Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (451)

Fever (335)

Cough (265)

Hypertension (152)

Respiratory distress (139)


Transmission

age categories (1172)

Transmission (1150)

fomite (565)

gender (495)

asymptotic cases (457)


Seroprevalence
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    Individualized Prediction of COVID-19 Adverse outcomes with MLHO

    Authors: Hossein Estiri; Zachary H. Strasser; Shawn N. Murphy

    id:2008.03869v1 Date: 2020-08-10 Source: arXiv

    The COVID-19 pandemic has devastated the world with health and economic wreckage. Precise estimates of the COVID-19 adverse outcomes on individual patients could have led to better allocation of healthcare resources and more efficient targeted preventive measures. We developed MLHO (pronounced as melo) for predicting patient-level risk of hospitalization, ICU admission, need for mechanical ventilation, and death MESHD from patients' past (before COVID-19 infection MESHD) medical records. MLHO is an end-to-end Machine Learning pipeline that implements iterative sequential representation mining and feature and model selection to predict health outcomes. MLHO's architecture enables a parallel and outcome-oriented calibration, in which different statistical learning algorithms and vectors of features are simultaneously tested and leveraged to improve prediction of health outcomes. Using clinical data from a large cohort of over 14,000 patients, we modeled the four adverse outcomes utilizing about 600 features representing patients' before-COVID health records. Overall, the best predictions were obtained from extreme and gradient boosting models. The median AUC ROC for mortality prediction was 0.91, while the prediction performance SERO ranged between 0.79 and 0.83 for ICU, hospitalization, and ventilation. We broadly describe the clusters of features that were utilized in modeling and their relative influence on predicting each outcome. As COVID-19 cases are re-surging in the U.S. and around the world, a Machine Learning pipeline like MLHO is crucial to improve our readiness for confronting the potential future waves of COVID-19, as well as other novel infectious diseases MESHD that may emerge in the near future.

    How Efficient is Contact Tracing TRANS in Mitigating the Spread of Covid-19? A Mathematical Modeling Approach

    Authors: T. A. Biala; Y. O. Afolabi; A. Q. M. Khaliq

    id:2008.03859v1 Date: 2020-08-10 Source: arXiv

    Contact Tracing TRANS (CT) is one of the measures taken by government and health officials to mitigate the spread of the novel coronavirus. In this paper, we investigate its efficacy by developing a compartmental model for assessing its impact on mitigating the spread of the virus. We describe the impact on the reproduction number TRANS $\mathcal{R}_c$ of Covid-19. In particular, we discuss the importance and relevance of parameters of the model such as the number of reported cases, effectiveness of tracking and monitoring policy, and the transmission TRANS rates to contact tracing TRANS. We describe the terms ``perfect tracking'', ``perfect monitoring'' and ``perfect reporting'' to indicate that traced contacts TRANS will be tracked while incubating, tracked contacts are efficiently monitored so that they do not cause secondary infections MESHD, and all infected persons are reported, respectively. We consider three special scenarios: (1) perfect monitoring and perfect tracking of contacts of a reported case, (2) perfect reporting of cases and perfect monitoring of tracked reported cases and (3) perfect reporting and perfect tracking of contacts of reported cases. Furthermore, we gave a lower bound on the proportion of contacts to be traced TRANS to ensure that the effective reproduction, $\mathcal{R}_c$, is below one and describe $\mathcal{R}_c$ in terms of observable quantities such as the proportion of reported and traced TRANS cases. Model simulations using the Covid-19 data obtained from John Hopkins University for some selected states in the US suggest that even late intervention of CT may reasonably reduce the transmission TRANS of Covid-19 and reduce peak hospitalizations and deaths MESHD. In particular, our findings suggest that effective monitoring policy of tracked cases and tracking of traced contacts TRANS while incubating are more crucial than tracing TRANS more contacts.

    Deciphering the state of immune silence in fatal COVID-19 patients

    Authors: Ido Amit; Pierre Bost; Francesco De Sanctis; Stefania Canè; Ugel Stefano; Katia Donadello; Monica Castellucci; Eyal David; Alessandra Fiore; Cristina Anselmi; Roza Barouni; Rosalinda Trovato; Simone Caligola; Alessia Lamolinara; Manuela Iezzi; Federica Facciotti; Anna Mazzariol; Davide Gibellini; Pasquale De Nardo; Evelina Tacconelli; Leonardo Gottin; Enrico Polati; Benno Schwikowski; Vincenzo Bronte

    doi:10.21203/rs.3.rs-56689/v1 Date: 2020-08-10 Source: ResearchSquare

    Since the beginning of the SARS-CoV-2 pandemic, COVID-19 has appeared as a unique disease MESHD with unconventional tissue and systemic immune features. While COVID-19 severe forms share clinical and laboratory aspects with various pathologies such as hemophagocytic lymphohistiocyto-sis, sepsis MESHD sepsis HP or cytokine release syndrome MESHD, their exact nature remains unknown. This is severely imped-ing the ability to treat patients facing severe stages of the disease MESHD. To this aim, we performed an in-depth, single-cell RNA-seq analysis of more than 150.000 immune cells isolated from matched blood SERO samples and broncho-alveolar lavage fluids of COVID-19 patients and healthy controls, and integrated it with clinical, immunological and functional ex vivo data. We unveiled an immune sig-nature of disease MESHD severity that correlated with the accumulation of naïve lymphoid cells in the lung and an expansion and activation of myeloid cells in the periphery. Moreover, we demonstrated that myeloid-driven immune suppression is a hallmark of COVID-19 evolution and arginase 1 expression is significantly associated with monocyte immune regulatory features. Noteworthy, we found mon-ocyte and neutrophil immune suppression loss associated with fatal clinical outcome in severe pa-tients. Additionally, our analysis discovered that the strongest association of the patients clinical outcome and immune phenotype is the lung T cell response. We found that patients with a robust CXCR6+ effector memory T cell response have better outcomes. This result is line with the rs11385942 COVID-19 risk allel, which is in proximity to the CXCR6 gene and suggest effector memory T cell are a primary feature in COVID-19 patients. By systemically quantifying the viral landscape in the lung of severe patients, we indeed identified Herpes-Simplex MESHD-Virus 1 (HSV-1) as a potential opportunistic virus in COVID-19 patients. Lastly, we observed an unexpectedly high SARS-CoV-2 viral load in an immuno-compromised patient, allowing us to study the SARS-CoV-2 in-vivo life cycle. The development of myeloid dysfunctions and the impairment of lymphoid arm establish a condition of immune paralysis MESHD paralysis HP that supports secondary bacteria and virus infection MESHD and can progress to “immune silence” in patients facing death MESHD.

    Assessment of Musculoskeletal Pain MESHD Pain HP, Fatigue MESHD Fatigue HP and Grip Strength in Hospitalized Patients with COVID-19

    Authors: Sansin Tuzun; Aslinur Keles; dilara okutan; Tugbay Yildiran; Deniz Palamar

    doi:10.21203/rs.3.rs-56548/v1 Date: 2020-08-10 Source: ResearchSquare

    IMPORTANCE Coronavirus disease MESHD 2019 (COVID-19) is an emerging disease MESHD that was declared as a pandemic by WHO. Although there are many retrospective studies to present clinical aspects of the COVID-19, still the involvement of the musculoskeletal system has not been deeply investigated.OBJECTIVE To classify the symptoms of musculoskeletal system in COVID-19 patients, to evaluate myalgia MESHD myalgia HP, arthralgia MESHD arthralgia HP and physical/ mental fatigue MESHD fatigue HP, to assess handgrip muscle strength, and to examine the relationship of these parameters with the severity and laboratory values of the disease MESHD. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study was performed at the IUC-Cerrahpaşa Pandemic Clinic. Hospitalized 150 adults TRANS with laboratory and radiological confirmation of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) according to WHO interim guidance were included in the study. Data were recorded from May 15,2020, to June 30, 2020.MAIN OUTCOMES AND MEASURES Demographic data, comorbidities, musculoskeletal symptoms, laboratory findings and CT scans were recorded. To determine the disease MESHD severity 2007 idsa/ats guidelines for community acquired pneumonia MESHD pneumonia HP was used. Myalgia MESHD Myalgia HP severity was calculated by numerical rating scale (NRS). Visual analog scale and Chalder Fatigue MESHD Fatigue HP Scale (CFS) were used for fatigue MESHD fatigue HP severity determination. Handgrip strength (HGS) was measured by Jamar hand dynamometer.RESULTS 103 patients (68.7%) were nonsevere and 47 patients (31.3%) were severe. The most common musculoskeletal symptom was fatigue MESHD fatigue HP (133 [85.3%]), followed by myalgia MESHD myalgia HP (102 [68.0%]), arthralgia MESHD arthralgia HP (65 [43.3%]) and back pain MESHD back pain HP (33 [22.0%]). Arthralgia MESHD Arthralgia HP, which was mostly notable at wrist (25 [16.7%]), ankle (24 [16.0%]) and knee (23 [15.3%]) joints, showed significant correlation with disease MESHD severity. There was severe myalgia MESHD myalgia HP according to NRS regardless of disease MESHD severity. The physical fatigue MESHD fatigue HP severity score was significantly higher in severe cases, whereas no relationship was found with mental fatigue MESHD fatigue HP score. Female patients with severe infection HP infection MESHD had lower grip strength with a mean value of 18.26 kg (P= .010) in dominant hand, whereas no relationship was found between disease MESHD severity and grip strength in male TRANS patients, but the mean values in both genders TRANS and in decades appears below the specified normative values. Lactate dehydrogenase (LDH) level and lymphocyte count were significantly correlated with lower grip strength. LDH, C-reactive protein (CRP) and D-dimer levels were above the normal range in patients with myalgia MESHD myalgia HP, arthralgia MESHD arthralgia HP and fatigue MESHD fatigue HP. CONCLUSIONS AND RELEVANCE Musculoskeletal symptoms are quite common aside from other multi-systemic symptoms in patients with COVID-19. Arthralgia MESHD Arthralgia HP, which is related to the disease MESHD severity, should be considered apart from myalgia MESHD myalgia HP. COVID-19 patients have severe ischemic myalgia MESHD myalgia HP regardless of the disease MESHD activity. Although there is a muscle weakness MESHD muscle weakness HP in all patients, the loss of muscle function is related with the disease MESHD activity especially in women. Muscular involvement in coronavirus disease MESHD is a triangle of myalgia MESHD myalgia HP, physical fatigue MESHD fatigue HP, and functional impairment.

    Association Between Antecedent Statin Use and Decreased Mortality in Hospitalized Patients with COVID-19

    Authors: Aakriti Gupta; Mahesh V. Madhavan; Timothy J. Poterucha; Ersilia M. DeFilippis; Jessica A. Hennessey; Bjorn Redfors; Christina Eckhardt; Behnood Bikdeli; Jonathan Platt; Ani Nalbandian; Pierre Elias; Matthew J. Cummings; Shayan N. Nouri; Matthew Lawlor; Lauren S. Ranard; Jianhua Li; Claudia Boyle; Raymond Givens; Daniel Brodie; Harlan M. Krumholz; Gregg W. Stone; Sanjum S. Sethi; Daniel Burkhoff; Nir Uriel; Allan Schwartz; Martin B. Leon; Ajay J. Kirtane; Elaine Y. Wan; Sahil A. Parikh

    doi:10.21203/rs.3.rs-56210/v1 Date: 2020-08-09 Source: ResearchSquare

    The coronavirus disease MESHD 2019 (COVID-19), caused by the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2), can result in a hyperinflammatory state, leading to acute respiratory distress HP syndrome MESHD (ARDS), myocardial injury, and thrombotic complications, among other sequelae. Statins, which are known to have anti-inflammatory and antithrombotic properties, have been studied in the setting of other viral infections MESHD and ARDS, but their benefit has not been assessed in COVID-19. Thus, we sought to determine whether antecedent statin use is associated with lower in-hospital mortality in patients hospitalized for COVID-19. This is a retrospective analysis of patients admitted with COVID-19 from February 1st through May 12th, 2020 with study period ending on June 11th, 2020. Antecedent statin use was assessed using medication information available in the electronic medical record. We constructed a multivariable logistic regression model to predict the propensity of receiving statins, adjusting for baseline socio-demographic and clinical characteristics, and outpatient medications. The primary endpoint included in-hospital mortality within 30 days. A total of 2626 patients were admitted during the study period, of whom 951 (36.2%) were antecedent statin users. Among 1296 patients (648 statin users, 648 non-statin users) identified with 1:1 propensity-score matching, demographic, baseline, and outpatient medication information were well balanced. Statin use was significantly associated with lower odds of the primary endpoint in the propensity-matched cohort (OR 0.48, 95% CI 0.36 – 0.64, p<0.001). We conclude that antecedent statin use in patients hospitalized with COVID-19 was associated with lower inpatient mortality. Randomized clinical trials evaluating the utility of statin therapy in patients with COVID-19 are needed.

    Efficacy and Outcomes of Lianhuaqingwen Capsule for Coronavirus Disease MESHD 2019: A Retrospective Propensity Score Matching Analysis

    Authors: zhiyong liu; Yongsheng Du; Jiankun Liu; Xiaolong Wei; Feiyang Zheng; Raomei LI; Shurong Zhang

    doi:10.21203/rs.3.rs-55928/v1 Date: 2020-08-08 Source: ResearchSquare

    Background: Coronavirus disease MESHD 2019 (COVID-19) has outbroken in Wuhan, China, in December, 2019, and became a global pandemic.No effective antiviral agents were approved for COVID-19. In this study, we aim to evaluate the efficacy and outcomes of Lianhuaqingwen (LH) capsulein patients with COVID-19.Methods:In this retrospective cohort study, we included 147 hospitalized patients with laboratory-confirmed severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD between February 4th and April 15th, 2020, in Wuhan Huoshen shan hospital. Patients were grouped as usual treatment alone or combination with LH capsules. Propensity score matching analysis were performed between two groups. Primary outcomes were mortality and duration of hospitalization time. Secondary outcomes included the recovery rate of chest radiological manifestations and abnormal laboratory examinations.Results: In two groups, 40 pairs patients were matched for analysis. The baseline information and clinical characteristics were comparable. 73 (91.25%) of all 80 patients were older than 50 years old. All patients in LH treatment group and 38 (95%) in usual treatment group were surviving respectively (P = 0.494). The hospitalization time of patients in LH treatment group was significantly shorter than usual treatment group (17.85±6.612vs.20.72±5.01 days, P = 0.032). After treatment, the rate of lung lesions detected by chest computerized tomography (CT) was lower in LH treatment group (30% vs. 55.0%, P = 0.024).Conclusion: LH capsules were associated with the improved clinical effects, and might be recommended in the treatment practices of COVID-19 patients. Moreover, further evaluation of LH capsules in large population randomized controlled trial is needed. 

    Prediction of Covid-19 Infections MESHD Through December 2020 for 10 US States Using a Two Parameter Transmission TRANS Model Incorporating Outdoor Temperature and School Re-Opening Effects

    Authors: Ty A Newell

    doi:10.1101/2020.08.06.20169896 Date: 2020-08-07 Source: medRxiv

    Covid-19 infection MESHD case predictions (total cases) are made for August through December 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC). A two-parameter model based on social distance index (SDI) and disease MESHD transmission TRANS efficiency (G) parameters is used to characterize SARS-CoV-2 disease MESHD disease spread TRANS spread. Current lack of coherent and coordinated US policy causes the US to follow a linear infection MESHD growth path with a limit cycle behavior that modulates the US between accelerating and decaying infection MESHD growth on either side of a linear growth path boundary. Four prediction cases are presented: 1) No school re-openings; fall HP season temperature effect 2) No school re-openings; no fall HP season temperature effect 3) School re-openings; fall HP season temperature effect 4) School re-openings; no fall HP season temperature effect Fall HP outdoor temperatures, in contrast to the 1918 pandemic, are predicted to be beneficial for dampening SARS-CoV-2 transmission TRANS in States as they pass through swing season temperature range of 70F to 50F. Physical re-opening of schools in September are predicted to accelerate infections MESHD. States with low current infectious case numbers (eg, NY) are predicted to be minimally impacted while States with high current infectious case numbers (eg, CA and FL) will be significantly impacted by school re-openings. Updated infection MESHD predictions will be posted monthly (Sept, Oct, Nov, Dec) with adjustments based on actual trends in SDI and G. Assessments related to outdoor temperature impact, school re-openings, and other public gathering re-openings will be discussed in updated reports.

    Association of mental disorders with SARS-CoV-2 infection MESHD infection and severe HP and severe health outcomes: a nationwide cohort study

    Authors: Ha-Lim Jeon; Jun Soo Kwon; So-Hee Park; Ju-Young Shin

    doi:10.1101/2020.08.05.20169201 Date: 2020-08-07 Source: medRxiv

    Background: No epidemiological data exists for the association between mental disorders and the risk of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD and coronavirus disease MESHD 2019 (COVID-19) severity. Aims: To evaluate the association between mental disorders and the risk of SARS-CoV-2 infection MESHD infection and severe HP and severe outcomes following COVID-19. Methods: We performed a cohort study using the Korean COVID-19 patient database based on the national health insurance data. Each patient with a mental or behavioral disorder (diagnosed during six months prior to the first SARS-CoV-2 test) was matched by age TRANS, sex, and Charlson comorbidity index with up to four patients without mental disorders. SARS-CoV-2 positivity risk and risk of death MESHD or severe events (intensive care unit admission, use of mechanical ventilation, and acute respiratory distress HP syndrome MESHD) post- infection MESHD were calculated using conditional logistic regression analysis. Results: Among 230,565 patients tested for SARS-CoV-2, 33,653 (14.6%) had mental disorders, 928/33,653 (2.76%) tested positive, and 56/928 (6.03%) died. In multivariate analysis with the matched cohort, there was no association between mental disorders and SARS-CoV-2 positivity risk (odds ratio [OR], 1.02; 95% confidence interval [CI], 0.92-1.12); however, a higher risk was associated with schizophrenia HP-related disorders (OR, 1.36; 95% CI, 1.02-1.81). Among confirmed cases TRANS, mortality risk significantly increased in patients with mental disorders (OR, 1.84, 95% CI, 1.07-3.15). Conclusion: Mental disorders are likely contributing factors of mortality following COVID-19. Although the infection MESHD infection risk TRANS infection risk TRANS risk did not increase in overall mental disorders, patients with schizophrenia HP-related disorders were more vulnerable to the infection MESHD.

    mRNA induced expression of human angiotensin-converting enzyme 2 in mice for the study of the adaptive immune response to severe acute respiratory syndrome MESHD coronavirus 2

    Authors: Mariah Hassert; Elizabeth Geerling; E. Taylor Stone; Tara L. Steffen; Alexandria Dickson; Madi S. Feldman; Jacob Class; Justin M. Richner; James D Brien; Amelia K Pinto

    doi:10.1101/2020.08.07.241877 Date: 2020-08-07 Source: bioRxiv

    The novel human coronavirus, severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has caused a pandemic resulting in nearly 20 million infections across MESHD the globe, as of August 2020. Critical to the rapid evaluation of vaccines and antivirals is the development of tractable animal models of infection MESHD. The use of common laboratory strains of mice to this end is hindered by significant divergence of the angiotensin-converting enzyme 2 (ACE2), which is the receptor required for entry of SARS-CoV-2. In the current study, we designed and utilized an mRNA-based transfection system to induce expression of the hACE2 receptor in order to confer entry of SARS-CoV-2 in otherwise non-permissive cells. By employing this expression system in an in vivo setting, we were able to interrogate the adaptive immune response to SARS-CoV-2 in type 1 interferon receptor deficient mice. In doing so, we showed that the T cell response to SARS-CoV-2 is enhanced when hACE2 is expressed during infection MESHD. Moreover, we demonstrated that these responses are preserved in memory and are boosted upon secondary infection MESHD. Interestingly, we did not observe an enhancement of SARS-CoV-2 specific antibody SERO responses with hACE2 induction. Importantly, using this system, we functionally identified the CD4+ and CD8+ peptide epitopes targeted during SARS-CoV-2 infection MESHD in H2b restricted mice. Antigen-specific CD8+ T cells in mice of this MHC haplotype primarily target peptides of the spike and membrane proteins, while the antigen-specific CD4+ T cells target peptides of the nucleocapsid, membrane, and spike proteins. The functional identification of these T cell epitopes will be critical for evaluation of vaccine efficacy in murine models of SARS-CoV-2. The use of this tractable expression system has the potential to be used in other instances of emerging infections MESHD in which the rapid development of an animal model is hindered by a lack of host susceptibility factors.

    Strategic anti-SARS-CoV-2 serology testing in a low prevalence SERO pandemic: The COVID-19 Contact (CoCo) Study in health care professionals

    Authors: Georg MN Behrens; Anne Cossmann; Metodi V Stankov; Bianca Schulte; Hendrik Streeck; Reinhold Foerster; Berislav Bosnjak; Stefanie Willenzon; Anna-Lena Boeck; Anh Thu Tran; Thea Thiele; Theresa Graalmann; Moritz Z. Kayser; Anna Zychlinsky Scharff; Christian Dopfer; Alexander Horke; Isabell Pink; Torsten Witte; Martin Wetzke; Diana Ernst; Alexandra Jablonka; Christine Happle

    doi:10.1101/2020.08.06.20169250 Date: 2020-08-07 Source: medRxiv

    Background: Serology testing is explored for epidemiological research and to inform individuals after suspected infection MESHD. During the COVID-19 pandemic, frontline healthcare professionals (HCP) may be at particular risk for infection TRANS risk for infection TRANS infection MESHD. No longitudinal data on functional seroconversion in HCP in regions with low COVID-19 prevalence SERO and low pre-test probability exist. Methods: In a large German university hospital, we performed weekly questionnaire assessments and anti-SARS-CoV-2 IgG measurements with various commercial tests, a novel surrogate virus neutralization test, and a neutralization assay using live SARS-CoV-2. Results: From baseline to week six, n=1,080 screening measurements for anti-SARS CoV-2 (S1) IgG from n=217 frontline HCP (65% female TRANS) were performed. Overall, 75.6% of HCP reported at least one symptom of respiratory infection MESHD. Self-perceived infection MESHD probability declined over time (from mean 20.1% at baseline to 12.4 % in week six, p<0.001). In sera of convalescent PCR-confirmed COVID-19 patients, we measured high anti-SARS-CoV-2 IgG levels, obtained highly concordant results from ELISAs SERO using e.g. the S1 spike protein domain and the nucleocapsid protein (NCP) as targets, and confirmed antiviral neutralization. However, in HCP the cumulative incidence for anti-SARS-CoV-2 (S1) IgG was 1.86% for positive and 0.93% for equivocal positive results over the six week study period. Except for one HCP, none of the eight initial positive results were confirmed by alternative serology tests or showed in vitro neutralization against live SARS CoV-2. The only true seroconversion occurred without symptoms and mounted strong functional humoral immunity. Thus, the confirmed cumulative incidence for neutralizing anti-SARS-CoV-2 IgG was 0.47%. Conclusion: When assessing anti-SARS-CoV-2 immune status in individuals with low pre-test probability, we suggest confirming positive results from single measurements by alternative serology tests or functional assays. Our data highlight the need for a methodical serology screening approach in regions with low SARS-CoV-2 infection MESHD rates.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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