD in some countries which could be attributed to mitigation efforts, lockdown strategies, health infrastructure, demographics and cultural habits. However, the lower rate of infection and death MESHD rates in mostly developing countries, which are not placed at higher levels in terms of healthcare facilities, is a very surprising observation. To address this issue, we hypothesize that this lower rate of infection is majorly been observed in countries which have a higher transmission TRANS/ prevalence SERO of protozoan parasite borne disease MESHD, malaria MESHD. We compared the COVID-19 spread and malaria MESHD endemicity of 108 countries which have shown at least 200 cases of COVID-19 till 18th April 2020. We found that the number of COVID-19 cases per million population correlates negatively with the malaria MESHD endemicity of respective countries. The malaria MESHD free countries not only have higher density of COVID-19 infections but also the higher case fatality rates as compared to highly malaria MESHD endemic countries. We also postulate that this phenomenon is due to natural immune response against malaria infection MESHD, which is providing a heterologous protection against the virus. Unfortunately, there is no licensed vaccine against SARS-CoV-2 yet, but this information will be helpful in design of future strategies against fast spreading COVID-19 disease.

    Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis

    Authors: Amobi Andrew Onovo; Akinyemi Atobatele; Abiye Kalaiwo; Christopher Obanubi; Ezekiel James; Pamela Gado; Gertrude Odezugo; Doreen Magaji; Dolapo Ogundehin; Michele Russell

    doi:10.1101/2020.04.27.20082057 Date: 2020-05-02 Source: medRxiv

    Introduction: Coronavirus disease 2019 (COVID-19) is an emerging infectious disease MESHD that was first reported in Wuhan, China, and has subsequently spread worldwide. Knowledge of coronavirus-related risk factors can help countries build more systematic and successful responses to COVID-19 disease outbreak. Here we used Supervised Machine Learning and Empirical Bayesian Kriging MESHD (EBK) techniques to reveal correlates and patterns of COVID-19 Disease outbreak in sub-Saharan Africa (SSA). Methods: We analyzed time series aggregate data compiled by Johns Hopkins University on the outbreak of COVID-19 disease across SSA. COVID-19 data was merged with additional data on socio-demographic and health indicator survey data for 39 of SSA 48 countries that reported confirmed cases TRANS and deaths from coronavirus between February 28, 2020 through March 26, 2020. We used supervised machine learning algorithm, Lasso for variable selection and statistical inference. EBK was used to also create a raster estimating the spatial distribution of COVID-19 disease outbreak. Results: The lasso Cross-fit partialing out predictive model ascertained seven variables significantly associated with the risk of coronavirus infection MESHD (i.e. new HIV infections MESHD among pediatric, adolescent, and middle- aged TRANS adult TRANS PLHIV, time (days), pneumococcal MESHD conjugate-based vaccine, incidence of malaria MESHD and diarrhea HP diarrhea MESHD treatment). Our study indicates, the doubling time in new coronavirus cases was 3 days. The steady three-day decrease in coronavirus outbreak rate of change (ROC) from 37% on March 23, 2020 to 23% on March 26, 2020 indicates the positive impact of countries' steps to stymie the outbreak. The interpolated maps show that coronavirus is rising every day and appears to be severely confined in South Africa. In the West African region (i.e. Burkina Faso, Ghana, Senegal, CotedIviore, Cameroon, and Nigeria), we predict that new cases and deaths MESHD from the virus are most likely to increase. Interpretation: Integrated and efficiently delivered interventions to reduce HIV MESHD, pneumonia HP pneumonia MESHD, malaria MESHD and diarrhea HP diarrhea MESHD, are essential to accelerating global health efforts. Scaling up screening and increasing COVID-19 testing capacity across SSA countries can help provide better understanding on how the pandemic is progressing and possibly ensure a sustained decline in the ROC of coronavirus outbreak. Funding: Authors were wholly responsible for the costs of data collation and analysis.

    In Vitro Virucidal Effect of Intranasally Delivered Chlorpheniramine Maleate Compound Against Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2)

    Authors: Gustavo Ferrer; Jonna Westover

    doi:10.21203/rs.3.rs-25854/v1 Date: 2020-04-28 Source: ResearchSquare

     Background. The initial global outbreak of the novel coronavirus disease MESHD 2019 (COVID-2019) pandemic, responsible for the severe acute respiratory syndrome MESHD 2 (SARS-CoV-2), was first reported in Wuhan, China, at the end of December 2019. COVID-19 shares similarities with the severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD, and it behaves similarly to influenza with a high intranasal viral load. The genome sequence of COVID-19 opened the opportunity for multiple in vitro and clinical trials, but we still do not have a clear path to treatment. Chlorpheniramine is a safe and effective antihistamine with potent antiviral activity against various strains of influenza A/B, thus suggesting that CPM has broad antiviral activity. We tested the virucidal potential of chlorpheniramine maleate (CPM) in a nasal spray composition currently in development as an anti- allergy HP allergy MESHD medication.Methods. The virucidal activity of chlorpheniramine maleate was tested using viral stock of SARS-CoV-2, USA-WA1/2020 strain in Vero 76 infected cells. The end-point titer (CCID50) values were calculated with the Reed-Muench (1948) equation. Three independent replicates of each sample were tested, and the average and standard deviation were calculated. Results were compared with untreated controls by one-way ANOVA with Dunnett’s multiple comparison test in GraphPad Prism (version 8) software. Results. After 25-minutes of contact time, the nasal spray reduced the levels of the virus from 4.2 to 1.7 log10 CCID50 per 0.1 mL, a statistically significant reduction of 2.5 log10 CCID50.Conclusions. This study demonstrates the strong virucidal effect against SARS-CoV-2 of a nasal spray containing chlorpheniramine maleate. Given that CPM has broad antiviral effects against influenza, virucidal effect against SARS-CoV-2, and coadjuvant effects with hydroxychloroquine in treating multidrug-resistant malaria MESHD with minimal side effects. We propose two further studies: a randomized placebo-controlled study of intranasally delivered chlorpheniramine in patients with mild to moderate SARS-CoV-2, and a second study aiming to determine the potential antiviral and adjuvant effects of CPM plus hydroxychloroquine, versus chloroquine alone, in hospitalized patients with SARS-CoV-2.   

    Multiple drivers of the COVID-19 spread: role of climate, international mobility, and region-specific conditions

    Authors: Yasuhiro Kubota; Takayuki Shiono; Buntarou Kusumoto; Junichi Fujinuma

    doi:10.1101/2020.04.20.20072157 Date: 2020-04-24 Source: medRxiv

    The novel Coronavirus Disease MESHD 2019 (COVID-19) has spread quickly across the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific susceptibility (BCG vaccination, malaria infection MESHD, and elderly TRANS population) and international traveller population (human mobility) in shaping the geographical patterns of COVID-19 cases across 1,055 countries/regions, and examined the sequential shift of multiple drivers of the accumulated cases from December, 2019 to April 12, 2020. The accumulated numbers of COVID-19 cases (per 1 million population) were well explained by a simple regression model. The explanatory power (R2) of the model increased up to > 70% in April 2020 as the COVID-19 spread progressed. Climate, host mobility, and host susceptibility largely explained the variance of the COVID-19 cases (per 1 million population), and their explanatory power improved as the pandemic progressed; the relative importance of host mobility and host susceptibility have been greater than that of climate. The number of days from outbreak onset showed greater explanatory power in the earlier stages of COVID-19 spread but rapidly lost its influence. Our findings demonstrate that the COVID-19 pandemic is deterministically driven by climate suitability, cross-border human mobility, and region-specific susceptibility. The present distribution of COVID-19 cases has not reached an equilibrium and is changing daily, especially in the Southern Hemisphere. Nevertheless, the present results, based on mapping the spread of COVID-19 and identifying multiple drivers of this outbreak trajectory, may contribute to a better understanding of the COVID-19 disease transmission risk TRANS and the measures against long-term epidemic.

    Repurposing of Chloroquine and Its Derivative, Hydroxychloroquine for COVID-19: Implications for People Living with HIV MESHD in Africa

    Authors: Chiagoziem Otuechere

    id:10.20944/preprints202004.0395.v1 Date: 2020-04-22 Source: Preprints.org

    The coronavirus disease MESHD 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 MESHD, has been declared by the World Health Organization (WHO) as a pandemic. Unfortunately, finding a vaccine or developing drugs from the scratch is a time-consuming luxury given the widespread and high fatality rates of the virus. In the short term, repurposing of drugs already in use seem to be the most rational step to quickly and effectively curb the virus. Several antiviral agents had been proposed as possible remedies, but the 4-aminoquinolines, Chloroquine (CHQ) and hydroxychloroquine (HCHQ) appear to be generating more interest. They are generic, cheaply available and have proven efficacy against malaria parasites MESHD in Africa. The human immunodeficiency HP immunodeficiency MESHD virus ( HIV MESHD), on the other hand, targets the immune system thereby reducing the patient’s ability to fight infections. Sadly, 68% of the global HIV burden occur in Africa. It is therefore anticipated that incidence of severe forms of COVID-19 could occur in Africa because of associated endemic conditions that compromise the immune system. With CHQ and HCHQ being considered for clinical use against COVID-19, there is a need to highlight their potential merits and confounding variables in the subgroup of patients with or without HIV MESHD.

    Myths and Facts: Chloroquine May Be A Potential Supportive/Therapeutic Drug in COVID-19 Treatment

    Authors: Muhammad Kashif; Muhammad Aamir; Sadia Minhas; Romeeza Tahir; Shah Jahan; Nadeem Afzal

    id:10.20944/preprints202004.0341.v1 Date: 2020-04-19 Source: Preprints.org

    Quinine and its less toxic derivatives have served humanity for decades as potent antimalarial drugs. Emergence of drug resistance has narrowed the usage of these drugs in malaria MESHD prevention and treatment. Fortunately, these drugs have roles in the treatment of other diseases as well including rheumatic disorders MESHD and viral infections MESHD. Quinine derivatives have proven antiviral effects, especially against human immunodeficiency HP immunodeficiency MESHD virus (HIV), Zika virus (ZiKV), herpes simplex virus (HSV), Ebola virus MESHD and dengue virus (DENV). The prophylactic and therapeutic role of Chloroquine/hydroxychroquine has become a topic of interest after the recent outbreak of novel Corona virus-19 (nCoV-19). This virus is also named severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) and WHO has officially named this disease as Corona virus disease MESHD 2019 (COVID-19). This lethal virus has affected almost 186 countries of the world till to date just in a period of four months of its outbreak. No approved antiviral drug is existed for the treatment of COVID-19. Therefore, this review is focused on potential prophylactic and therapeutic role of chloroquine/hydroxychlroquine for COVID-19.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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