Corpus overview


MeSH Disease

Human Phenotype

Fever (8)

Pneumonia (6)

Cough (4)

Hypertension (4)

Anosmia (3)


    displaying 1 - 10 records in total 64
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    High SARS-CoV-2 seroprevalence SERO in Health Care Workers but relatively low numbers of deaths MESHD in urban Malawi

    Authors: Marah Grace Chibwana; Khuzwayo Chidiwa Jere; Jonathan Mandolo; Vincent Katunga-Phiri; Dumizulu Tembo; Ndaona Mitole; Samantha Musasa; Simon Sichone; Agness Lakudzala; Lusako Sibale; Prisca Matambo; Innocent Kadwala; Rachel Louise Byrne; Alice Mbewe; Ben Morton; Chimota Phiri; Jane Mallewa; Henry C Mwandumba; Emily R Adams; Stephen B Gordon; Kondwani Charles Jambo

    doi:10.1101/2020.07.30.20164970 Date: 2020-08-01 Source: medRxiv

    Background In low-income countries, like Malawi, important public health measures including social distancing or a lockdown, have been challenging to implement owing to socioeconomic constraints, leading to predictions that the COVID-19 pandemic would progress rapidly. However, due to limited capacity to test for severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD, there are no reliable estimates of the true burden of infection MESHD and death MESHD. We, therefore, conducted a SARS-CoV-2 serosurvey amongst health care workers (HCW) in Blantyre city to estimate the cumulative incidence of SARS-CoV-2 infection MESHD in urban Malawi. Methods Five hundred otherwise asymptomatic TRANS HCWs were recruited from Blantyre City (Malawi) from 22nd May 2020 to 19th June 2020 and serum samples SERO were collected all participants. A commercial ELISA SERO was used to measure SARS-CoV-2 IgG antibodies SERO in serum SERO. We run local negative samples (2018 - 2019) to verify the specificity of the assay. To estimate the seroprevalence SERO of SARS CoV-2 antibodies SERO, we adjusted the proportion of positive results based on local specificity of the assay. Results Eighty-four participants tested positive for SARS-CoV-2 antibodies SERO. The HCW with a positive SARS-CoV-2 antibody SERO result came from different parts of the city. The adjusted seroprevalence SERO of SARS-CoV-2 antibodies SERO was 12.3% [CI 9.0-15.7]. Using age TRANS-stratified infection MESHD fatality estimates reported from elsewhere, we found that at the observed adjusted seroprevalence SERO, the number of predicted deaths MESHD was 8 times the number of reported deaths MESHD. Conclusion The high seroprevalence SERO of SARS-CoV-2 antibodies SERO among HCW and the discrepancy in the predicted versus reported deaths MESHD, suggests that there was early exposure but slow progression of COVID-19 epidemic in urban Malawi. This highlights the urgent need for development of locally parameterised mathematical models to more accurately predict the trajectory of the epidemic in sub-Saharan Africa for better evidence-based policy decisions and public health response planning.

    Persistence of anti- SARS-CoV-2 antibodies SERO in non-hospitalized COVID-19 convalescent health care workers

    Authors: Margherita Bruni; Valentina Cecatiello; Angelica Diaz-Basabe; Georgia Lattanzi; Erika Mileti; Silvia Monzani; Laura Pirovano; Francesca Rizzelli; Clara Visintin; Giuseppina Bonizzi; Marco Giani; Marialuisa Lavitrano; Silvia Faravelli; Federico Forneris; Flavio Caprioli; Pier Giuseppe Pelicci; Gioacchino Natoli; Sebastiano Pasqualato; Marina Mapelli; Federica Facciotti

    doi:10.1101/2020.07.30.20164368 Date: 2020-08-01 Source: medRxiv

    Background. Coronavirus disease MESHD-19 (COVID-19) is a respiratory illness caused by the Severe Acute Respiratory Syndrome MESHD CoronaVirus 2 (SARS-CoV-2), a novel beta-coronavirus. Although antibody SERO response to SARS-CoV-2 can be detected early during the infection MESHD, several outstanding questions remain to be addressed regarding magnitude and persistence of antibody SERO titer against different viral proteins and their correlation with the strength of the immune response, as measured by serum SERO levels of pro-inflammatory mediators. Methods. An ELISA assay SERO has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length nucleocapsid protein (N protein). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies SERO as well as soluble pro-inflammatory mediators in the sera. Results. Specificity and sensitivity SERO of the ELISA assays SERO were high for anti-RBD IgG and IgA (92-97%) and slightly lower for IgM and the Spike and N proteins (70-85%). The ELISA SERO allowed quantification of IgM, IgG and IgA antibody SERO responses against all the viral antigens tested and showed a correlation between magnitude of the antibody SERO response and disease MESHD severity. Non-hospitalized subjects showed lower antibody SERO titers and blood SERO pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested SERO. Noteworthy, in non-severe COVID-19 infections MESHD, antibody SERO titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance. Conclusions. Rapid decline in antibody SERO titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection MESHD, suggesting that antibody SERO-mediated protection against re- infection MESHD with SARS-CoV-2 is of short duration. These results suggest caution in use serological testing SERO to estimate the prevalence SERO of SARS-CoV-2 infection MESHD in the general population.

    A Non-Adaptive Combinatorial Group Testing Strategy to Facilitate Healthcare Worker Screening During the Severe Acute Respiratory Syndrome MESHD Coronavirus-2 (SARS-CoV-2) Outbreak

    Authors: John Henry McDermott; Duncan Stoddard; Peter Woolf; Jamie M Ellingford; David Gokhale; Algy Taylor; Leigh AM Demain; William G Newman; Graeme Black

    doi:10.1101/2020.07.21.20157677 Date: 2020-07-30 Source: medRxiv

    Background: Regular SARS-CoV-2 testing of healthcare workers (HCWs) has been proposed to prevent healthcare facilities becoming persistent reservoirs of infectivity. Using monoplex testing, widespread screening would be prohibitively expensive, and throughput may not meet demand. We propose a non-adaptive combinatorial (NAC) group-testing strategy to increase throughput and facilitate rapid turnaround via a single round of testing. Methods: NAC matrices were constructed for sample sizes of 700, 350 and 250 with replicates of 2, 4 and 5, respectively. Matrix performance SERO was tested by simulation under different SARS-CoV-2 prevalence SERO scenarios of 0.1-10%, with each simulation ran for 10,000 iterations. Outcomes included the proportions of re-tests required and the proportion of true negatives identified. NAC matrices were compared to Dorfman Sequential (DS) approaches. A web application ( was designed to decode results. Findings: NAC matrices performed well at low prevalence SERO levels with an average number of 585 tests saved per assay in the n=700 matrix at a 1% prevalence SERO. As prevalence SERO increased, matrix performance SERO deteriorated with n=250 most tolerant. In simulations of low to medium (0.1%-3%) prevalence SERO levels all NAC matrices were superior, as measured by fewer repeated tests required, to the DS approaches. At very high prevalence SERO levels (10%) the DS matrix was marginally superior, however both group testing approaches performed poorly at high prevalence SERO levels. Interpretation: This testing strategy maximises the proportion of samples resolved after a single round of testing, allowing prompt return of results to staff members. Using the methodology described here, laboratories can adapt their testing scheme based on required throughput and the current population prevalence SERO, facilitating a data-driven testing strategy.

    EUAdb: a resource for COVID-19 test development

    Authors: Alyssa Woronik; Henry W Shaffer; Karin Kiontke; Jon M Laurent; Ronald Zambrano; Jef D Boeke; David H.A. Fitch

    doi:10.1101/2020.07.30.228890 Date: 2020-07-30 Source: bioRxiv

    Due to the sheer number of COVID-19 ( coronavirus disease MESHD 2019) cases, the prevalence SERO of asymptomatic TRANS cases and the fact that undocumented cases appear to be significant for transmission TRANS of the causal virus, SARS-CoV-2 ( severe acute respiratory syndrome MESHD coronavirus 2), there is an urgent need for increased SARS-CoV-2 testing capability that is both efficient and effective1. In response to the growing threat of the COVID-19 pandemic in February, 2020, the FDA (US Food and Drug Administration) began issuing Emergency MESHD Use Authorizations (EUAs) to laboratories and commercial manufacturers for the development and implementation of diagnostic tests1. So far, the gold standard assay for SARS-CoV-2 detection is the RT-qPCR (real-time quantitative polymerase chain reaction) test2. However, the authorized RT-qPCR test protocols vary widely, not only in the reagents, controls, and instruments they use, but also in the SARS-CoV-2 genes they target, what results constitute a positive SARS-CoV-2 infection MESHD, and their limit of detection (LoD). The FDA has provided a web site that lists most of the tests that have been issued EUAs, along with links to the authorization letters and summary documents describing these tests1. However, it is very challenging to use this site to compare or replicate these tests for a variety of reasons. First, at least 12 of 18 tests that were issued EUAs prior to March 31, 2020, are not listed there. Second, the data are not standardized and are only provided as longhand prose in the summary documents. Third, some details (e.g. primer sequences) are absent from several of the test descriptions. Fourth, for tests provided by commercial manufacturers, summary documents are completely missing. To address at least the first three issues, we have developed a database, EUAdb (, that holds standardized information about EUA-issued tests and is focused on RT-qPCR diagnostic tests, or "high complexity molecular-based laboratory developed tests"1. By providing a standardized ontology and curated data in a relational architecture, we seek to facilitate comparability and reproducibility, with the ultimate goal of consistent, universal and high-quality testing nationwide. Here, we document the basics of the EUAdb data architecture and simple data queries. The source files can be provided to anyone who wants to modify the database for his/her own research purposes. We ask that the original source of the files be made clear and that the database not be used in its original or modified forms for commercial purposes.

    Comorbidities associated with regional variations in COVID-19 mortality revealed by population-level analysis

    Authors: Hongxing Yang; Fei Zhong

    doi:10.1101/2020.07.27.20158105 Date: 2020-07-29 Source: medRxiv

    Coronavirus disease MESHD 2019 (COVID-19), caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-Cov-2), has developed into a global health crisis. Understanding the risk factors for poor outcomes of COVID-19 is thus important for successful management and control of the pandemic. However, the progress and severity of the epidemic across different regions show great differentiations. We hypothesized the origination of these differences are based on location-dependent variations in underlying population-wide health factors. Disease MESHD prevalence SERO or incidence data of states and counties of the United States were collected for a group of chronic diseases MESHD, including hypertension MESHD hypertension HP, diabetes, obesity MESHD obesity HP, stroke MESHD stroke HP, coronary heart disease MESHD, heart failure MESHD, physical inactivation, and common cancers (e.g., lung, colorectal, stomach, kidney and renal). Correlation and regression analysis identified the prevalence SERO of heart failure MESHD as a significant positive factor for region-level COVID-19 mortality. Similarly, the incidence of gastric cancer and thyroid cancer were also identified as significant factors contributing to regional variation in COVID-19 mortality. To explore the implications of these results, we re-analyzed the RNA-seq data for stomach adenocarcinoma MESHD (STAD) and colon carcinoma MESHD carcinoma HP (COAD) from The Cancer Genome Atlas (TCGA) project. We found that expression of genes in the immune response pathways were more severely disturbed in STAD than in COAD, implicating higher probability for STAD patients or individuals with precancerous chronic stomach diseases MESHD to develop cytokine storm once infected with COVID-19. Taken together, we conclude that location variations in particular chronic diseases MESHD and cancers contribute significantly to the regional variations in COVID-19 mortality.

    Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints

    Authors: Manjula Gunawardana; Jessica Breslin; John M Cortez; Sofia Rivera; Simon Webster; F Javier Ibarrondo; Otto O Yang; Richard B Pyles; Christina M Ramirez; Amy P Adler; Peter A Anton; Marc M Baum

    doi:10.1101/2020.07.25.20160812 Date: 2020-07-28 Source: medRxiv

    Background The rapid spread of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) and the associated coronavirus disease MESHD 2019 (COVID-19) have precipitated a global pandemic heavily challenging our social behavior, economy, and healthcare infrastructure. Public health practices currently represent the primary interventions for managing the spread of the pandemic. We hypothesized that frequent, longitudinal workplace disease MESHD surveillance would represent an effective approach to controlling SARS-CoV-2 transmission TRANS among employees and their household members, reducing potential economic consequences and loss of productivity of standard isolation methods, while providing new insights into viral-host dynamics. Methodology and Findings On March 23, 2020 a clinical study (OCIS-05) was initiated at a small Southern California organization. Results from the first 3 months of the ongoing study are presented here. Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. Only participants testing negative were allowed to enter the "safe zone" workplace facility. Optional blood SERO samples were collected at baseline and throughout the 3-month study. Serum SERO virus-specific antibody SERO concentrations (IgG, IgM, and IgA) were measured using a selective, sensitive, and quantitative ELISA assay SERO developed in house. A COVID-19 infection MESHD model, based on traditional SEIR compartmental models combined with Bayesian non-linear mixed models and modern machine learning, was used to predict the number of employees and household members who would have become infected in the absence of workplace surveillance. Two study participants were found to be infected by SARS-CoV-2 during the study. One subject, a household member, tested positive clinically by RT-qPCR prior to enrollment and experienced typical COVID-19 symptoms that did not require hospitalization. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody SERO concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples SERO collected at three timepoints. A single, unrelated employee became positive for SARS-CoV-2 RNA over the course of the study, but remained asymptomatic TRANS with low associated viral RNA copy numbers. The participant did not have detectable serum SERO IgM and IgG concentrations, and IgA concentrations decayed rapidly (half-life: 1.3 d). The employee was not allowed entry to the safe zone workplace until testing negative three consecutive times over 7 d. No other employees or household members contracted COVID-19 over the course of the study. Our model predicted that under the current prevalence SERO in Los Angeles County without surveillance intervention, up to 7 employees (95% CI = 3-10) would have become infected with at most 1 of them requiring hospitalizations and 0 deaths MESHD. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic TRANS participants. The surveillance plan outlined here is scalable and transferrable. The study represents a powerful example on how an innovative public health initiative can be dovetailed with scientific discovery.

    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.

    Low Seroprevalence SERO of SARS-CoV-2 in Rhode Island Blood SERO Donors Determined using Multiple Serological Assay SERO Formats

    Authors: Daniel J Nesbitt; Daniel Jin; Joseph W Hogan; Philip A Chan; Melissa J Simon; Matthew Vargas; Ewa King; Richard C Huard; Utpala Bandy; Christopher D Hillyer; Larry L Luchsinger

    doi:10.1101/2020.07.20.20157743 Date: 2020-07-26 Source: medRxiv

    Epidemic projections and public health policies addressing Coronavirus disease MESHD (COVID)-19 have been implemented without data reporting on the seroconversion of the population since scalable antibody testing SERO has only recently become available. We measured the percentage of severe acute respiratory syndrome MESHD- Coronavirus-2 (SARS-CoV-2) seropositive individuals from 2,008 blood SERO donors drawn in the state of Rhode Island (RI). We utilized multiple antibody testing SERO platforms, including lateral flow immunoassays SERO (LFAs), enzyme-linked immunosorbent assays SERO ( ELISAs SERO) and high throughput serological assays SERO (HTSAs). We report than an estimated seropositive rate of RI blood SERO donors of approximately 0.6% existed in April-May of 2020. These data imply that seroconversion, and thus infection MESHD, is likely not widespread within this population. Daily new case rates peaked in RI in late April 2020. We conclude that IgG LFAs and HTSAs are suitable to conduct seroprevalence SERO assays in random populations. More studies will be needed using validated serological tests SERO to improve the precision and report the kinetic progression of seroprevalence SERO estimates.

    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.

    Humoral Response Dynamics Following Infection MESHD with SARS-CoV-2

    Authors: Louis Grandjean; Anja Saso; Arturo Ortiz; Tanya Lam; James Hatcher; Rosie Thistlethwaite; Mark Harris; Timothy Best; Marina Johnson; Helen Wagstaffe; Elizabeth Ralph; Annabelle Mai; Caroline Colijn; Judith Breuer; Matthew Buckland; Kimberly Gilmour; David Goldblatt; - The Co-Stars Study Team

    doi:10.1101/2020.07.16.20155663 Date: 2020-07-21 Source: medRxiv

    Introduction: Severe Acute Respiratory Syndrome MESHD Coronavirus-2 ( SARS-CoV-2) specific antibodies SERO have been shown to neutralize the virus in-vitro. Understanding antibody SERO dynamics following SARS-CoV-2 infection MESHD is therefore crucial. Sensitive measurement of SARS-CoV-2 antibodies SERO is also vital for large seroprevalence SERO surveys which inform government policies and public health interventions. However, rapidly waning antibodies SERO following SARS-CoV-2 infection MESHD could jeopardize the sensitivity SERO of serological testing SERO on which these surveys depend. Methods: This prospective cohort study of SARS-CoV-2 humoral dynamics in a central London hospital analyzed 137 serial samples collected from 67 participants seropositive to SARS-CoV-2 by the Meso-Scale Discovery assay. Antibody SERO titers were quantified to the SARS-CoV-2 nucleoprotein (N), spike (S-)protein and the receptor-binding-domain (RBD) of the S-protein. Titers were log-transformed and a multivariate log-linear model with time-since- infection MESHD and clinical variables was fitted by Bayesian methods. Results: The mean estimated half-life of the N- antibody SERO was 52 days (95% CI 42-65). The S- and RBD- antibody SERO had significantly longer mean half-lives of 81 days (95% CI 61-111) and 83 days (95% CI 55-137) respectively. An ACE-2-receptor competition assay demonstrated significant correlation between the S and RBD- antibody SERO titers and ACE2-receptor blocking in-vitro. The time-to-a-negative N- antibody test SERO for 50% of the seropositive population was predicted to be 195 days (95% CI 163-236). Discussion: After SARS-CoV-2 infection MESHD, the predicted half-life of N- antibody SERO was 52 days with 50% of seropositive participants becoming seronegative to this antibody SERO at 195 days. Widely used serological tests SERO that depend on the N- antibody SERO will therefore significantly underestimate the prevalence SERO of infection MESHD following the majority of infections MESHD.

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MeSH Disease
Human Phenotype

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